Updates on the genomic evaluation program G R

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Updates on the genomic evaluation program G. R. Wiggans Animal Improvement Programs Laboratory Agricultural

Updates on the genomic evaluation program G. R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD george. [email protected] usda. gov Council on Dairy Cattle Breeding meeting prequel 1) ( G. R. Wiggans 2009

Goals l Increase accuracy of genomic evaluations l Provide accurate evaluations on schedule l

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

Calling genotypes at AIPL l l l Labs FTP intensity data from scanner to

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

Nomination application l Requester required to record animals to be genotyped w Records bar

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 Council on Dairy Cattle Breeding meeting prequel 4) ( G. R. Wiggans 2009

Genotype storage l Genotypes stored as 0, 1, 2, or 5 Count of A

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

Genotype checking l l Genotyped marked not usable if w Conflict with parents or

Genotype checking l 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 Problems reported to lab and requester Council on Dairy Cattle Breeding meeting prequel 6) ( G. R. Wiggans 2009

Preparation for evaluation l Genotypes added or with updated pedigree extracted l Combined with

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 Council on Dairy Cattle Breeding meeting prequel 7) ( G. R. Wiggans 2009

Processing at traditional evaluation l l l For estimation of SNP effects, previous Interbull

Processing at traditional evaluation l l l 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 Council on Dairy Cattle Breeding meeting prequel 8) ( G. R. Wiggans 2009

Plan to redo genotype calls l l Reprocess all 20, 000+ genotypes to obtain

Plan to redo genotype calls l l 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 Council on Dairy Cattle Breeding meeting prequel 9) ( G. R. Wiggans 2009

Schedule of genomic evaluations l l l Current frequency = approximately every 2 months

Schedule of genomic evaluations l l l 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 Council on Dairy Cattle Breeding meeting prequel 10) ( G. R. Wiggans 2009

Effect of Interbull on schedule l l l Interbull proposes providing converted genomic evaluations,

Effect of Interbull on schedule l l l 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) Council on Dairy Cattle Breeding meeting prequel 11) ( G. R. Wiggans 2009

Improved genotype management l Hope to enable parentage checking by labs using 116 publicly

Improved genotype management l Hope to enable parentage checking by labs using 116 publicly available parentage SNP Would enable labs to detect sample switches w Could lead to earlier correction w l l Breed associations could provide online checking service to labs 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 Council on Dairy Cattle Breeding meeting prequel 12) ( G. R. Wiggans 2009

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

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

Predictor animals Breed Bulls Holstein 7, 600 Jersey 1, 807 Brown Swiss 655 Council

Predictor animals Breed Bulls Holstein 7, 600 Jersey 1, 807 Brown Swiss 655 Council on Dairy Cattle Breeding meeting prequel 14) ( Cows 2, 711 337 41 Total 10, 311 2, 144 696 G. R. Wiggans 2009

Brown Swiss l l l 117 genotypes received from Switzerland through exchange Encouraging results

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

Increase number of predictor animals l l l Automatic increase as genotyped bulls in

Increase number of predictor animals l l l 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 Council on Dairy Cattle Breeding meeting prequel 16) ( G. R. Wiggans 2009

Genotype status of active Holsteins Group All Not genotyped From participating AI organizations Other

Genotype status of active Holsteins Group All Not genotyped From participating AI organizations Other AI organizations Council on Dairy Cattle Breeding meeting prequel 17) ( No. 713 210 15 195 G. R. Wiggans 2009

Missing sires of genotyped Holsteins Progeny (no. ) 1 2 3 4 5 6

Missing sires of genotyped Holsteins Progeny (no. ) 1 2 3 4 5 6 7 8 9 10– 111 Council on Dairy Cattle Breeding meeting prequel 18) ( Bulls (no. ) 210 57 22 12 7 7 12 3 2 14 G. R. Wiggans 2009

Ungenotyped bulls, 10+ progeny Controlling AI Bull ID number organization HODEU 000345379222 204 HOFRA

Ungenotyped bulls, 10+ progeny Controlling AI Bull ID number organization HODEU 000345379222 204 HOFRA 002217051448 2139 HOUSA 000125349240 555 HONLD 000255749372 HOUSA 000002289236 HOCAN 000000391661 HOUSA 000002280338 HOUSA 000121883236 15 HOCAN 000000400985 HOFRA 005994022699 2139 HONLD 000343990114 Non-AI HOCAN 000000394485 HONLD 000160325582 HOGBR 000000587438 Council on Dairy Cattle Breeding meeting prequel 19) ( Genotyped Bull name progeny (no. ) Jardin 111 Roumare 61 Zade 30 11 Altalucky Mike 1 Cash 21 70 Skychief 7 Elation 16 14 Mil-Joy Wade Vixen 73 Milestone Jesther 13 Barnkamper Support 72 Mystic 1 Swinger 29 Lookout 29 16 14 10 10 12 10 G. R. Wiggans 2009

Ways to increase accuracy l Add predictor animals w l Use more SNP w

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

Animal ID with sex-code proposal l l Sex code helpful in some situations Interbull

Animal ID with sex-code proposal l l 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) Council on Dairy Cattle Breeding meeting prequel 21) ( G. R. Wiggans 2009

Proposed Changes l Labs enabled to validate sample ID against nominations w Nomination required

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 Council on Dairy Cattle Breeding meeting prequel 22) ( G. R. Wiggans 2009

Financial support l l National Research Initiative grants, USDA NAAB (Columbia, MO) w ABS

Financial support l l National Research Initiative grants, USDA NAAB (Columbia, MO) w ABS Global (De. Forest, 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 Council on Dairy Cattle Breeding meeting prequel 23) ( G. R. Wiggans 2009