1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2008 AIPL Centennial (1)G.R. Wiggans Implementing and improving genomic evaluations

2. G.R. Wiggans 2008 AIPL Centennial (2) Genomic evaluation procedure l Nominate animals for genotyping l Collect blood, hair, ear tissue, or semen l Extract DNA and genotype l Assign genotypes from image files l Check genotypes for call rate, parent-progeny consistency, and X homozygosity for bulls l Collect parent averages/estimated breeding values (EBV) l Calculate evaluations l Distribute evaluations to requesters

3. G.R. Wiggans 2008 AIPL Centennial (3) Nominate animals l Participating artificial-insemination (AI) organizations have 5-year exclusive rights to evaluate bulls genomically l Each AI organization genotypes its first-choice flushes, which usually avoids duplicate genotypes l Web-based system being developed to collect nominations w Avoid duplication w Confirm validity of identification (ID) and pedigree l Breed associations developing cow genotyping service

4. G.R. Wiggans 2008 AIPL Centennial (4) DNA sources l Semen from Cooperative Dairy DNA Repository primary source of historical DNA l Cow genotypes primarily from associated research projects l Blood and hair the most common sources of DNA for calves and cows l Bulls in waiting genotyped from semen l Ear tissue being evaluated but has not been used l Some DNA from samples collected for parentage testing

5. G.R. Wiggans 2008 AIPL Centennial (5) DNA laboratories l Research w Bovine Functional Genomics Laboratory (BFGL), USDA (Beltsville, MD) w University of Alberta (Edmonton, AB, Canada) w University of Missouri (Columbia, MO) w Illumina (San Diego, CA) l Commercial w GeneSeek (Lincoln, NE) w Genetics & IVF Institute (Fairfax, VA) w Genetic Visions (Middleton, WI) w DNA LandMarks (Saint-Jean-sur-Richelieu, QC, Canada) w Maxxam Analytics (Mississauga, ON, Canada) w ABS (DeForest, WI, through SyGen/PIC, Franklin, KY )

6. G.R. Wiggans 2008 AIPL Centennial (6) Assign genotypes l Each laboratory sends image files to BFGL l Methods developed to achieve consistent and high call rates l Direct reporting of genotypes to AIPL planned for December 2008

7. G.R. Wiggans 2008 AIPL Centennial (7) Check genotypes l 90% call rate required l Each parent-progeny pair checked for conflicting homozygotes l Maternal grandsire (MGS) also checked with higher threshold of conflicts l Cases with many conflicts or no parent genotyped checked against all genotyped animals for possible parent l Heterozygous SNP on X counted (none expected for bulls)

8. G.R. Wiggans 2008 AIPL Centennial (8) Collect parent averages/EBV l Combined U.S.-Canadian analysis requires comparable evaluations for all animals l Interbull evaluations used for bulls l Canadian Dairy Network provides evaluations of Canadian genotyped cows and maternal ancestors of genotyped animals l Holstein USA provides type evaluations l Previous Interbull evaluations used at traditional triannual evaluation releases

9. G.R. Wiggans 2008 AIPL Centennial (9) Reliability of evaluations l Reliability from inverse of a matrix with order the number of genotyped animals l Approximation necessary as number of genotyped animals increases l Daughter equivalents discounted by 0.6 to represent better the reliability of 2003 data in predicting bulls first evaluated in 2008

10. G.R. Wiggans 2008 AIPL Centennial (10) Accurate genomic evaluations l Estimates of SNP effects required l Evaluations with high reliability provide the most information l Recent animals more useful than ones from earlier generations l Reliability of genomic evaluations increases with number of predictor animals

11. G.R. Wiggans 2008 AIPL Centennial (11) Genotyped animals (October 2008) BreedBullsCowsPredictors Holstein12,2752,4457,821 Jersey1,2053691,428 Brown Swiss3653359

12. G.R. Wiggans 2008 AIPL Centennial (12) Schedule l Calculate SNP effects with each of 3 annual traditional evaluations l Calculate genomic evaluations once or more between traditional evaluations, monthly? w Recalculate SNP effects if significant number of predictor animals added w Use existing SNP effects if only young animals added

13. G.R. Wiggans 2008 AIPL Centennial (13) Official release in 2009 l Added information from genomic evaluations propagated to evaluations of descendents without genotypes l National Association of Animal Breeders (NAAB) to manage bull-owner notification and sharing among AI organizations l Public release of genomic evaluations w Cows soon after calculated w Bulls when enrolled with NAAB or Canadian AI organization w Shared by agreement with owner

14. G.R. Wiggans 2008 AIPL Centennial (14) Improvements l Employ bar codes on sample containers to reduce errors and improve lab efficiency w Widely used l Rely on breed associations to resolve parent-progeny genotype conflicts w Will happen, especially if parentage verification is switched from microsatellites to SNP l Enroll animals that might be genotyped at birth to avoid ID issues when genotyped w Needs to be required; low cost enrollment available

15. G.R. Wiggans 2008 AIPL Centennial (15) Plans to increase accuracy l Genotype more predictor bulls l Reach 1,500 Brown Swiss through foreign collaboration? l Increase genotyped Jerseys from both domestic animals and possible foreign collaboration l Investigate across-breed analysis to allow data from Holsteins to improve accuracy for Jerseys and Brown Swiss

16. G.R. Wiggans 2008 AIPL Centennial (16) Implications l Extraordinarily rapid implementation of genomic evaluations l Young bull acquisition and marketing as well as cow selection now based on genomic evaluations l Industry groups taking responsibility for genotyping and validation

17. G.R. Wiggans 2008 AIPL Centennial (17) Financial support l National Research Initiative grants, USDA l NAAB (Columbia, MO) w ABS Global (DeForest, WI) w Accelerated Genetics (Baraboo, WI) w Alta (Balzac, AB) w Genex (Shawano, WI) w New Generation Genetics (Fort Atkinson, WI) w Select Sires (Plain City, OH) w Semex Alliance (Guelph, ON) w Taurus-Service (Mehoopany, PA) l Agricultural Research Service, USDA