1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2011 National Breeders Roundtable (1) Dairy Cattle Genomic Evaluation Program Update

2. Wiggans2011 National Breeders Roundtable (2) National Dairy Genetic Evaluation Program l Collaboration between ARS and Dairy industry l Dairy Industry partners w DHI Milk recording w Breed Associations w Artificial Breeding organizations w Other farm service organizations

3. Wiggans2011 National Breeders Roundtable (3) Expanding Industry Role l Collaboration of: w ARS - Animal Improvement Programs Lab w Council on Dairy Cattle Breeding l Council – Plan to provide staff for data collection, database management, calculation and distribution of evaluations l AIPL – Focus on research and Development

4. Wiggans2011 National Breeders Roundtable (4) History of genomic evaluations l Dec. 2007 BovineSNP50 BeadChip available l Apr. 2008 First unofficial evaluation released l Jan. 2009 Genomic evaluations official for Holstein and Jersey l Aug. 2009 Official for Brown Swiss l Sept. 2010 Unofficial evaluations from 3K chip released l Dec. 2010 3K genomic evaluations official

5. Wiggans2011 National Breeders Roundtable (5) Genomic Evaluations l Genotype calves l Calculate evaluation l Select intensively l Reduces cost of finding top bulls l Increases rate of genetic progress

6. Wiggans2011 National Breeders Roundtable (6) Data & evaluation flow Animal Improvement Programs Laboratory, USDA AI organizations, breed associations Dairy producers DNA laboratories samples genotypes nominations evaluations

7. Wiggans2011 National Breeders Roundtable (7) Changes in last 12 Months l New Chips w Low density 3K, 2900 SNP w High Density − Illumina 777,062 SNP − Affymetrics 648,855 SNP l Collaboration with Italy and Great Britain l Adjustment of cow evaluations to improve compatibility with those of bulls l Improved accuracy of imputation

8. Wiggans2011 National Breeders Roundtable (8) HD - $20050K - $100 3K - $45 Chip Types HD 50K 3K $200 $100 $45

9. Wiggans2011 National Breeders Roundtable (9) Cow adjustment – background l Genotyped cows adjusted starting April 2010 l Required to prevent distortions in SNP effect estimates by making genotyped cows and bulls comparable l Made PTA of genotyped cows not comparable (lower) than those of non-genotyped cows l Industry requested adjustment on non- genotyped cows for April 2011 evaluation.

10. Wiggans2011 National Breeders Roundtable (10) Cow adjustment l Make evaluations of non-genotyped cow more like those of genotyped cows l Reduce variation to that of bulls l Subtract 40% of within year parent average deviation l Additional adjustment for genotyped cows l Discontinue using foreign cow evaluations in predictor population

11. Wiggans2011 National Breeders Roundtable (11) Imputation l Based on splitting the genotype into individual chromosomes (maternal & paternal contributions) l Missing SNP approximated by tracking inheritance from ancestors and descendents l Imputed Dams increase predictor population l 3K & 50K genotypes merged by imputing SNP not on 3K

12. Wiggans2011 National Breeders Roundtable (12) Imputation improvements l Use multiple segment lengths to detect common haplotypes l Long segments increase chance that matching haplotype came from a common ancestor l Shorter segments improve fill in l 2 -3 percentage points increase in accuracy achieved

13. Wiggans2011 National Breeders Roundtable (13) High density (HD) genotypes l Illumina Bovine HD BeadChip available w 777,962 SNP w Collaborations with GBR, ITA, & CAN to provide genotypes w Over 400 genotypes from research projects in database

14. Wiggans2011 National Breeders Roundtable (14) l Affymetrics HD w 648,855 SNP w Research project to determine usefulness w Optimized for genetic coverage w Over 100,00 SNP in common with Illumina High density (HD) genotypes

15. Wiggans2011 National Breeders Roundtable (15) Use of HD l Some increase in accuracy from better tracking of QTL l Potential for across breed evaluations l Requires few new HD genotypes once adequate base for imputation developed l Imputation improvements were particularly beneficial in imputing HD

16. Wiggans2011 National Breeders Roundtable (16) 3K chip l 2900 SNP mostly from SNP50 chip w 14 Y Chr SNP included for sex validation w Evenly spaced across 30 Chr l Developed to reduce cost of genotyping l 2614 SNP used after removing poor performers l Rapid adoption, 4,731 animal genotypes submitted for May genomic evaluation

17. Wiggans2011 National Breeders Roundtable (17) Genotype processing improvements l Labs submit genotypes for automated checking for: w Nomination issues w Genotype calling issues w Sample ID errors l Reports of conflicts enhanced w Excel compatible format w Additional ID information l Online pedigree correction

18. Wiggans2011 National Breeders Roundtable (18) Parentage validation and discovery l Parent-progeny conflicts detected w Reported to breeds and requesters w Correct sire usually detected l Maternal Grandsire checking w SNP at a time checking w Haplotype checking more accurate l Breeds moving to accept SNP in place of microsatellites

19. Wiggans2011 National Breeders Roundtable (19) Genotyped Holsteins Date Young animals** All animals Bulls*Cows* Bulls Heifers 04-10 9,770 7,415 16,007 8,63041,822 08-1010,430 9,37218,65211,02149,475 09-1010,611 9,45319,38913,33352,786 10-1010,616 9,78720,18415,28855,877 11-1010,61910,17520,83617,09558,727 12-1011,29312,82521,16118,33663,615 01-1111,19413,58222,56722,99970,342 02-1111,19613,93523,33026,27074,731 03-1111,71314,38224,50529,92980,529 04-1112,15211,22425,20236,54585,123 05-1112,42911,83426,13940,99691,398 *Traditional evaluation **No traditional evaluation

20. Wiggans2011 National Breeders Roundtable (20) May Genotypes – Holstein and Jersey 0 500 1000 1500 2000 2500 3000 3500 200020012002200320042005200620072008200920102011 Birth Year Number of Genotyped Animals HolsteinJersey

21. Wiggans2011 National Breeders Roundtable (21) May Genotypes − Holstein MalesFemales

22. Wiggans2011 National Breeders Roundtable (22) May Genotypes − Jersey 0 100 200 300 400 500 600 700 800 900 1000 3K50K Chip Type Number of Genotyped Jerseys MalesFemales

23. Wiggans2011 National Breeders Roundtable (23) Holstein Bulls 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 200020012002200320042005200620072008200920102011 Birth Year Number of Bulls Total10 HerdsGenotypedBoth

24. Wiggans2011 National Breeders Roundtable (24) Determination of Reliability l Sum of genomic relationships with the predictor animals weighted by reliability l Call rate l Expected imputation error rate l Reliability of parent average w Larger impact if dam not genotyped

25. Wiggans2011 National Breeders Roundtable (25) Reliabilities for young Holsteins* *Animals with no traditional PTA in April 2011 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 404550556065707580 Reliability for PTA protein (%) Number of animals 3K genotypes 50K genotypes

26. Wiggans2011 National Breeders Roundtable (26) Use of genomic evaluations l Determine which young bulls to bring into AI service l Use to select mating sires l Pick bull dams l Market semen from 2-year-old bulls

27. Wiggans2011 National Breeders Roundtable (27) Use of 3K genomic evaluations l Sort heifers for breeding w Flush w Sexed semen w Beef bull l Confirm parentage to avoid inbreeding l Predict inbreeding depression better l Precision mating considering genomics (future)

28. Wiggans2011 National Breeders Roundtable (28) Future

29. Wiggans2011 National Breeders Roundtable (29) Increase in accuracy l Genotyped bulls get traditional evaluation when 5 years old l Possible genotyping of 10,000 bulls with semen in CDDR l Collaboration with more countries l Use of more SNP from HD chips l Full sequencing

30. Wiggans2011 National Breeders Roundtable (30) Application to more traits l Animal’s genotype is good for all traits l Traditional evaluations required for accurate estimates of SNP effects l Traditional evaluations not currently available for heat tolerance or feed efficiency l Research populations could provide data for traits that are expensive to measure l Will resulting evaluations work in target population?

31. Wiggans2011 National Breeders Roundtable (31) Summary l Extraordinarily rapid implementation of genomic evaluations l Young-bull acquisition and marketing now based on genomic evaluations l Genotyping of many females because of 3K chip l Application of HD chips being developed

32. Wiggans2011 National Breeders Roundtable (32)