why do we need more genotypes and phenotypes?
DESCRIPTION
Why Do We Need More Genotypes and Phenotypes?. How Much Data, and What Cost?. Traditional data sources 55 million pedigree records 28 million US cows with lactations 57 million daughters of MACE bulls Current and future data sources 50K genotypes on 50,119 animals - PowerPoint PPT PresentationTRANSCRIPT
2007
Paul VanRaden Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA
2009
Why Do We Need More Why Do We Need More Genotypes and Phenotypes?Genotypes and Phenotypes?
Council on Dairy Cattle Breeding, April 2010 (2) Paul VanRaden200
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How Much Data, and What Cost?How Much Data, and What Cost?
Traditional data sources• 55 million pedigree records• 28 million US cows with lactations• 57 million daughters of MACE bulls
Current and future data sources• 50K genotypes on 50,119 animals• 3K, 850K, etc. genotypes• Additional traits, more herds
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Value of PhenotypesValue of Phenotypes
Contribution = ∑ (REL – Rpa)• 10,000 HO bulls, 77% REL, 40% Rpa• 8,000 HO cows, 46% REL, 36% Rpa• Cows supply 18% of genomic info
Recent phenotypes slightly more valuable than past generations
Foreign useful if correlations high• CAN HO, CHE BS, DNK JE, etc.
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Genotyped Animals (n=42,653)Genotyped Animals (n=42,653)In North America as of February 2010In North America as of February 2010
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2000
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6000
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1000019
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1970
1990
1992
1994
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2006
2008
2010
Year of Birth
Nu
mb
er
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An
ima
ls Predictor
Predictee
Young
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Most Holstein GenotypesMost Holstein GenotypesFeb 2010Feb 2010
Country Reference bulls
Germany 17,000
Netherlands 16,000
France 16,000
Scandinavia (DFS) 16,000
United States 9,300
Canada 8,800
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Validation ResultsValidation Results
EuroGenomics reliabilities about 5% higher than in North America• Plan to be official in August 2010• > 10% REL gain from exchange• Similar regressions, slightly < 1.0
Validation expects regressions < 1 with selective genotyping of bulls• Means of genotyped vs. nongenotyped• Most countries genotyped all recent bulls
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Genomic Validation TestsGenomic Validation Tests
Predict 2010 daughter data using 2006 PA or genomic PTA• DYD2010 = apa + bpa PA2006 + e
• DYD2010 = apta + bpta PTA2006 + e
Statistics from Jorjani, 2010 Interbull Genomics Workshop• Foreign average includes DEU, FRA, NLD,
DFS, JPN, POL, NZL, and CAN• FRA not latest data (10,000 bulls)
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Regressions and Gains in RRegressions and Gains in R22 When predicting last 4 years of dataWhen predicting last 4 years of data
Regression Gain in R2
Trait USA Foreign USA Foreign
Yield .91 .85 24 22
SCS .80 .97 15 23
Longevity 1.10 .98 15 8
Final score .89 .90 15 15
Udd depth .90 1.01 30 31
Stature .98 .98 26 30
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Reliability from Additional DataReliability from Additional Data
Young bull REL for:
Options to add data: Yield SCS DPR
10,000 current bulls 72 68 60
+7,500 with 50 dtrs 84 81 73
+7,500 with 100 dtrs 85 82 76
+16,000 from Europe 87 85 79
7,500 N. American bulls = 1500 / year over next 5 years
Or,
Or,
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Foreign GenotypesForeign Genotypes
“A potentially related issue is bartering for genotypes from other countries. If you will be sharing genotypes eventually, it would be advantageous to get genotypes on their bulls in return, particularly soon.” G.R. Wiggans, July 2008
“We are unanimously opposed to this idea.” CDDR Steering Committee, Oct 2008
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REL using Only 3K, 50K, or 850KREL using Only 3K, 50K, or 850Kwith increasing numbers of bullswith increasing numbers of bulls
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PA only 2,500 10,000 25,000 100,000
3K
50K
850K
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Expected REL with HaplotypingExpected REL with Haplotyping
Actual 3K subset of 50K genotypes• Correlation (50K, 3K) was .95 to .97• REL PA = 35% , 3K = 63% , 50K = 70%
Simulated 500K genotypes• REL, all animals 50K = 82.6%, 500K = 84%• REL improved only if >4,000 had 500K
Gains in reliability above PA• 3K chip gives >80% of 50K REL gain• 50K chip gives >96% of 500K REL gain
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Compare Young, Proven Bulls in 2006Compare Young, Proven Bulls in 2006
Bulls ranked by 2006 Net Merit• Computed from August 2006 data• Cow adjustments not included
– Genomic PTAs on ftp since Nov 2009:Genomic PTAs on ftp since Nov 2009:– ftp://aipl.arsusda.gov/pub/outgoing/validftp://aipl.arsusda.gov/pub/outgoing/valid
ation0608.zipation0608.zip
• Base adjusted using: (NM – 132) * 1.13
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Top Proven Bulls in 2006Top Proven Bulls in 2006
2006 Net Merit (adj) 2010 NM$
Dtrs Trad Gen Dtrs Gen
O Man 1,317 653 646 58,474 724
OBrian 94 385 496 1,351 456
Billion 73 470 461 3,685 232
Jet Stream 108 444 458 10,600 392
Alton 108 484 452 6,688 541
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Top Young Bulls in 2006Top Young Bulls in 2006
2006 NM$ (adj) 2010 Net Merit
Name Trad Gen Dtrs Trad Gen
Freddie 467 762 73 834 827
Awesome 472 731 90 524 576
Garrett 509 688 132 572 559
Fortunato 523 669 103 410 481
Logan 521 646 104 630 588
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Use Young Bulls MoreUse Young Bulls More
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ConclusionsConclusions
Genomic PTAs are improving
New haplotyping program allows mixing 3K, 50K, and 850K SNPs
Foreign data free if you trade
Benefits of additional phenotypes are shared by all breeders. Should costs also be shared?