1. G.R. Wiggans, T. A. Cooper* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD George.Wiggans@ars.usda.gov Tabatha.Cooper@ars.usda.gov Paul.Vanraden@ars.usda.gov ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (1) Cow Adjustments for Genomic Predictions of Holstein and Jersey Bulls

2. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (2) Introduction l Most countries use only bull PTAs in genomic prediction equations l Information from genotyped cows was not increasing reliability of yield traits l Inflated PTA values of cows cause genomic predictions to suffer in accuracy l Solution was to make cow contributions comparable to those from bulls

3. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (3) DGV vs Traditional PTA (Bulls) DGV – evaluation based on genomics only Traditional PTA – no genomics -226 0 226 454 680 907 -70125267360436501568636716847 PA Milk (kg) Milk (kg) Bull DGVBull Traditional PTA

4. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (4) DGV vs Traditional PTA (Cows) -454 -226 0 226 434 680 907 1134 -324129261360435501568641722878 PA Milk (kg) Milk (kg) Cow DGVCow Traditional PTA DGV – evaluation based on genomics only Traditional PTA – no genomics

5. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (5) Adjustments Needed 0 226 454 680 907 1134 0.40.61.02.5 Daughter Equivalent (progeny) Std. Dev of Dereg M.S. (Milk, kg) Cow Bull -181 -91 0 91 181 272 362 680 20002001200220032004200520062007 Birth year Milk (kg) Cow Bull Variance Adjustment Mean Adjustment

6. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (6) Cow Adjustment l Deregressed Mendelian Sampling (MS) = (PTA-PA) / f(REL) l Adj. MS =.84*MS - 784 l Adj. PTA = f(REL)*(Adj. MS+ PA n ) + (1- f(REL)*PA n ) f(REL) = weight in PTA from own records and progeny Breed MilkFatProtein SDMeanSDMeanSDMean Holstein0.84-7840.72-27.50.77-23.0 Jersey0.72-6430.67-31.40.67-24.2

7. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (7) DGV vs Traditional PTA (Cows) PA Milk (kg) Milk (kg) Cow DGVCow Traditional PTAAdjusted Traditional PTA -454 -226 0 226 434 680 907 1134 -324129261360435501568641722878 DGV – evaluation based on genomics only Traditional PTA – no genomics

8. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (8) Validation Populations l Predictor population - Animals with August 2006 evaluations − No Females − Unadjusted − Adjusted l Predicted population – Bulls with no evaluation in August 2006 but did have an evaluation in June 2010

9. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (9) Effects on Regression (ß) TraitNo FemalesUnadjustedAdjusted Milk0.910.870.91 Fat0.950.870.96 Protein0.890.830.88 % Fat0.991.001.02 % Protein0.880.890.90 Deregressed value = α + ß·PTA

10. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (10) Interbull Validation of Regression TraitExpectedUnadjustedAdjusted Protein0.90 +.020.830.88 Within 2 SE of expected to pass Fail Validation Test Pass Validation Test

11. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (11) Effects on Bias TraitNo FemalesUnadjustedAdjusted Milk-127.5-117.0-8.7 Fat-6.9-5.8-1.9 Protein-2.5-1.81.3 % Fat-0.005 -0.002 % Protein0.007 0.008 Bias = actual - predicted

12. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (12) Effects on Genomic Reliability TraitNo FemalesUnadjustedAdjusted Milk66.564.667.5 Fat72.469.873.1 Protein63.060.663.7 % Fat85.3 85.8 % Protein76.076.478.0

13. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (13) Unadjusted Protein SNP effects Abs (SNP Effect)

14. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (14) Unadjusted Protein SNP effects (PAR) Abs (SNP Effect)

15. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (15) Adjusted Protein SNP effects (PAR) Abs (SNP Effect)

16. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (16) Adjusted Protein SNP effects (PAR) Abs (SNP Effect)

17. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (17) Milk SNP effects

18. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (18) Fat SNP effects

19. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (19) Benefit of Adjustment l Regressions closer to 1 l Reduction in Bias l Gain in Genomic Reliability l SNP estimates less affected by sex l Similar benefits for Jersey

20. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (20) The future l Investigate solutions to the problem of not being able to compare genotyped and non- genotyped cows − Reduce heritability − Add dam-herd interaction − Varying heritability by herd − Vary adjustments by sub-population l Increased genotyping with 3K chip will change genotyped population, which may necessitate modification of adjustment

21. ADSA · PSA · AMPA · CSAS · ASAS Joint Annual Meeting July 2010 (21) Thank You! l Dr. John Cole – SNP effect graphics l AIPL Staff