Updates on the genomic evaluation program

1. Updates on the genomic evaluation program

2. Goals • Increase accuracy of genomic evaluations • Provide accurate evaluations on schedule • Provide reliable tracking of use of genotypes

3. Calling genotypes at AIPL • Labs FTP intensity data from scanner to AIPL • AIPL staff trained to run GenomeStudio using lab-specific cluster files and eliminating poor-quality SNP • Call rate of 90% required for any SNP genotype to be reported

4. Nomination application • Requester required to record animals to be genotyped • Records bar code or other sample ID • Determines if animal in pedigree table • Allows labs to check ID • Provides ID of recipient of genomic evaluation • Updated with disposition of genotype

5. Genotype storage • Genotypes stored as 0, 1, 2, or 5 • Count of A allele • 5 = Missing • Genotypes identified by chip bar code and position to allow multiple genotypes per animal and reassignment • 58,336 SNP per genotype stored in long-character object giving 1 row per genotype

6. Genotype checking • Genotyped marked not usable if • Conflict with parents or progeny • Heterozygous count on X chromosome wrong for sex • Duplicate of other animal that’s not a twin, split, or clone • Non-pedigree parent-progeny relationship • Problems reported to lab and requester

7. Preparation for evaluation • Genotypes added or with updated pedigree extracted • Combined with existing master file • Checks for conflicts and duplicates repeated • Evaluations of females requested from Canada • Evaluations and parent averages assembled from domestic, Interbull, and Canadian evaluations

8. Processing at traditional evaluation • For estimation of SNP effects, previous Interbull evaluation used for bulls if Interbull evaluation was official • Final genomic evaluations calculated using current Interbull evaluation in selection-index combination step • Parent Average reported is from evaluations used in estimation of SNP effects

9. Plan to redo genotype calls • Reprocess all 20,000+ genotypes to obtain calls on low MAF SNP • Lower minimum MAF from 5% to 2% • Provide SNP for Jerseys and Brown Swiss that are monomorphic for Holsteins • Provide genotypes on full set of 116 parentage SNP

10. Schedule of genomic evaluations • Current frequency = approximately every 2 months • With successful genotype calling at AIPL and regular submissions from labs, more frequent evaluations possible • Labs need a steady flow of samples to genotype to avoid overload at cutoff

11. Effect of Interbull on schedule • Interbull proposes providing converted genomic evaluations, test run input due soon • For traditional evaluations, genomic evaluation must be completed by Interbull submission time (data cutoff for labs earlier) • Interbull will provide both traditional and genomic evaluations (output data doubled)

12. Improved genotype management • Hope to enable parentage checking by labs using 116 publicly available parentage SNP • Would enable labs to detect sample switches • Could lead to earlier correction • Breed associations could provide online checking service to labs • Conflict reports generated at receipt of genotypes at AIPL (before start of evaluation) • Chance of correction before start of evaluation • Nomination query updated as genotypes stored

13. Genotyped Holsteins in evaluations

14. Predictor animals

15. Brown Swiss • 117 genotypes received from Switzerland through exchange • Encouraging results from test using 2004 data to predict current PTA • Official release planned for August 2009

16. Increase number of predictor animals • Automatic increase as genotyped bulls in waiting receive traditional evaluations • Genotype bull dams • Genotype sires of sons and sires with many genotyped progeny • Exchange genotypes with other countries • Allow other AI organizations to genotype active bulls

17. Genotype status of active Holsteins

18. Missing sires of genotyped Holsteins

19. Ungenotyped bulls, 10+ progeny Controlling AI Genotyped Bull ID number organization Bull name progeny (no.) HODEU000345379222 204 Jardin 111 HOFRA002217051448 2139 Roumare 61 HOUSA000125349240 555 Zade 30 HONLD000255749372 11 Altalucky Mike 29 HOUSA000002289236 1 Cash 21 HOCAN000000391661 70 Skychief 16 HOUSA000002280338 7 Elation 16 HOUSA000121883236 14 Mil-Joy Wade Vixen 15 HOCAN000000400985 73 Milestone 14 HOFRA005994022699 2139 Jesther 13 HONLD000343990114 Non-AI Barnkamper Support 12 HOCAN000000394485 72 Mystic 10 HONLD000160325582 1 Swinger 10 HOGBR000000587438 29 Lookout 10

20. Ways to increase accuracy • Add predictor animals • Impute genotypes of missing animals • Use more SNP • Impute missing SNP • Improve methods of estimation of SNP effects • Haplotyping • Improved models

21. Animal ID with sex-code proposal • Sex code helpful in some situations • Interbull and Canada include sex code in ID following country code • In XML files and other genomic-related exchange formats, sex code could be included in ID • In sample ID, trailing sex code has been allowed (could be discontinued)

22. Proposed Changes • Labs enabled to validate sample ID against nominations • Nomination required for genotype to be processed • Brown Swiss evaluations to be official • Various opportunities exist to increase accuracy • Genotype calling to be done at AIPL • Control over schedule

23. 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) • Brown Swiss Association (Beloit, WI) • Agricultural Research Service, USDA