1. G.R. Wiggans* and P.M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *george.wiggans@ars.usda.gov G.R. WiggansADSA 2010 (1) Improved reliability approximation for genomic evaluations in the United States Abstr. 617

2. G.R. WiggansADSA 2010 (2) Reliability (REL) l Measure of amount of information in an evaluation l Squared correlation between EBV and true breeding value l May be expressed as daughter equivalents (DE = k*Rel/(1-Rel), where k = variance ratio) l Diagonal element of inverse of coefficient matrix l Approximation used when computing inverse is too time consuming

3. G.R. WiggansADSA 2010 (3) Approximation of REL l Time to compute inverse increases cubically with number of genotyped animals l When inversion discontinued in 2009, all animals given same contribution from genomics l Genomic relationship (G) with predictor animals measures information contributed l REL of predictor animal evaluation used for weighting

4. G.R. WiggansADSA 2010 (4) Approximation procedure l Convert traditional reliability to DE l Remove contribution from parents l Convert back to reliability for weighting genomic relationship l Sum weighted relationships across predictor animals ( ∑ G w ). Similar to genomic future inbreeding

5. G.R. WiggansADSA 2010 (5) Conversion of ∑ G w to reliability l August 2009 reliabilities from inverse converted to DE and genomic contribution (DE g ) extracted l DE g predicted from ∑ G w for 3 Holstein groups w 8,353 bulls with traditional evaluations w 3,559 cows with traditional evaluations w 16,135 animals without traditional evaluations

6. G.R. WiggansADSA 2010 (6) Conversion of ∑ G w (continued) l Straight line fit well except for low ∑ G w w Floor set at 30 DE g l Slopes and floor differ by breed l Applicable across traits because same k used to calculate DE g

7. G.R. WiggansADSA 2010 (7) Coefficients to predict DE g BreedFloor Bulls*Cows* Young animals** Holstein Jersey 200.0580.056 0.051 100.0880.086 0.072 Brown Swiss 60.122 0.085 *Traditional evaluation **No traditional evaluation

8. G.R. WiggansADSA 2010 (8) Genotyped Holsteins Date Young animals** All animals Bulls*Cows* Bulls Heifers 04-097,600 2,711 9,690 1,94321,944 01-108,974 4,348 14,061 6,03133,414 02-109,378 5,086 15,328 7,62037,412 04-109,770 7,415 16,007 8,63041,822 05-109,958 7,940 16,594 9,77244,264 06-109,958 8,122 17,507 10,71346,300 07-109,963 8,186 18,187 11,30947,645 *Traditional evaluation **No traditional evaluation

9. G.R. WiggansADSA 2010 (9) REL for 18,187 young Holstein bulls 0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000 60616465666768697071727374757677787980 REL (%) for mlk yield Bulls (no.)

10. G.R. WiggansADSA 2010 (10) REL (%) for Holsteins born ≥2005 Trait Young animals** Bulls*Cows* Bulls Heifers Milk87 80 76 Protein87 79 76 Productive life72 68 65 64 Somatic cell score80 74 71 Daughter pregnancy rate68 65 62 PTA type79 74 70 Service-sire calving ease82 71 72 70 Daughter calving ease74 68 67 66 Service-sire stillbirth66 60 59 58 Daughter stillbirth67 62 59 Net merit79 73 70 Animals, n1,262 4,487 18,117 11,171 *Traditional evaluation **No traditional evaluation

11. G.R. WiggansADSA 2010 (11) G matrix l Computing time increases by (number of SNP)*(number of genotyped animals) 2 l Options for calculating genomic relationships w Get faster computer w Run program in parallel w Compute relationships before evaluations w Calculate only for new animals; store old ones w Calculate based only on SNP from 3K chip w Use Eigenvalues & Eigenvectors to reduce processing l If G used to calculate EBV greater precision needed

12. G.R. WiggansADSA 2010 (12) Genotype quality and reliability l Problems – greater with imputation w Missing genotypes w Genotype incorrect l Remedies w Discount for missing SNP genotypes w Consider if parents were genotyped w Discount uniformly for 3K chip

13. G.R. WiggansADSA 2010 (13) Implementation of 3K chip l Chip expected to ship this week l 2,882 usable SNP, plus 14 on Y Chromosome l Unofficial evaluations expected Sept. 7 l Large initial use expected l New genotyping laboratories

14. G.R. WiggansADSA 2010 (14) Conclusions l Improved REL approximation implemented April 2010 l REL reduced for animals less related to predictor population w MN control-line bulls w Foreign bulls l Approximation relies on G matrix l Modification planned to account for loss in accuracy from imputation

15. G.R. WiggansADSA 2010 (15) Brought to you by AIPL Staff