Albert De Vries

Department of Animal SciencesUniversity of Florida

Gainesville, FL 32608devries@ufl.edu

Genomic Testing: Where is the Greatest Economic

Value?

USDA-NIFA Dairy Genomics Workshop, Okeechobee, FL, December 7, 2016

Genomic test predicts future performance

Must have a planPlan may be profitable

Acknowledgments• Dairy farmers• Allied industry• University/USDA colleagues, students• Funding:

This work is financially supported by USDA-NIFA AFRI grant award 2013-68004-20365 titled “Improving Fertility of Dairy Cattle Using Translational Genomics”.

Outline1. Genetics 1012. Genomic testing: where is the value?

Avoid inbreeding Sell surplus calves/heifers Use sexed and/or beef semen Genetic progress and culling Better reproduction Optimization What is next?

3. Take home messages

AGIL meeting with BARC and NEA management, November 5 2014 (5) Paul VanRaden

Trait

Relative emphasis in USDA index (%)PD$1971

MFP$1976

NM$1994

NM$2000

NM$2003

NM$2006

NM$2010

NM$2014

Milk 52 27 6 5 0 0 0 -1Fat 48 46 2

521 22 23 19 22

Protein … 27 43

36 33 23 16 20

Longevity

… … 20

14 11 17 22 19

SCS … … –6 –9 –9 –9 –10 –7Udder … … … 7 7 6 7 8Feet/Leg … … … 4 4 3 4 3Body Size

… … … –4 –3 –4 –6 –5

Preg Rate

… … … … 7 9 11 7

Calving … … … … 4 6 5 5Heifer CR … … … … … … … 2Cow CR … … … … … … … 1

Changes in trait selection across time

Net Merit (NM$) = USDA genetic selection index

2014 revision: 12 traits

Lifetime value of genetic worth ($) compared to cow born in 2010

Variation: $194 standard deviation of true transmitting ability $388 standard deviation of true breeding value

University of Florida genomic testing

Clarifide Plus and Igenity Essential

Net Merit 9 calves PTA EBV=2xPTA Worst: $253 $506 Best: $530 $1060

Difference: $227 $554

Best calf is expected to be $554 more profitable than worst calf ($185 per lactation)

“Identify top genetics IVF/ET sell top genetics”

“Identify low genetics sell, or use as ET recipients”

No IVF/ET? “Genomic test the heifers, identify the elite individuals and breed those heifers to sexed

semen”

Avoid inbreeding

• Genetic progress = genetic variation x selection intensity x √(reliability of test)

• Genetic progress per year = genetic progress between generations / generation interval

How good the ranking is:• Pedigree info.• Genomic test info.

Natural genetic differences

How picky we can be

Genetic progress 101Breeders equation

-300-200-100

0100200300400500600700

0 500 1000 1500 2000 2500 3000 3500 4000

PTA

net m

erit

($)

Age (days)

Heifers

Cows

PTA Net Merit distributionFL farm, 539 heifers, 1058 cows (no genomic

testing)Standard deviation PTA ≈ $125Standard deviation EBV ≈ $250

True genetic variation > Estimated genetic variation

Dr. Kent Weigel UW (2011)

True breeding value of selected animals ($)

$350 genetic standard deviation Net Merit

10% 30% 50% 70% 90%10% 194 128 88 55 2230% 336 222 153 95 3750% 434 287 197 123 4870% 514 339 234 145 5790% 583 385 265 165 65

Animals selected

Reliability of test

How to calculate value of genomic testing?

• Try to include all important factors:– Genetic age trend, genetic variation,

inseminations, milk production, feed, prices, reproduction, culling, stillbirth, cost of testing, …

– Sell surplus worst heifer calves– Not included: inbreeding, bad matings – Reliabilities: 0%, “some”, “a lot” ($0), genomic

($50)• Do math …• Bottom line: profit per milking cow per year

– And many other results

Scenario 1: Only conventional semen

reference

+$14+$26

+$15 = $42 - $27

• Only conventional semen• 12% surplus heifer calves sold• “genomic” profit per milking cow per year: $431

reliability

Scenario 1: Only conventional semen

reference

+$26+$47

+$26 = $76 - $50

• Per dairy calf:

reliability

Scenario 2: top 50% heifers sexed semen

reference

+$22+$41

+$37

• Top 50% heifers with sexed semen, remainder conventional• 18% surplus heifer calves sold• “genomic” profit per milking cow per year: $449

reliability

Genetic variation matterssexed semen on top 50% heifers (Scenario 2)

EBV (PTA)Standard deviation

Reliability

Sire matters too• Increase in sire PTA to break-even with genomic

profit/milking cow per year• Net Merit, $350 breeding value• Top 50% heifers with sexed semen (Scenario 2)

+$50

+$20-$6

Reliability

Genetic progress and culling

• Increase cow cull rate instead of selling surplus heifers?

Net Merit genetic trends (PTA)

https://www.cdcb.us/eval/summary/trend.cfm

2010 – 2014:Sire of cow PTA: $58/yearCow PTA: $47/yearDam of cow PTA: $35/year

Conclusion culling - genetics

• After review of existing work: Increased genetic progress in sires should increase cow cull rates by a few percent at most.

But• Selective breeding within the herd,

and selection of calves, may capture some additional genetic progress, depending on level of reproduction.

Pregnancy rate (%)6,795 Holstein dairy herdsMostly eastern USANovember 2016DairyMetrics, www.drms.org

19.1%

Source: Overton and Cabrera (2017).

Figure 1

Value of increased pregnancy rates ($/cow/year)

6 model studies

Valuing change in reproduction

• Herd budget spreadsheet– …, calves, heifers, cows, milk, feed, repro, culling,

insemination, prices, genetics, …• 3 x 2 = 6 policies:

– 3: “Traditional”, constant cull rate, no surplus calves– 2: Conventional semen only, sexed semen + genomic

testing– Sell surplus calves, vary cull rate (if needed)

• Change reproduction:– Vary probability of estrus detection and/or probability of

conception for free– Calculate results: …, cull rate, surplus calves, profit, …

Surplus female dairy calves6 policies:

Profit per milking cow per year

6 policies:

Optimization• Best breeding mix (sexed, conventional,

beef)– Increase in pregnancy rate– Increase in crossbred calf price

Effect of beef price: User• Crossbred calf $225, $300, or $375 (Purebred:

$150)• Genetics: traditional or genomic test• Breeding mix: User-defined (sexed, conventional,

beef) $225 $300

$375

Profit/milking cow/year

Effect of beef price: Optimal

• Crossbred calf $225, $300, or $375 (Purebred: $150)

• Genetics: traditional or genomic test• Breeding mix: Optimal (sexed, conventional, beef)

$225 $300

$375

Profit/milking cow/year

Effect of better repro: User• Pregnancy rate: 14%, 20%, or 28%• Genetics: traditional or genomic test• Breeding mix: User-defined (sexed, conventional,

beef)14% 20% 28%

Profit/milking cow/year

Effect of better repro: Optimal

• Pregnancy rate: 14%, 20%, or 28%• Genetics: traditional or genomic test• Breeding mix: Optimal (sexed, conventional, beef)

≈14% ≈20%

≈28%

Profit/milking cow/year

Timing of costs and returns• Pregnancy rate: 28%• Genetics: traditional vs. genomic test• Breeding mix: Optimal (sexed, conventional, beef)• Δ Profit/milking cow/year = $57 (genomic –

traditional)

Profit/milking cow/year

What is next?• All shown results preliminary• Many factors, prices play a role• Results on your farm will be different• It is complicated, need professional

advice• Best strategies emerging

Take home messages• Genomic testing is here to stay• Genomic testing of females on the farm can

be profitable, maybe• Better reproduction makes testing more

profitable• Value of testing will likely increase when we

learn how to best use the information

Thank youdevries@ufl.edu