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2002
Curt Van TassellCurt Van TassellGene Evaluation and Mapping Laboratory andAnimal Improvement Programs LaboratoryAgricultural Research Service, USDA, Beltsville, MDcurtvt@aipl.arsusda.gov
Application of Application of Genetic Markers to Genetic Markers to
Dairy CattleDairy Cattle
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OverviewOverview
Traditional selection
Genetic markers
Granddaughter design
Resource populations
QTL identification
EST sequencing
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IntroductionIntroduction
Traditional dairy cattle breeding has assumed that an infinite number of genes each with very small effect control most traits of interest
Logical to expect some “major” genes with large effect; these genes are usually called quantitative trait loci (QTL)
The QTL locations are unknown! Genetic markers can provide information
about QTL
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Traditional Selection ProgramsTraditional Selection Programs
Estimate genetic merit for animals in a population
Select superior animals as parents of future generations
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Genetic Improvement: Genetic Improvement: Challenges and TechnologiesChallenges and Technologies
Traditional selectionTraditional selection
Gene mapping and Gene mapping and marker assisted selectionmarker assisted selection
TransgenicsTransgenics
Abundant Genetic variationAbundant Genetic variation
Limited genetic variationLimited genetic variation
Little or no genetic variationLittle or no genetic variation
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Application of Genetic MarkersApplication of Genetic Markers
Identify genetic markers that are associated with changes in genetic merit
Use marker assisted selection (MAS) to make selection decisions before phenotypes are available
Adjust genetic merit for genetic markers
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Useful Genetic Markers:Useful Genetic Markers:
Allow marker inheritance to be followed across generations
Many different types of marker alleles well represented in the population
Marker and QTL are close together so that recombination between marker and QTL is rare
Best case is when we know the QTL - then it is the marker!
m q
M Q
MarkerLocus
QuantitativeTrait Locus
{ {
LinkageDistance
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ParentalChromosomes
RecombinantChromosomes
MarkerLocus
QuantitativeTrait Locus
{ {
m q
M q
m Q
M Q
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ParentalChromosomes
A B C D E F
a b c d e f
RecombinantChromosomes
*******
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Genetic MarkersGenetic Markers
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Genetic Markers!!Genetic Markers!!
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Genetic MarkersGenetic Markers
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Bull
Granddaughter DesignGranddaughter Design
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Granddaughter DesignGranddaughter Design
Sons
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Granddaughter DesignGranddaughter Design
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Granddaughter DesignGranddaughter Design
DNA
Genetic
Merit
Data
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Resource Populations:Resource Populations: Cooperative Dairy DNA Repository (CDDR)Cooperative Dairy DNA Repository (CDDR) The CDDR is an ongoing collection of all
bulls entering progeny tests Includes all breeds Useful for QTL mapping in dairy cattle using
a granddaughter design and for complex pedigree analysis
Currently (6/01): Six North American studs contributing semen 9789 bulls in the collection 128 families with at least 25 sons
Compare GeneticMerit
QTL IdentificationQTL Identification
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3.51.7 -0.1 -2.5 -6.20.7
QTL IdentificationQTL Identification
Bull
Sons
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USDA-ARS ProgressUSDA-ARS Progress
Over 160 markers studied in over 1000 animals from 8 families
Evaluated all available traits: Conformation traits, M, F, P, SCS, PL, and calving ease
Genome-wide scan across all families was recently completed
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Marker Association ResultsMarker Association ResultsChromosome Trait
3 Protein Percentage4 Strength
Body Depth5 Dairy Form6 Protein PercentageProtein Percentage7 Somatic Cell Score
12 Foot AngleRear Legs (Rear View)
14 Fat PercentageProtein PercentatgeFore Udder AttachmentFront Teat Placement
16 Udder Depth18 Rump Angle20 Protein Percentatge22 Rump Angle27 Dairy FormDairy Form
0
4
8
12
16
20
0 20 40 60
DF M F PF% P% PL SCS
Family 8 interval analysis resultsFamily 8 interval analysis results
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What is an EST?What is an EST?
ATG TAAmRNA
ESTs
AAAAAAAAA
5’ AAAAAAAAATTTTTTTTTT3’
5’ 3’
5’3’
cDNA
Tissue Biopsy
mRNA isolation
RT-PCR
Sequencing of cDNA clones
Bioinformatics
Bovine Sequence database
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USDA-ARS Bovine EST ProjectsUSDA-ARS Bovine EST Projects
Initial goal: Single pass sequencing of 5 bovine cDNA libraries
4 axis libraries @ MARC = 80,000 EST 1 mammary library @ BARC = 10,000 EST
Mammary cDNA library has stages from prepubertal, mid-gestation, late gestation, cholostrogenesis, lactation, infected lactation, and early and late involution.
Sample diverse developmental stages and morphological cell types to maximize diversity and minimize redundancy
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Status ARS EST sequencingStatus ARS EST sequencing
GenBank dbEST database submissions: 231,577 total cattle gene-related
sequences >150,000 cattle ESTs generated by USDA 120,745 cattle sequences 1-4BOV cDNA
libraries (MARC) 23,202 cattle sequences 5BOV cDNA
library (BARC)
EST Sequence Analysis & AssemblyEST Sequence Analysis & Assembly
AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGACATTACCTAGG
AGCTTTAAGCCATACCTTAGGACATTACCTAGG
GCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTC
AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGAC
AGCTTTAAGCCATACCTTAGGGTCAGCTTTAAGCCATACCTTAGGACATTACCTAGG
TC
EST1EST2EST3EST4
TIGR Bovine Gene Index:TIGR Bovine Gene Index:
Over 67,000 unique sequence elementsOver 67,000 unique sequence elements
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Unique Cattle SequencesUnique Cattle Sequences
Rat Gene Index
11,077
28,61718,292
36,7
34
10,1
75
44,367
2,542
31,67115,238
22,760
24,149
Human Gene Index
Mouse Gene Index
Human Golden Path
TOGA
Over 17,000 “no hit” bovine sequence elements.
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ConclusionsConclusions
Marker assisted selection is an evolutionary improvement over traditional selection methods. It allows more accurate estimation genetic merit of animals
Evidence of important QTL has been found
EST sequencing has been very successful
Lots of interesting findings from EST project that will need additional research
Recommended