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Implementation of dairy cattle breeding policy in
Ethiopia ndash some reflections on complementary strategies
Sipke Joost Hiemstra
13 April 2018 Addis Ethiopia
Centre for Genetic Resources the Netherlands (CGN)
My background ndash animal breeding
Director - Centre for Genetic Resources the Netherlands (CGN)
Plant Genetic Resources
Forest Genetic Resources
Animal Genetic Resources
FAO Global Strategy NationalCoordinator for Animal Genetic Resources
Chair of European Regional Focal Point (ERFP) European Network of National Coordinators
1 Identification characterization and selection of indigenous breeds for dairy production
2 Improving the genetic potential of indigenous animals through crossbreeding with exotic dairy breeds
3 Establishing dairy cattle production and multiplication centers
4 Import and export of dairy animal breeds shall be regulated
Ethiopia - Dairy cattle breeding policy and strategy
3
Which dairy animals and animal characteristics for which Ethiopian
production system - Breeding goal
Structure and implementation of breeding programs
Cross-breeding strategies
Improvement and maintenance of indigenous breeds
Taking advantage of novel approaches and technologies
Conclusions - pathways towards implementation of complementary
strategies
This presentation
4
Animal breeding
Very simple
Select the best animals
Usemate the best animals in further breeding
Disseminate the best
But maintain genetic diversity
What is best
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
My background ndash animal breeding
Director - Centre for Genetic Resources the Netherlands (CGN)
Plant Genetic Resources
Forest Genetic Resources
Animal Genetic Resources
FAO Global Strategy NationalCoordinator for Animal Genetic Resources
Chair of European Regional Focal Point (ERFP) European Network of National Coordinators
1 Identification characterization and selection of indigenous breeds for dairy production
2 Improving the genetic potential of indigenous animals through crossbreeding with exotic dairy breeds
3 Establishing dairy cattle production and multiplication centers
4 Import and export of dairy animal breeds shall be regulated
Ethiopia - Dairy cattle breeding policy and strategy
3
Which dairy animals and animal characteristics for which Ethiopian
production system - Breeding goal
Structure and implementation of breeding programs
Cross-breeding strategies
Improvement and maintenance of indigenous breeds
Taking advantage of novel approaches and technologies
Conclusions - pathways towards implementation of complementary
strategies
This presentation
4
Animal breeding
Very simple
Select the best animals
Usemate the best animals in further breeding
Disseminate the best
But maintain genetic diversity
What is best
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
1 Identification characterization and selection of indigenous breeds for dairy production
2 Improving the genetic potential of indigenous animals through crossbreeding with exotic dairy breeds
3 Establishing dairy cattle production and multiplication centers
4 Import and export of dairy animal breeds shall be regulated
Ethiopia - Dairy cattle breeding policy and strategy
3
Which dairy animals and animal characteristics for which Ethiopian
production system - Breeding goal
Structure and implementation of breeding programs
Cross-breeding strategies
Improvement and maintenance of indigenous breeds
Taking advantage of novel approaches and technologies
Conclusions - pathways towards implementation of complementary
strategies
This presentation
4
Animal breeding
Very simple
Select the best animals
Usemate the best animals in further breeding
Disseminate the best
But maintain genetic diversity
What is best
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Which dairy animals and animal characteristics for which Ethiopian
production system - Breeding goal
Structure and implementation of breeding programs
Cross-breeding strategies
Improvement and maintenance of indigenous breeds
Taking advantage of novel approaches and technologies
Conclusions - pathways towards implementation of complementary
strategies
This presentation
4
Animal breeding
Very simple
Select the best animals
Usemate the best animals in further breeding
Disseminate the best
But maintain genetic diversity
What is best
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Animal breeding
Very simple
Select the best animals
Usemate the best animals in further breeding
Disseminate the best
But maintain genetic diversity
What is best
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
The success of (Dutch) animal breeding programs
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Breeding circle
7
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Starting point
8
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Ethiopia ndash range of climates and production systems
Altitude
Mean daily
temperature
Rainfall distribution
throughout the year
Feed availability
Farm management
Small scale farms
Mediumlarge scale
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Breeding goal
Local circumstances and external factors
Market (consumers society)
Climate
Feed availability
Cost price
Which traits are really important in the next 10-15 years
Many options
Milk yield
Fertility
Heat tolerance
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Economic models
Economic Value
0
5
10
15
20
25
30
0 10 20 30 40 50
Trait
Prof
it
1 unit
EVprofit function
Figure 81 The use of a profit function to derive economic values The economic value (EV) of a trait is the increase in profit that results from a
single unit increase of the trait value
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example Higher milk production per cow andor
improved longevity
Price in KES
Case 1
Price in KES
Case 2
Explanation andor assumptions
Heifer raising costs or investment to
purchase a heifer 300000 300000
To be calculated or estimated
Productive life in years 3 5 Just two cases in a common range
Depreciation per year 100000 60000
Margin of extra year longevity 0 +40000 Less costs means higher margin
Price in KESExplanation andor assumptions
Price per extra kg milk35
Milk price on market
Cost of extra feed
23
Feed costs of 30 KES per kg concentrates
065 kg concentrates needed for 10 kg of
milk extra
Margin of extra kg milk+12
For Kenya - J Zijlstra Wageningen Livestock Research
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
We donrsquot want this situation
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Specialists and generalists
Well-controlledAverageHarsh amp dynamic
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Another example Netherlands What type of cow
is optimal ndash specialized dairy or dual purpose
bull Reduction of green house gas emissions kg milk
bull By increasing milk production
bull By increasing longevity
bull HOWEVER
bull Benefits of higher milk production are much lower when taking into account both milk and beefveal production from dairy farms
bull Higher milk production per cow lower beefveal production more import of beefveal
bull Specialized beef production systems are less efficient
bull Dual purpose breeds are endangered but WHYVellinga and de Vries 2018
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example Is the Dorper the superior breed
Dorper Fast growing
Red Maasai Slow growing
0
200
400
600
800
1000
1200
1400
hot-humid semi-arid
Gro
wth
(g
day)
Dorper
Red Masai
Re-ranking The Dorper is superior in semi-arid conditions but the Red Maasai is superior in hot and humid areas
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example Is the Dorper the superior breed
Dorper big but sensitive
Red Maasai small but heat resistant0
005
01
015
02
025
03
hot-humid semi-arid
An
nu
al
mo
rta
lity
ra
te
Dorper
Red Masai
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Another dimension Role of livestock added value
of livestock products or feedfood competition
(H van Zanten 2016)
18Centre for Genetic Resources the Netherlands (CGN)
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Human edible protein ratio =
Output of human edible protein Input human edible proteins via feed
New protein efficiency traits in breeding goals
19Centre for Genetic Resources the Netherlands (CGN)
(Van Zanten 2016)
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example
the Netherlands
Change in
breeding goal
over time
20
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Collection of information Breeding values
21
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Which traits are important
Trait Production Functional
Kg milk -006 0
Kg fat 07 0
Kg protein 42 0
Longevity 0 7
Udder Health 0 15
Fertility 0 25
Trait production Functional
kg milk 263 -98
kg fat 16 -8
kg protein 12 -4
Longevity -09 30
Udder Health -03 26
Fertility -18 17
Breeding goal Selection response
What do we learn from this1 Sign of economic value is not always equal to sign of selection response (milk fertility)2 Index with only 3 traits influences nearly every trait (weighting factor of zero does not mean zero change)
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example
the Netherlands
Change in
breeding goal
over time
23
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
24
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Genetic improvement
Selecting the best animals as parents of the next generation
Every generation again
This leads to a stepwise (cumulative) genetic improvement
Genetic improvement euro
=
Accuracy x Intensity x Genetic standard deviation
Generation interval
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example mass selection and ΔG
Growth in beef cattle
h2 = 035 P = 02 kgday
generation interval L= 5 years
selection of 25 of fastest
growing individuals
Intensity p = 025 i = 1271
Accuracy rIHmass = h = 035 = 059
Genetic std A = h P = 059 x 02 = 0118 kgday
G = (1271 x 059 x 0118)5 = 00177 (kgday)yrL
irG AIH
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
How heritable is the trait under selection
(ie the trait in the breeding goal)
How much genetic variation for that trait is
there in the population
What is the average accuracy of the EBV
and thus the accuracy of selection
What proportion of the animals will be selected for breeding
In case genetic gain is to be expressed per year rather than per
generation how long is a generation
Factors determining success of selection decisions
27
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Four selection paths
1 Sires to breed males (SS) Selection of the best progeny tested bulls
to breed ldquoyoung bullsrdquo (AI-company)
2 Sires to breed females (SD) Selection of progeny tested bulls to breed cows on farms
(AI-company + farmer)
3 Dams to breed males (DS) Selection of the very best cows to breed ldquoyoung bullsrdquo
(AI-company)
4 Dams to breed females (DD) selection of cows to breed the next generation of cows (farmer)
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Evaluation
29
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example
the Netherlands
Genetic
improvement
over time
30
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Holstein
CRV-breeding
program
Netherlands
31
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Conservation and genetic improvement of the most valuable
indigenous breeds
Upgrading of indigenous cattle to more productive 50 crossbreds
Development of synthetic indigenous-exotic breed
Importing suitable breeds (semen embryorsquos heifers )
Some key questions based on breeding goal discussion
- What do farmers consider as the optimal blood level 50 75
- Upgrading of local animals to 50 exotic whatrsquos next
Parallel breeding strategies needed to achieve
the national goal and to meet farmers needs
32
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Which breeds ndash How to make optimal use of the
genetic resources pool ndash a broad genetic base
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Livestock breeds ndash the global picture (FAO 2015)
34Centre for Genetic Resources the Netherlands (CGN)
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Threats to livestock genetic diversity (FAO 2015)
35Centre for Genetic Resources the Netherlands (CGN)
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
What happened in the Netherlands
change in population size 1979 - 2007
0
20
40
60
80
100
120
1979
1981
1983
1985
1987
1989
1991
1993
1995
1997
1999
2001
2003
2005
2007
1979
100
Blaarkop
Fries Hollands ZB
Fries Hollands R
MRY incl Brandrood
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
37
Ethiopian breeds
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Upgrading of less productive breeds
Quickly trying tosolve problems at farm level
Making use of heterosis effects
Long term strategy
Crossbreeding Advantages
39
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Rotational cross
Rotational cross A x (B x (A x B)))
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
International pool of genetic products (eg CRV)
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
J Gibson
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Milk production by animals with different proportions of exotic genotypes (dairyness)
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)
Herd environment level
Kenya
21-35 36-60 61-875 gt875
0
2
4
6
8
10
12
Level-1 Level-2 Level-3
Dai
ly m
ilk y
ield
(l
day
)Herd environment level
Uganda
21-35 36-60 61-875 gt875
High grade cattle only showed substantially better milk yields than other grades in the highest production environment
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Daily milk production for different dairy groups of animals within countries
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly M
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Kenya
Class 2 Class 3 Class 4 Class 5
0
1
2
3
4
5
6
7
8
9
10
0 1 2 3 4 5
Dai
ly m
ilk y
ield
(l
day
)
Lactation Stage (100-day intervals)
Uganda
Class-1 Class-2 Class-3 Class-4 Class-5
Lactation curves for animals were generally flat
with no evidence of a peak in early lactation
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
G Leroy R Baumung P Boettcher B Scherf I
Hoffmann 2015
45
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Synthetic
FxA crosses
(goal=50)
Arsi Cows (A)Friesian Bulls (F)
X
50F50A
375F625A
25F75A
4375F5625A
46875F53125A
50F 50A
Foundation stock
selection
Dissemination to
participating herds
Dissemination to
participating herds
selection
selection
selection
Dissemination to
participating herds
Dissemination to
participating herds
Dissemination to
participating herds
10th generation
4th generation
3rd generation
1st generation
nucleus participating herds
2nd generation
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
DNA technology
Reproductive technologies
Taking advantage of new technologies in
breeding programmes
47Centre for Genetic Resources the Netherlands (CGN)
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
AI versus Natural mating
Uptake of AI is low (so far)
Technical results should improve
Novel technologies
Keep it simple
Reproductive technologies
48
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Large scale SNP genotyping is available
CAGTCAGTCGTACCAGTCT
CAGTCAGTAGTACCAGTCT
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Determine breed composition
Combine production and SNP data to determine which breedanimal combinations perform best under different conditions
Genomic selection
Genotyping for
50
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
KenyaUganda - PCA results based on 566k chip - Admixture
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Selecting the best animals for instance
animal 1 A A G T A T T A T C T T hellip
A A G T A T T A T C T T hellip
animal 2 A A G T A T T A T C T T hellip
A A G A A T T A T C T T hellip
This A gives +02 kg milk -1 fertility etc
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Genomic Selection ndash accelerating genetic progress
Genomic breeding values
(GEBVs)
Estimate SNP
effects
Reference population
Selection candidates
Genomic Selection
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Traditional versus genomic selection
Factors Genomic selection
Accuracy +++ ++
Intensity + +++
Genetic variation
Generation interval -- ++
Traditional = Progeny testing
Impact on genetic improvement
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Can we use GS in developing countries where
pedigree recording is lacking
Screen the population
Select number of herds with information on performance on cows
Take a DNA sample on these cows
Young bulls in your nucleus
Take a DNA sample
Estimate EBV based on DNA profile
Select the best bulls for nucleus and dissemination
Link performance to
EBV through DNA
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Genomic selection in small populations or specific
context (Kariuki 2017)
56 -
2000
4000
6000
8000
10000
12000
14000
PT15 PT30 GS15 GS30
Retu
rn
s (
00
0) E
uros
4
7
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Inbreeding - risks for small populations
57
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Directly in the trait itself
Reduction in Additive genetic variance after selection (Falconer Chapter 11)
Use of a small group of related individuals as parents reduces the genetic diversity
Affects other traits as well
Loss of diversity due to selection
Proportion Heritability
selected 090 070 050 030 010
5 22 40 57 74 91
20 30 45 61 77 92
50 43 55 68 81 94
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Loss of genetic diversity through genetic drift
Change in frequency and loss of alleles by chance due to sampling of a limited numbers of individuals
Less individuals sampled -gt more genetic drift
Loss of diversity is predictable but which diversity is not predictable
Frequency
Black 10
White 11
Yellow 9
Green 10
Blue 10
Brown 2
Red 5
Before After
10 -
11 6
9 2
10 1
10 1
2 -
5 -
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Not only in
ldquosmall populationsrdquo
Holstein
CRV-breeding
program
Netherlands
60
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
On inbreeding
Inbreeding depression inbred individuals perform less well
Genetic defects are more common in inbred individuals
Inbreeding always increases in closed population
The smaller the population the higher the inbreeding rate
Uneven distribution of offspring over parents causes more inbreeding
Use of few bulls
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Measures
Two principles
Larger population size
More even distribution of offspring over ancestors
Provide access to more unrelated bulls
Gene banks
Avoid excessive use of single bulls
Limit inseminations bull
Limit sons available for breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Example Netherlands - Gene bank supports
conservation of endangered breeds
Dutch Friesian Red and White
bull lt 400 purebred cows
bull gt 40 (old) bulls in gene bank
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Collections CGN ndash Dutch gene bank farm animals
CGN Gene bank collections = reproductive material
Semen (+ embryorsquos oocytesovarian tissue)
Blood samples
ldquoCore collectionsrdquobreed
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Conclusions ndash pathways towards implementation
ldquoNational breeding program and national infrastructurerdquo should support
the relevant complementary strategies
Upgrading
Development of synthetic breeds
Conservation and improvement of indigenous breeds
More effective and efficient AI delivery system needed
AI centres should make available semen of lsquoexotic bullsrsquo lsquocrossbred bullsrsquo
aacutend lsquoindigenous bullsrsquo
Investment in performance recording will pay off in the long run
selection of best animalsbull dams at private farms for further breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
Conclusions ndash pathways towards implementation Import of semen or semen production in Ethiopia
Importing 100 exotic semen or importing young bulls is probably economically more
profitable than sourcing 100 exotic bulls for AI at Ethiopian (nucleus breeding) farms
No need to buy the most expensive semen ndash probably not the best for Ethiopian farmer
Use the national infrastructure of breeding and research farms for
Conservation and improvement of selected indigenous breeds
Development of synthetic breeds
Performance recording and research
Selection of bull-damsbulls for AI
Dissemination of natural mating bulls and heifers to farmers
67
Looking forward to discuss collaboration in dairy breeding
67
Looking forward to discuss collaboration in dairy breeding