1. 2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA Paul.VanRaden@ars.usda.gov 2008 Genomic Prediction Results

2. NAAB DSEC April 2008 (2) Paul VanRaden 2008 Measuring Genetic Similarity  Cattle genome sequenced in 2004 30 chromosome pairs (including X,Y) 3 billion letters from each parent  Illumina Bovine SNP50 TM Chip 58,000 genetic markers in 2007 39,835 used in genomic predictions Cost about $200 per animal

3. NAAB DSEC April 2008 (3) Paul VanRaden 2008 How Related are Relatives?  Example: Full sibs are expected to share 50% of their DNA on average, with SD of 5% may actually share 40% to 60% of their DNA because each inherits a different mixture of chromosome segments from the two parents. SD 3.5% reported previously was low

4. NAAB DSEC April 2008 (4) Paul VanRaden 2008 Simulated Results (Apr 2007)  1777 older and 500 younger bulls  10,000 SNPs and 100 QTLs  Reliability vs parent average REL 58% vs 36% for young bulls Higher REL if major loci and Bayesian methods used, lower if many loci (>100) affect trait

5. NAAB DSEC April 2008 (5) Paul VanRaden 2008 Simulated Results (2008)  8271 older and 1984 younger bulls  40,000 SNPs and 500 QTLs  Provided timing, memory test  Reliability vs parent average REL 79% vs 37% expected for young bulls 76% vs 37% observed in simulation

6. NAAB DSEC April 2008 (6) Paul VanRaden 2008 Genotyped Bulls (Feb 2007) from Cooperative Dairy DNA Repository  DNA of bulls stored in Beltsville (BFGL)  2560 proven bulls used to computed predictions Bulls born 1994-1996 with >75% reliability of Net Merit Plus ancestor bulls born 1952-1993  659 later bulls used to test predictions Born 2001 with >75% reliability of Net Merit

7. NAAB DSEC April 2008 (7) Paul VanRaden 2008 Proposed Genotyping (Apr 2007) Data cutoff

8. NAAB DSEC April 2008 (8) Paul VanRaden 2008 Current Genotyped Animals (n=6005)

9. NAAB DSEC April 2008 (9) Paul VanRaden 2008 Acknowledgments  Funding: NRI grants 2006-35205-16888, 16701 CDDR Contributors (NAAB, Semex)  Genotyping and DNA extraction: BFGL, U. Missouri, U. Alberta, GeneSeek, GIFV, and Illumina  Computing from AIPL staff

10. NAAB DSEC April 2008 (10) Paul VanRaden 2008 Genomic Methods  Direct genomic evaluation Inversion for linear prediction, REL Iteration for nonlinear prediction  Combined genomic evaluation Traditional PA or PTA, subset PA or PTA, and direct genomic combined by REL in 3 x 3 selection index Nonlinear genomic predictions used

11. NAAB DSEC April 2008 (11) Paul VanRaden 2008 Nonlinear and Linear Regressions for marker allele effects

12. NAAB DSEC April 2008 (12) Paul VanRaden 2008 Actual Results (Feb 2007 data)  August 2003 PTAs for 2650 older bulls to predict January 2008 daughter deviations for 569 younger bulls (total = 3119 bulls)  Results computed for 27 traits: 5 yield, 5 health, 16 conformation, and Net Merit  Nonlinear A used, B didn’t work

13. NAAB DSEC April 2008 (13) Paul VanRaden 2008 Marker P-Values for Net Merit

14. NAAB DSEC April 2008 (14) Paul VanRaden 2008 Marker Effects for Net Merit

15. NAAB DSEC April 2008 (15) Paul VanRaden 2008 Marker Effects for Milk

16. NAAB DSEC April 2008 (16) Paul VanRaden 2008 Marker Effects for Final Score

17. NAAB DSEC April 2008 (17) Paul VanRaden 2008 Reliabilities and R-square values comparing traditional to genomic predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Net Merit 821365418 Milk 3044385416 Fat 1539386527 Protein 3143385113 Fat % 2858387234 Protein % 3251386628

18. NAAB DSEC April 2008 (18) Paul VanRaden 2008 Reliabilities and R-square values comparing traditional to genomic predictions Squared corr (x100) Reliability TraditionalGenomic Trait PAGenomicPARealizedGain Prod Life 919284719 SCS 723325422 DPR 1523254015 SCE 192331365 DCE 242731365 Final Score 243228379

19. NAAB DSEC April 2008 (19) Paul VanRaden 2008 Expected vs Observed Reliability  Reliability for predictee bulls Average across traits: 57% expected vs. 48% observed vs. 30% PA Observed range 72% (fat pct) to 36% PTA regressions.8 to.9 of expected  Redo 2003 cutoff using April data  Develop REL and PTA adjustments

20. NAAB DSEC April 2008 (20) Paul VanRaden 2008 Clones and Identical Twins 21HO2121, 21HO2125, 21HO2100, CAN6139300, CAN6139303 TraditionalGenomic BullDtrsNM$RELNM$REL Triton - ETN98-36382-37191 Triad - ETN26-30668-37091 Trey - ETN108-39583-37191 Loyalty108-18578-19687 Lauriet83-20376-19687

21. NAAB DSEC April 2008 (21) Paul VanRaden 2008 X, Y, Pseudo-autosomal SNPs 487 SNPs 35 SNPs 0 SNPs 35 SNPs

22. NAAB DSEC April 2008 (22) Paul VanRaden 2008 SNPs on X Chromosome  Each animal has two evaluations Expected genetic merit of daughters Expected genetic merit of sons Difference is sum of effects on X SD =.1 σ G, smaller than expected  Correlation with sire’s daughter vs. son PTA difference was significant (P<.0001), regression close to 1.0

23. NAAB DSEC April 2008 (23) Paul VanRaden 2008 SNP Density Comparison 2130 older and 261 younger bulls REL of PA Genomic REL Trait10K20K40K Net Merit35454948 Milk37495251 Fat37525557 Protein37525453 Productive Life28444542 SCS31444547 Dtr Preg Rate21444946

24. NAAB DSEC April 2008 (24) Paul VanRaden 2008 Genetic Evaluation Advances and increases in genetic progress YearAdvance% Gain 1935Daughter-dam comparison100 1962Herdmate comparison50 1974Modified cont. comparison5 1977Protein evaluated4 1973Records in progress10 1989Animal model4 1994Net merit, PL, and SCS50 2008Genomic selection>40

25. NAAB DSEC April 2008 (25) Paul VanRaden 2008 Conclusions  Genomic predictions significantly better than parent average (P <.0001) for all 26 traits tested  Gains in reliability from 2650 bulls (Feb data) equivalent on average to 9 daughters with records  April data included 5285 proven bulls, more analysis needed