Estimation of US Yorkshire breed composition using genomic data

The Yorkshire breed uses white coat color as a selection requirement to indicate breed purity. In this study, genomic information from chromosomal regions, as well as the whole genome, was applied to estimate breed composition of purebred Yorkshire animals. Genotypes for approximately 60,000 SNP from the Illumina PorcineSNP60 BeadChip (60K) were available for reference animals for which the genetic background was known, study animals that included Yorkshire sires (Tes_York, n = 889), and known crossbred animals that had Yorkshire heritage (Tes_U, n = 12). Haplotypes of SNP flanking the KIT (Dominant white locus) and MC1R (Melanocortin receptor 1) genes were developed for reference animals for the Duroc, Hampshire, Landrace, Yorkshire, and Pietrain breeds. For the KIT region, haplotypes observed in Yorkshire reference animals were also found in 84 and 7% of the haplotypes in Landrace and Pietrain reference animals, respectively. They were not found in Duroc or Hampshire reference animals. The sensitivity and specificity of haplotype analysis was 0.93 and 0.75, respectively. In addition, whole genome SNP information was used in regression analyses to further differentiate breed composition. Using 60K, 90% of regression coefficients for Yorkshire, indicating relative Yorkshire composition, ranged from 0.791 to 1.073 and 0.524 to 1.06 in Tes_York and Tes_U, respectively. Regression coefficients for 90% of Hampshire ranged from -0.029 to 0.052 and -0.005 to 0.379 in Tes_York and Tes_U, respectively. Animals in Tes_U were likely of Yorkshire and Hampshire breed origin. The sensitivity and specificity of regression analysis was 0.96 and 0.58, respectively. Combining haplotype and regression analyses, 810 Tes_York animals were accepted as purebred Yorkshire. Genomic information can be used as a tool to describe an animal's breed composition and reduce the need for progeny testing for white coat color verification.