Transition of genomic evaluation from a research project

Transition of genomic evaluation from a research project to a production system Abstr. 278 G. R. Wiggans*1, P. M. Van. Raden 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 2 Improvement Programs and Bovine Functional Genomics Laboratories, Agricultural Research Service, USDA, Beltsville, MD *george. wiggans@ars. usda. gov ADSA – 2009 (1)

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

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 (Genome. Studio software) ADSA – 2009 (3) Wiggans

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

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

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

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

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

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

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

SNP selection l l MAF >1% for at least 1 breed 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 ADSA – 2009 (11) Wiggans

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

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

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

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

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

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) Thanks! from the bovine g-nome 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 ADSA – 2009 (17) Wiggans