1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov Select Sires‘ Holstein Sire Evaluation Committee – 2011 (1) USDA genetic evaluation update

2. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (2) Changes for April l Adjustment of yield evaluations for all cows l Improved imputation l Chip type and genomic inbreeding added to output l Multitrait heifer and cow conception rates

3. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (3) 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.

4. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (4) Cow adjustment l Make evaluations of non-genotyped cow more like those of genotyped cows l Make similar to bull evaluations l Reduce variation to that of bulls l Subtract 40% of within year parent average deviation l Additional adjustment for genotyped cows

5. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (5) Cow adjustment for genomics l Cow PTA compared to bull only direct genomic values l Cows with reliability from records and progeny > 55 further adjusted l Canadian and other foreign cow evaluations excluded from estimation of SNP effects w Not adjusted by all cow adjustment w Receive larger adjustment for own evaluation and for use in Parent Average

6. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (6) Cow adjustment

7. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (7) Comparison of top 100 Cows Mean (lbs)Standard deviation MinimumMaximum Holstein Unadjusted PTA Milk for top 100 cows Non-genotyped226839611753105 Genotyped178336811012719 Adjusted PTA Milk for the same 100 cows Non-genotyped18713389502544 Genotyped17984247812636 Jersey Unadjusted PTA Milk for top 100 cows Non-genotyped14876315933834 Genotyped11543114141866 Adjusted PTA Milk for the same 100 cows Non-genotyped12806183413441 Genotyped12953244662119

8. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (8) 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

9. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (9) 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

10. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (10) 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 l Affymetrics HD w 648,855 SNP w Optimized for genetic coverage w NAAB negotiating plan for use

11. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (11) 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

12. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (12) 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, 4,288 animal genotypes submitted for April genomic evaluation

13. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (13) 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

14. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (14) 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 *Traditional evaluation **No traditional evaluation

15. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (15) April Genotypes – Holstein 0 500 1000 1500 2000 1998-200620072008200920102011 Birth year Number of Genotypes 3K Females3K Males50K Females50K Males

16. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (16) April Genotypes - Jersey 0 50 100 150 200 250 2001-200620072008200920102011 Birth year Number of Genotypes 3K Females3K Males50K Females50K Males

17. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (17) Holstein Bulls 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 200020012002200320042005200620072008200920102011 Birth Year Number of Bulls Total10 HerdsGenotypedBoth

18. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (18) Reliabilities for young animals* *Animals with no traditional PTA in March 2011

19. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (19) 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

20. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (20) 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

21. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (21) 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)

22. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (22) Future

23. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (23) 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

24. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (24) 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?

25. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (25) 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

26. WiggansSelect Sires‘ Holstein Sire Evaluation Committee – 2011 (26)