G.R. Wiggans* 1, P.M. VanRaden 1, L.R. Bacheller 1, F.A. Ross, Jr. 1, M.E. Tooker 1, J.L. Hutchison 1, T.S. Sonstegard 2, and C.P. Van Tassell 1,2 1 Animal Improvement Programs and 2 Bovine Functional Genomics Laboratories, Agricultural Research Service, USDA, Beltsville, MD ADSA – 2009 (1) Transition of genomic evaluation from a research project to a production system Abstr. 278

Wiggans ADSA – 2009 (2) Genomic evaluation system l Provides timely evaluations of young bulls for purchasing decisions l Increases accuracy of evaluations of bull dams l Assists in selection of service sires, particularly for low-reliability traits

Wiggans ADSA – 2009 (3) Obtaining genotypes l Collect tissue sample (hair and blood most common for calves) l Extract DNA l Bind DNA to chip (12 samples/chip) l Scan chip to create intensity files l Call genotypes (GenomeStudio software)

Wiggans ADSA – 2009 (4) Before clustering adjustment 86% call rate

Wiggans ADSA – 2009 (5) After clustering adjustment 100% call rate

Wiggans ADSA – 2009 (6) Calling genotypes l Genotypes called by Tad Sonstegard, BFGL, through April 2009 l AIPL staff trained to run GenomeStudio l Cluster files shared with 4 commercial labs to promote call harmonization l Labs began providing genotypes in June

Wiggans ADSA – 2009 (7) Managing sample ID l Web query established for nominations w Indicates missing pedigrees w Designates who receives evaluation w Provides sample status, including rejection reasons l Query used by labs to convert sample ID to registration number and detect ID entry errors

Wiggans ADSA – 2009 (8) Genotype storage l Single row per sample l Genotype usability determined, pedigree change triggers a recheck l Counts of validated parents and progeny maintained to indicate reliability of ID assignment l Multiple genotypes per animal allowed l Genotypes with invalid ID assignment stored but not usable l DNA source (blood, semen, or hair) stored

Wiggans ADSA – 2009 (9) Genotype usability l Genotype consistent with parents (few SNP conflicts) l No genomic parent-progeny relationships not in pedigree found l Not identical to another animal (unless identical twin, split embryo, or clone) l X heterozygosity w For bulls, low for X chromosome specific SNP w For cows, high unless both X chromosomes from same ancestor

Wiggans ADSA – 2009 (10) Loading genotype database l 50,972 SNP called l Calling redone to provide genotypes for this set l Many corrections required to make sample ID match l Genotypes from Illumina, University of Missouri, University of Alberta, and Switzerland also included

Wiggans ADSA – 2009 (11) SNP selection l MAF >1% for at least 1 breed l Based on MAF of 50% (Threshold more restrictive as MAF decreases) w Call rate of >90% w Parent-progeny conflicts of <1% l Not a duplicate l 43,385 SNP selected across breed

Wiggans ADSA – 2009 (12) Evaluation preparation l Pedigree file created w Checked for missing ancestors w Pedigree requested for missing ancestors l Canadian evaluations obtained for cows l Type evaluations obtained for Holsteins

Wiggans ADSA – 2009 (13) Genomic evaluation calculation l Automated evaluation system l Jobs dispatched based on successful completion of prerequisites and processor availability l Most traits run in parallel

Wiggans ADSA – 2009 (14) Genomic evaluation news l Evaluations official w Holstein and Jerseys (January 2009) w Brown Swiss (August 2009) l June 2009 trait changes w Net Merit $ as sum of traits, not individual w Holstein feet & legs and rear teat placement added l Current Interbull evaluation added at final selection-index step triannually

Wiggans ADSA – 2009 (15) Plans l Monthly release of genomic evaluations if practical

Wiggans ADSA – 2009 (16) Summary l Simplification of genotype processing w Web-based nomination and validation w Genotype calling by labs w Database table to store genotypes l Evaluation improvement w Incorporation of current Interbull evaluation at end w Canadian type evaluations for cows

Wiggans ADSA – 2009 (17) 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 Cattle Breeders’ Association (Beloit, WI) l Agricultural Research Service, USDA Thanks! from the bovine g-nome