2012 Annual Report
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.