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United States Department of Agriculture

Agricultural Research Service

Research Project: EVALUATION OF GENOTYPES FROM AFFYMETRIX® AXIOM® GENOME-WIDE BOS 1 ARRAY PLATES
2012 Annual Report


1a.Objectives (from AD-416):
Determine the characteristics of genotypes from Affymetrix® Axiom® Genome-Wide BOS 1 Array Plates.


1b.Approach (from AD-416):
Analyze genotypes from 2,000 Holstein bulls to assess the accuracy of the genotyping and the ability to impute the full set of genotypes.


3.Progress Report:

The project is related to in-house objective 3.A [develop methodology for calculation of genome-enhanced breeding values using single-nucleotide polymorphism (SNP) genotypes]. The correspondence between genotypes from Illumina and Affymetrix high-density (HD) marker panels was investigated. Seventy animals with genotypes from both the Illumina BovineSNP50 BeadChip and the Affymetrix Axiom Genome-Wide BOS 1 Array Plate enabled determination of which SNPs.
1)gave the same genotypes,.
2)required reversing the genotype coding, or.
3)had more than one discrepancy between the two marker panels and, therefore, were designated as unreliable. Because the Illumina BovineSNP50 genotypes has only 54,609 SNPs, only about half of the 113,000 SNPs that are in common between the Illumina BovineHD BeadChip and the Affymetrix BOS 1 Array Plate could be evaluated. The SNP comparisons enabled Affymetrix HD genotypes for 19 bulls without other genotypes to be included in USDA genomic evaluations of dairy cattle. A project to compare 300 bulls with both Illumina and Affymetrix HD genotypes has been planned, but implementation depends on the contributors of semen and financing reaching agreement on the details.


Last Modified: 12/20/2014
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