1. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD george.wiggans@ars.usda.gov Select Sires’ Sire Committee meeting (1) 2008 Routine genomic predictions

2. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (2) Getting started l Select animals to genotype l Assign identification to animals l Collect tissue samples l Extract DNA l Check DNA quality and standardize concentration on mother plate l Propagate to daughter plates

3. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (3) Infinium ® II assay protocol © 2006 Illumina, Inc.− For research use only Source: Infinium® II Assay Workflow, Illumina ® SNP Genotyping

4. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (4) Evaluation workflow l Check genotypes for inheritance errors l Calculate genomic relationships l Infer missing genotypes l Estimate SNP effects

5. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (5) Evaluation workflow – cont. l Combine genomic information with parent average w Based on gain from genomics over parent average for animals with genotypes l Apply to all traits l Distribute results

6. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (6) First genomic evaluation l 832 animals nominated for genotyping l Over 4,700 predictor bulls from US and Canada l Embryo flushes w AI organization with first choice arranged for genotyping w Genotypes shared by agreement between studs

7. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (7) First genomic evaluation – cont. l Calves must have unique ID w Holstein offers Easy-ID program l Samples sent to GeneSeek for extraction l BFGL genotypes animals with chips purchased through cooperative research and development agreement l AIPL calculates genomic evaluations

8. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (8) First genomic evaluation – cont. l April 1 distribution to cooperators w Evaluations sent to AI organizations that paid for chip w Evaluation mailed to owner of animal l Future schedule at least every 2 months

9. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (9) Proposed mailer (text) This report contains results obtained from studying DNA of bull HOUSA00000000001, GENOMICS EXTRAORDINARE-ET, born in 2007. Breeders can now determine which genes each animal inherited and include this completely new source of information in genetic evaluations. Predicted transmitting abilities have used pedigrees to calculate probabilities about the genes that relatives share. A new DNA chip developed by the USDA Bovine Functional Genomics Laboratory, Illumina, and other research partners can read >50,000 single nucleotide polymorphisms (SNPs) evenly distributed across all 30 chromosomes to determine which alleles are shared. Genetic effects for each SNP were estimated using DNA of 3,119 proven Holstein bulls contributed by members of the National Association of Animal Breeders and by Semex in Canada. The sum of these genetic effects is used to adjust an animal's PTA for each trait and for net merit. Genomic predictions (on reverse side of this letter) for genotyped Holsteins are being distributed to owners to aid in selection decisions, but these should not yet be used in advertising. More research and education is needed before genomic predictions replace official PTAs. Scientific articles describing the statistical methods and results from both simulated and real genomic data are available from http://aipl.arsusda.gov/News/News.htm. The AIPL and BFGL will work closely with industry partners to implement this new technology.

10. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (10) Proposed mailer (tables) Health traits Trait namePTAPAPTA RELPA REL Net merit 3424766439 Daughter pregnancy rate –1.3–1.15334 Productive life 0.80.35433 Somatic cell score 3.103.195936

11. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (11) Proposed mailer (tables) – cont. Yield traits Trait namePTAPAPTA RELPA REL Milk 144218436640 Fat 31 62 6640 Fat % –0.08–0.026640 Protein 45616640 Protein % 0.000.026640

12. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (12) Proposed mailer (tables) – cont. Calving traits Trait namePTAPAPTA RELPA REL Sire calving ease 7.16.65631 Daughter Calving ease 7.15.9 5231

13. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (13) Proposed mailer (tables) – cont. Type traits Trait namePTAPAPTA RELPA REL Final score 1.30.65731 Dairy form 2.00.9 5731 Fore udder attachment 0.7 5731 Rear udder height 1.10.85731 Rear legs (rear view) 2.01.35230 etc.

14. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (14) Future plans l Use genomic information to update evaluations of animals not genotyped (3 times each year) l Genomic evaluations calculated and released more frequently (monthly? weekly?) l Bull evaluations made public when bull enrolled with NAAB l Cow evaluations made public immediately at USDA web site l January 2009 target for public release

15. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (15) Genomic selection (New Zealand) l Identify top 30,000 bull calves annually based on parent average l Genotype by 6 days old with 768 SNP l Genotype top 500 bull calves with 50k SNP chip l Keep top 100 bull calves

16. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (16) Genomic selection (NZ) – cont. l At 1 year, limited progeny test to check for undesirable recessives l At 2 years, market as part of DNA team l When progeny tested, graduate best to progeny-proven team

17. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (17) Research topics l Differential inclusion of X-chromosome effects to predict bulls vs cows l Contribution of cows to accuracy of genomic prediction l Benefit of genotyping more predictor bulls l Optimum methods for combining genomic and current evaluation

18. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (18) Research topics – cont. l Practicality of screening and parentage verification with low-cost, low-SNP number assay l Potential of freely sharing enough SNP for accurate parentage discovery l Computational methods to improve accuracy, such as haplotyping

19. G.R. Wiggans 2008 Select Sires’ Sire Committee meeting (19) Summary l Genomic prediction has great promise l Extensive changes in bull acquisition and marketing and in cow selection expected l Routine genotyping and validation will become industry rather than research responsibilities l We are trying to develop a system that makes this new information work for everyone