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United States Department of Agriculture

Agricultural Research Service

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle

Authors
item Wiggans, George
item Cooper, Tabatha
item Null, Daniel
item Vanraden, Paul

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: April 21, 2014
Publication Date: August 17, 2014
Citation: Wiggans, G.R., Cooper, T.A., Null, D.J., Van Raden, P.M. 2014. Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle. World Congress of Genetics Applied in Livestock Production. Vancouver, Canada, Aug. 17–22. 3 pp.

Technical Abstract: A small increase in the accuracy of genomic evaluations of dairy cattle was achieved by increasing the number of SNP used to 61,013. All the 45,195 SNP used previously were retained, and 15,818 SNP were selected from higher density genotyping chips if the magnitude of the SNP effect was among the top 1,000 effects of the added SNP for at least 1 trait. The imputation of the additional SNP was based on 4,037 GeneSeek Genomic Profiler HD and 2,262 Illumina BovineHD genotypes available as of March 2013. Markers for 7 mutation tests based on recessive codes provided by breed associations were included in the SNP set. For Holsteins, the mean gain in reliability across all traits from using the additional SNP was 0.5 percentage points. Correlations of new with previous predictions were close to 0.99 for all traits. The new SNP set improves the value of genomic testing.

Last Modified: 10/23/2014
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