1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george.wiggans@ars.usda.gov 2009 G.R. WiggansCouncil on Dairy Cattle Breeding meeting prequel (1) Updates on the genomic evaluation program

2. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (2) Goals l Increase accuracy of genomic evaluations l Provide accurate evaluations on schedule l Provide reliable tracking of use of genotypes

3. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (3) Calling genotypes at AIPL l Labs FTP intensity data from scanner to AIPL l AIPL staff trained to run GenomeStudio using lab-specific cluster files and eliminating poor-quality SNP l Call rate of 90% required for any SNP genotype to be reported

4. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (4) Nomination application l Requester required to record animals to be genotyped w Records bar code or other sample ID w Determines if animal in pedigree table l Allows labs to check ID l Provides ID of recipient of genomic evaluation l Updated with disposition of genotype

5. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (5) Genotype storage l Genotypes stored as 0, 1, 2, or 5 w Count of A allele w 5 = Missing l Genotypes identified by chip bar code and position to allow multiple genotypes per animal and reassignment l 58,336 SNP per genotype stored in long- character object giving 1 row per genotype

6. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (6) Genotype checking l Genotyped marked not usable if w Conflict with parents or progeny w Heterozygous count on X chromosome wrong for sex w Duplicate of other animal that’s not a twin, split, or clone w Non-pedigree parent-progeny relationship l Problems reported to lab and requester

7. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (7) Preparation for evaluation l Genotypes added or with updated pedigree extracted l Combined with existing master file l Checks for conflicts and duplicates repeated l Evaluations of females requested from Canada l Evaluations and parent averages assembled from domestic, Interbull, and Canadian evaluations

8. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (8) Processing at traditional evaluation l For estimation of SNP effects, previous Interbull evaluation used for bulls if Interbull evaluation was official l Final genomic evaluations calculated using current Interbull evaluation in selection- index combination step l Parent Average reported is from evaluations used in estimation of SNP effects

9. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (9) Plan to redo genotype calls l Reprocess all 20,000+ genotypes to obtain calls on low MAF SNP l Lower minimum MAF from 5% to 2% l Provide SNP for Jerseys and Brown Swiss that are monomorphic for Holsteins l Provide genotypes on full set of 116 parentage SNP

10. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (10) Schedule of genomic evaluations l Current frequency = approximately every 2 months l With successful genotype calling at AIPL and regular submissions from labs, more frequent evaluations possible l Labs need a steady flow of samples to genotype to avoid overload at cutoff

11. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (11) Effect of Interbull on schedule l Interbull proposes providing converted genomic evaluations, test run input due soon l For traditional evaluations, genomic evaluation must be completed by Interbull submission time (data cutoff for labs earlier) l Interbull will provide both traditional and genomic evaluations (output data doubled)

12. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (12) Improved genotype management l Hope to enable parentage checking by labs using 116 publicly available parentage SNP w Would enable labs to detect sample switches w Could lead to earlier correction l Breed associations could provide online checking service to labs l Conflict reports generated at receipt of genotypes at AIPL (before start of evaluation) w Chance of correction before start of evaluation w Nomination query updated as genotypes stored

13. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (13) Genotyped Holsteins in evaluations

14. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (14) Predictor animals BreedBullsCowsTotal Holstein7,6002,71110,311 Jersey1,8073372,144 Brown Swiss65541696

15. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (15) Brown Swiss l 117 genotypes received from Switzerland through exchange l Encouraging results from test using 2004 data to predict current PTA l Official release planned for August 2009

16. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (16) Increase number of predictor animals l Automatic increase as genotyped bulls in waiting receive traditional evaluations l Genotype bull dams l Genotype sires of sons and sires with many genotyped progeny l Exchange genotypes with other countries l Allow other AI organizations to genotype active bulls

17. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (17) Genotype status of active Holsteins GroupNo. All713 Not genotyped210 From participating AI organizations15 Other AI organizations195

18. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (18) Missing sires of genotyped Holsteins Progeny (no.)Bulls (no.) 1210 257 322 412 57 67 7 83 92 10–11114

19. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (19) Ungenotyped bulls, 10+ progeny Controlling AIGenotyped Bull ID numberorganizationBull nameprogeny (no.) HODEU000345379222 204Jardin 111 HOFRA0022170514482139Roumare61 HOUSA000125349240 555Zade30 HONLD00025574937211Altalucky Mike29 HOUSA000002289236 1Cash21 HOCAN00000039166170Skychief16 HOUSA000002280338 7Elation16 HOUSA00012188323614Mil-Joy Wade Vixen15 HOCAN00000040098573Milestone14 HOFRA0059940226992139Jesther13 HONLD000343990114Non-AIBarnkamper Support12 HOCAN00000039448572Mystic10 HONLD000160325582 1Swinger10 HOGBR00000058743829Lookout10

20. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (20) Ways to increase accuracy l Add predictor animals w Impute genotypes of missing animals l Use more SNP w Impute missing SNP l Improve methods of estimation of SNP effects w Haplotyping w Improved models

21. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (21) Animal ID with sex-code proposal l Sex code helpful in some situations l Interbull and Canada include sex code in ID following country code l In XML files and other genomic-related exchange formats, sex code could be included in ID l In sample ID, trailing sex code has been allowed (could be discontinued)

22. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (22) Proposed Changes l Labs enabled to validate sample ID against nominations w Nomination required for genotype to be processed l Brown Swiss evaluations to be official l Various opportunities exist to increase accuracy l Genotype calling to be done at AIPL w Control over schedule

23. G.R. Wiggans 2009 Council on Dairy Cattle Breeding meeting prequel (23) 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 Brown Swiss Association (Beloit, WI) l Agricultural Research Service, USDA