Implementing and improving genomic evaluations

1. Implementing and improving genomic evaluations

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

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

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

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

6. Assign genotypes • Each laboratory sends image files to BFGL • Methods developed to achieve consistent and high call rates • Direct reporting of genotypes to AIPL planned for December 2008

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

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

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

10. Accurate genomic evaluations • Estimates of SNP effects required • Evaluations with high reliability provide the most information • Recent animals more useful than ones from earlier generations • Reliability of genomic evaluations increases with number of predictor animals

11. Genotyped animals (October 2008)

12. Schedule • Calculate SNP effects with each of 3 annual traditional evaluations • Calculate genomic evaluations once or more between traditional evaluations, monthly? • Recalculate SNP effects if significant number of predictor animals added • Use existing SNP effects if only young animals added

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

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

15. Plans to increase accuracy • Genotype more predictor bulls • Reach 1,500 Brown Swiss through foreign collaboration? • Increase genotyped Jerseys from both domestic animals and possible foreign collaboration • Investigate across-breed analysis to allow data from Holsteins to improve accuracy for Jerseys and Brown Swiss

16. Implications • Extraordinarily rapid implementation of genomic evaluations • Young bull acquisition and marketing as well as cow selection now based on genomic evaluations • Industry groups taking responsibility for genotyping and validation

17. Financial support • National Research Initiative grants, USDA • NAAB (Columbia, MO) • ABS Global (DeForest, WI) • Accelerated Genetics (Baraboo, WI) • Alta (Balzac, AB) • Genex (Shawano, WI) • New Generation Genetics (Fort Atkinson, WI) • Select Sires (Plain City, OH) • Semex Alliance (Guelph, ON) • Taurus-Service (Mehoopany, PA) • Holstein Association USA (Brattleboro, VT) • American Jersey Cattle Association (Reynoldsburg, OH) • Agricultural Research Service, USDA