What’s Coming in Genomic Evaluations and How It Affects You

1. What’s Coming in Genomic Evaluations and How It Affects You

2. What are genomic evaluations? • DNA extracted from blood, hair, or semen • ~40,000 genetic markers (SNPs) evaluated • For each SNP, difference in PTA between animals with one allele compared to the other is estimated • Genomic evaluation combines SNP effect estimates with existing PA or PTA • Genomic data contribute ~11 daughter equivalents to reliability

3. What is a SNP? • Single-nucleotide polymorphism • Place on the chromosome where animals differ in the nucleotides (A, C, T, or G) they have • Usually not part of the gene that controls a trait – quantitative trait locus (QTL) • With enough SNPs, association between SNP alleles and QTL alleles gives useful evaluations • SNPs chosen to be distributed evenly and have both alleles well represented in population

4. Genomic vs. traditional PTA • Genotype can be thought of as source of information like parents, progeny, and records • Official PTA will have a indicator if they include a genomic contribution • One genotype is used to calculate genomic evaluations for all 29 traits • Genomic evaluations used the same way as traditional PTA • Expected to increase rate of genetic improvement because of a large decrease in generation interval

5. What’s happened so far • Illumina BovineSNP50™ BeadChip developed • Accuracy of genomic information assessed by using 2003 evaluations of bulls born before 2000 to predict 2008 evaluations of young bulls • Test evaluations began to provide genomic evaluations of bull calves in April • Jersey results released in October • New results released every 2 months • Nearly 15,000 animals genotyped through October

6. Genotyped animals (October 2008)

7. How to get animals genotyped • Participating AI organizations have 5-year exclusive right to evaluate bulls genomically • Each AI organization genotypes first-choice flushes, thereby usually avoiding duplicate genotypes • Web-based system being developed to collect nominations • Avoid duplication • Confirm validity of ID and pedigree • Breed associations developing cow genotyping service

8. What can go wrong • Sample doesn’t provide adequate DNA quality or quantity • Genotype has many SNPs that can’t be determined (90% call rate required) • Genotype conflicts with parent(s) • Pedigree error • Sample ID error • Laboratory error • Genotype checked against all others to find true parent

9. Collaboration with Canada • Semex • Supported since beginning of genomics research • Contributed valuable genotypes to first accuracy test • Genotypes will be shared between AIPL and Canadian Dairy Network • AIPL and University of Guelph collaboration

10. Collaboration with Canada (cont.) • Canadian and U.S. evaluations of genotyped animals expected to have same accuracy because same set of predictor animals used • Canada expects official release of genomic evaluations in April 2009 • Young animals expected to be evaluated only by one country • Common procedures between 2 countries assist in industry acceptance

11. 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 )

12. Use of genomic evaluations • AI organizations determine which young bulls to buy • Considered in selection of mating sires • Impact on bull dam selection will increase • May be used to market semen from 2-year-old bulls

13. January 2009 • Genomic evaluations become official • Genotyped ancestors contribute their evaluations to descendents • Evaluations of all genotyped females are public • Evaluations of males enrolled with NAAB or ≥24 months old are public • Young-bull genomic evaluations may be shared among AI organizations or disclosed by owner

14. Impact on producers • Young-bull evaluations will have accuracy of early first-crop evaluations • AI organizations may market genomically evaluated 2-year-olds • Genotypes for bull dams likely to be required • Rate of genetic improvement likely to increase by up to 50% • Progeny-test programs will change

15. 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

16. Improvements • Require bar codes on sample containers to reduce errors and improve lab efficiency • Establish routine system to detect, report, and resolve parent-progeny genotype conflicts • Enroll animals that might be genotyped at birth to minimize ID issues when genotyped • Reduce processing time by enabling labs to report genotypes directly to AIPL

17. Plans to increase accuracy • Genotype more predictor bulls (most active bulls expected to be genotyped soon) • 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

18. International implications • All major dairy countries investigating genomic selection • Interbull meeting in January to discuss how genomic evaluations should be integrated • AI organizations need to find balance between competitive benefits from treating genotypes as proprietary versus sharing • Importing countries must change rules to allow for genomically evaluated young bulls

19. Low-cost genotyping research • Develop a genetic test that’s cheap enough to enable use for most animals • Provide parentage verification/discovery • Provide genetic estimate useful for first-stage screening • 384 SNPs proposed for first test • High throughput procedures being developed

20. Longer-term possibilities • Determine inheritance of individual chromosome segments (haplotyping) • May allow better tracking of QTL • Approximate genotypes of missing ancestors to increase predictor population • Increase number of SNPs or even use entire DNA sequence

21. Implications • Extraordinarily rapid implementation of genomic evaluations • Young bull acquisition and marketing now based on genomic evaluations • Increase in diversity of bull dams considered • Industry groups taking responsibility for genotyping and validation

22. 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