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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #303160
Title: Increasing the number of single nucleotide polymorphisms used in genomic evaluations of dairy cattle

Author
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: 4/21/2014
Publication Date: 8/17/2014
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.

Interpretive Summary:

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.