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ARS Home » Research » Publications at this Location » Publication #236741
Title: Transition of genomic evaluation from a research project to a production system

Author
item Wiggans, George
item Vanraden, Paul
item Bacheller, Lillian
item Ross Jr, Frank
item Sonstegard, Tad
item GE MEERMAN, G - UNIV OF GRONINGEN
item Van Tassell, Curtis - Curt

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/4/2009
Publication Date: 7/12/2009
Citation: Wiggans, G.R., Van Raden, P.M., Bacheller, L.R., Ross Jr, F.A., Sonstegard, T.S., Ge Meerman, G., Van Tassell, C.P. 2009. Transition of genomic evaluation from a research project to a production system. Journal of Dairy Science. 92(E-Suppl. 1):313-314(abstr. 278).

Interpretive Summary:

Technical Abstract: Genomic data began to be included in official USDA genetic evaluations of dairy cattle in January 2009. Numerous changes to the evaluation system were made to enable efficient management of genomic information, to incorporate it in official evaluations, and to distribute evaluations. Artificial-insemination and breed organizations can use an online query to designate animals to be genotyped, to determine if the animal has already been nominated, and to check for the reason if a genotype was rejected. Four commercial laboratories provide genotypes. A genomic sample scanner generates large files of intensity data, which are used to determine the genotype of each single-nucleotide polymorphism (SNP). A technique to adjust jointly for sample and SNP effects may improve call rate and allow automation of adjustment for differences among scanners and reagent batches. Genotypes for 58,336 SNP are stored in a database table with 1 row per animal genotype. Genotypes rejected from evaluation because of parentage conflicts are stored to allow easy recovery if the conflict is resolved. For evaluation, genotypes for new animals and those with pedigree changes are extracted, combined with verified genotypes from the previous evaluation, and searched for conflicts. Validated genotypes are shared with Canada. Data for all ancestors of genotyped animals are collected, and missing pedigrees and foreign cow evaluations prior to addition of genomic data are obtained. The most recent evaluations from the Interbull Centre (Uppsala, Sweden) are combined with genomic data into a single evaluation that includes all available information. The US Jersey and Brown Swiss breed associations have sought additional animals to genotype, and the Brown Swiss association has arranged to share genotypes with European countries. The evaluation system is being streamlined to provide genomic evaluations that meet industry needs and can be produced with available resources.