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2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD

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Presentation on theme: "2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD"— Presentation transcript:

1 2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD Paul.VanRaden@ars.usda.gov 2011 Overview of current genomic selection in dairy cattle populations

2 FASS annual meeting, July 2011 (2) Paul VanRaden 2011 Topics - 1  Current status of dairy genomics Data available within each breed Potential of cow reference genotypes National vs. international evaluation  Future strategies All-breed and crossbred evaluation Higher density marker sets

3 FASS annual meeting, July 2011 (3) Paul VanRaden 2011 Topics - 2  Potential for genotype imputation Number of high density genotypes required per breed Impute 1.2 million from 2 different 600K chips Impute 3K and 6K together Impute sequence from high density  New recessive defects discovered

4 FASS annual meeting, July 2011 (4) Paul VanRaden 2011 Dairy Breeds and Crosses

5 FASS annual meeting, July 2011 (5) Paul VanRaden 2011 Reference Bulls by Breed BreedBullsDatabase Holstein16,000North America+ (USA-CAN-ITA-GBR) 18,000EuroGenomics (DEU-FRA-NLD-DFS) 10,000Not yet merged (many other countries) Red Dairy Cattle8,000 1,000 Scandinavia (DNK-FIN-SWE-NOR) Not yet merged (CAN, NZL) Jersey6,000Not yet merged (USA, DNK, NZL) Brown Swiss5,000Interbull (DEU-CHE-ITA-USA-FRA-SLV) Fleckvieh3,000(DEU-AUT) Montbeliarde2,000(FRA) Others0Not started yet

6 FASS annual meeting, July 2011 (6) Paul VanRaden 2011 Gain in Genomic Reliability for young animals ReferenceHeritability Bulls.30.10.03 50,000+49+50+52 15,000+35+34 5,000+20+18+17 1,500+8+7+6 500+3+2 Parent Avg REL373430 Traditional REL907565

7 FASS annual meeting, July 2011 (7) Paul VanRaden 2011 Cows in Reference Population  More females than males are being genotyped and will get phenotypes 70,687 females as of July 2011 50,393 males, most will be culled  1-step method will include cows  Test reliability from cow genotypes  Cows only, Bulls only, Cows+Bulls

8 FASS annual meeting, July 2011 (8) Paul VanRaden 2011 Correlations with Bull-Only GPTA Genetic Evaluation From: TraitTraditionalCows OnlyCows + Bulls Milk.73.81.97 Protein.76.79.96 Fat Percent.62.90.98 Productive Life.67.75.97 Som. Cell Score.56.75.97 Dtr Preg Rate.66.61.96 Final Score.78.85.96 Stature.75.87.98 Udder Depth.58.78.98

9 FASS annual meeting, July 2011 (9) Paul VanRaden 2011 National vs. International Delivery  Simple genotype exchange < 6 months to deliver results Flexible implementation by countries Same schedule + monthly updates  Interbull Brown Swiss project > 2 years to deliver results, no monthly Poor schedule, no 3K predictions Disconnected from other breeds

10 FASS annual meeting, July 2011 (10) Paul VanRaden 2011 All-Breed Genomic Evaluation  All breeds in same database  Multi-trait, correlated SNP effects 50K data = ~.3 corr, +1% REL 700K data = ~.7 corr, +10% REL (guess)  Potential to genotype crossbreds Useful for introgression or synthetic  Will major breed subsidize minor?

11 FASS annual meeting, July 2011 (11) Paul VanRaden 2011 Accuracy of Imputing High Density HD genotypes simulated within each breed

12 FASS annual meeting, July 2011 (12) Paul VanRaden 2011 High Density Imputation  Accuracy of HD imputation ~1% less using young animals vs. famous bulls  Two different chips >600K are now available (Illumina, Affymetrix) Overlap 50K chip + 60K other SNPs Test if double genotyping of some animals is needed

13 FASS annual meeting, July 2011 (13) Paul VanRaden 2011 Imputation with Two 600K Chips Bulls with both chips (n) 050200500 ChipAnimalsImputation accuracy 50K61,61598.5398.5698.5998.52 600K chip 11,00098.9699.1299.3899.49 600K chip 21,00098.0299.3899.3999.43 Both 600K chips n N/A99.7699.8399.88 Optimum imputation if 200 bulls genotyped with both 600K chips

14 FASS annual meeting, July 2011 (14) Paul VanRaden 2011 Simulated Sequences  Impute 30 million SNPs from 600K 2.9 billion monomorphic removed  Animals: 217 sequenced, 100 HD  Computer time and memory: 1 hr simulation, 3.3 hr imputation 25 Gbytes simulation, 30 imputation  Accuracy = 99.2% correct

15 FASS annual meeting, July 2011 (15) Paul VanRaden 2011 Imputation with 3K and 6K  Possible new 6K chip with double the markers of 3K, higher accuracy 99% for 6K vs. 96% for 3K for HO 98% for 6K vs. 95% for 3K for JE 98% for 6K vs. 94% for 3K for BS  Include 3K SNPs or choose new?  Imputation best with most overlap

16 FASS annual meeting, July 2011 (16) Paul VanRaden 2011 Recessive Defect Discovery  Check for homozygous haplotypes 7 to 90 expected but none observed 5 of top 11 are potentially lethal 936 to 52,449 carrier sire by carrier MGS fertility records 3.1% to 3.7% lower conception rates Some slightly higher stillbirth rates  Confirmed Brachyspina same way

17 FASS annual meeting, July 2011 (17) Paul VanRaden 2011 Potential Recessive Lethals Name Chrom- osome Loca- tion Carrier FreqSource Ancestors BTAMbase% HH1558-664.5Pawnee Farm Arlinda Chief HH2192-974.6Willowholme Mark Anthony HH3890-954.7Glendell Arlinda Chief, Gray View Skyliner JH11513-1823.4Observer Chocolate Soldier BH1741-4714.0West Lawn Stretch Improver

18 FASS annual meeting, July 2011 (18) Paul VanRaden 2011 Conclusions - 1  Small populations cannot keep up with Holsteins  All-breed genomic evaluations: Benefit all breeds if sufficient animals genotyped and phenotyped in each Enable crossbred or synthetic breed selection Identify favorable alleles in other breeds not yet present in Holstein

19 FASS annual meeting, July 2011 (19) Paul VanRaden 2011 Conclusions - 2  Data collected should be exchanged to increase return on investment Reduce costs via experimental design Cow genotypes are useful if numbers of bulls are small  Accurate imputation key to success: Can impute between two different 600K chips within breed Need ~1000 higher density genotypes in each breed  Recessive defects found in each breed

20 FASS annual meeting, July 2011 (20) Paul VanRaden 2011 Acknowledgments  Dan Null, Katie Olson, and Jana Hutchison for discovering harmful recessive haplotypes  George Wiggans for testing 6K marker sets

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