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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION Title: Genomic Evaluations in the United States and Canada: A Collaboration

Authors
item Wiggans, George
item Sonstegard, Tad
item Vanraden, Paul
item Matukumalli, L - GEORGE MASON UNIV
item Schnabel, R - UNIV OF MISSOURI
item Taylor, J - UNIV OF MISSOURI
item Chesnais, J - SEMEX ALLIANCE
item Schenkel, F - UNIV OF GUELPH
item Van Tassell, Curtis

Submitted to: International Committee on Animal Recording(ICAR)
Publication Type: Proceedings
Publication Acceptance Date: June 16, 2008
Publication Date: January 12, 2009
Citation: Wiggans, G.R., Sonstegard, T.S., Van Raden, P.M., Matukumalli, L.K., Schnabel, R.D., Taylor, J.F., Chesnais, J.P., Schenkel, F.S., Van Tassell, C.P. 2009. Genomic Evaluations in the United States and Canada: A Collaboration. International Committee on Animal Recording (ICAR). ICAR Tech Ser. 13:347–353. 2009.

Interpretive Summary: Researchers in quantitative and molecular genetics in the United States and Canada have collaborated to develop and implement genomic evaluations and plan to integrate them into their national genetic evaluations for dairy cattle. In collaboration with Illumina, Inc., the BovineSNP50 BeadChip was developed to genotype over 50,000 single nucleotide polymorphisms (SNP) in a single assay. In a field test, SNP effects were estimated using current evaluations on 5285 genotyped bulls and cows. Genomic evaluations were calculated for these animals and another 750 without evaluations by combining the SNP effects with the parent averages for production, functional, calving, and type traits. The estimated SNP effects will be updated 3 times/year with the national genetic evaluations. In 2009, genomic evaluations are expected to become official and additional accuracy of genomic evaluations of genotyped animals propagated to relatives without genotypes. Methods to exchange genomically enhanced evaluations across countries need to be developed. Genomic evaluations will allow for substantial change in selection of bulls and cows for breeding programs.

Technical Abstract: Researchers in quantitative and molecular genetics in the United States and Canada have collaborated to develop and implement genomic evaluations and plan to integrate them into their national genetic evaluations for dairy cattle. Collaboration started with the Cooperative Dairy DNA Repository (CDDR) through contributions of semen from seven major artificial insemination (AI) companies in North America. In collaboration with Illumina, Inc., the BovineSNP50 BeadChip was developed to genotype over 50,000 single nucleotide polymorphisms (SNP) in a single assay. To determine the accuracy of genomic prediction, 2003 evaluations of bulls born before 1999 were used to predict the 2008 evaluations of bulls born in 2001 and 2002. Based on promising results, 6 AI organizations nominated over 750 animals to be genotyped for the initial application of genomic evaluation. Over 6100 genotypes were processed to check for parent-progeny DNA conflicts and impute some of the missing genotypes. SNP effects were estimated using current evaluations on 5285 genotyped bulls and cows. Genomic evaluations of the nominated animals were calculated by combining the SNP effects with the parent averages for production, functional, calving, and type traits. The estimated SNP effects will be updated 3 times/year with the national genetic evaluations. Additional runs, as needed, will provide evaluations for newly genotyped animals using the previously estimated SNP effects. In 2009, genomic evaluations are expected to become official and additional accuracy of genomic evaluations of genotyped animals propagated to relatives without genotypes. Release of genomic evaluations of bulls may be delayed until they are enrolled with the National Association of Animal Breeders or enter a Canadian AI stud. Methods to exchange genomically enhanced evaluations across countries need to be developed. Genomic evaluations will allow for substantial change in selection of bulls and cows for breeding programs.

Last Modified: 12/22/2014
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