1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2008 G.R. WiggansDHI-Provo Herd Management Conference (1) What’s Coming in Genomic Evaluations and How It Affects You

2. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (2) What are genomic evaluations? l DNA extracted from blood, hair, or semen l ~40,000 genetic markers (SNPs) evaluated l For each SNP, difference in PTA between animals with one allele compared to the other is estimated l Genomic evaluation combines SNP effect estimates with existing PA or PTA l Genomic data contribute ~11 daughter equivalents to reliability

3. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (3) What is a SNP? l Single-nucleotide polymorphism l Place on the chromosome where animals differ in the nucleotides (A, C, T, or G) they have l Usually not part of the gene that controls a trait – quantitative trait locus (QTL) l With enough SNPs, association between SNP alleles and QTL alleles gives useful evaluations l SNPs chosen to be distributed evenly and have both alleles well represented in population

4. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (4) Genomic vs. traditional PTA l Genotype can be thought of as source of information like parents, progeny, and records l Official PTA will have a indicator if they include a genomic contribution l One genotype is used to calculate genomic evaluations for all 29 traits l Genomic evaluations used the same way as traditional PTA l Expected to increase rate of genetic improvement because of a large decrease in generation interval

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

6. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (6) Genotyped animals (October 2008) BreedBullsCowsPredictors Holstein12,2752,4457,821 Jersey1,2053691,428 Brown Swiss3653359

7. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (7) How to get animals genotyped l Participating AI organizations have 5-year exclusive right to evaluate bulls genomically l Each AI organization genotypes first-choice flushes, thereby usually avoiding duplicate genotypes l Web-based system being developed to collect nominations w Avoid duplication w Confirm validity of ID and pedigree l Breed associations developing cow genotyping service

8. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (8) What can go wrong l Sample doesn’t provide adequate DNA quality or quantity l Genotype has many SNPs that can’t be determined (90% call rate required) l Genotype conflicts with parent(s) w Pedigree error w Sample ID error w Laboratory error w Genotype checked against all others to find true parent

9. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (9) Collaboration with Canada l Semex w Supported since beginning of genomics research w Contributed valuable genotypes to first accuracy test l Genotypes will be shared between AIPL and Canadian Dairy Network l AIPL and University of Guelph collaboration

10. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (10) Collaboration with Canada (cont.) l Canadian and U.S. evaluations of genotyped animals expected to have same accuracy because same set of predictor animals used l Canada expects official release of genomic evaluations in April 2009 l Young animals expected to be evaluated only by one country l Common procedures between 2 countries assist in industry acceptance

11. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (11) 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 )

12. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (12) Use of genomic evaluations l AI organizations determine which young bulls to buy l Considered in selection of mating sires l Impact on bull dam selection will increase l May be used to market semen from 2- year-old bulls

13. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (13) January 2009 l Genomic evaluations become official l Genotyped ancestors contribute their evaluations to descendents l Evaluations of all genotyped females are public l Evaluations of males enrolled with NAAB or ≥24 months old are public l Young-bull genomic evaluations may be shared among AI organizations or disclosed by owner

14. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (14) Impact on producers l Young-bull evaluations will have accuracy of early first-crop evaluations l AI organizations may market genomically evaluated 2-year-olds l Genotypes for bull dams likely to be required l Rate of genetic improvement likely to increase by up to 50% l Progeny-test programs will change

15. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (15) 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

16. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (16) Improvements l Require bar codes on sample containers to reduce errors and improve lab efficiency l Establish routine system to detect, report, and resolve parent-progeny genotype conflicts l Enroll animals that might be genotyped at birth to minimize ID issues when genotyped l Reduce processing time by enabling labs to report genotypes directly to AIPL

17. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (17) Plans to increase accuracy l Genotype more predictor bulls (most active bulls expected to be genotyped soon) 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

18. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (18) International implications l All major dairy countries investigating genomic selection l Interbull meeting in January to discuss how genomic evaluations should be integrated l AI organizations need to find balance between competitive benefits from treating genotypes as proprietary versus sharing l Importing countries must change rules to allow for genomically evaluated young bulls

19. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (19) Low-cost genotyping research l Develop a genetic test that’s cheap enough to enable use for most animals l Provide parentage verification/discovery l Provide genetic estimate useful for first-stage screening l 384 SNPs proposed for first test l High throughput procedures being developed

20. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (20) Longer-term possibilities l Determine inheritance of individual chromosome segments (haplotyping) w May allow better tracking of QTL l Approximate genotypes of missing ancestors to increase predictor population l Increase number of SNPs or even use entire DNA sequence

21. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (21) Implications l Extraordinarily rapid implementation of genomic evaluations l Young bull acquisition and marketing now based on genomic evaluations l Increase in diversity of bull dams considered l Industry groups taking responsibility for genotyping and validation

22. G.R. Wiggans 2008 DHI-Provo Herd Management Conference (22) 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 Holstein Association USA (Brattleboro, VT) l American Jersey Cattle Association (Reynoldsburg, OH) l Agricultural Research Service, USDA