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Increasing the Number of Single Nucleotide Polymorphisms Used in Genomic Evaluations of Dairy Cattle

Wednesday, August 20, 2014: 12:00 PM
Bayshore Grand Ballroom E-F (The Westin Bayshore)
George R. Wiggans , Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD
Tabatha A Cooper , Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD
Daniel J Null , Animal Improvement Programs Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD
Paul M VanRaden , Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD
Recorded Presentation (mp4)
Abstract Text: 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.

Keywords:

single nucleotide polymorphism

genomic evaluation

dairy cattle

genetics

See more of: Developing Effective Dairy Genomic Selection Programs for Traits or Breeds that Lack Massive Reference Populations
See more of: Species Breeding: Dairy cattle
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