Estimation of genome-wide and locus-specific breed composition in pigs1

Abstract

Abstract Advances in pig genomic technologies enable implementation of new methods to estimate breed composition, allowing innovative and efficient ways to evaluate and ensure breed and line background. Existing methods to test for homozygosity at key loci involve test mating the animal in question and observing phenotypic patterns among offspring, requiring extensive resources. In this study, whole-genome pig DNA microarray data from over 8,000 SNP was used to profile the composition of U.S. registered purebred pigs using a refined linear regression method that enhances the interpretation of coefficients. In a simulation analysis, a strong correlation between true and estimated breed composition was observed (R2 = 0.94). Applying these methods to 930 Yorkshire animals registered with the National Swine Registry, 95% were estimated to have a “genome-wide” Yorkshire breed composition of at least 0.825 or 82.5%, with similar performance for evaluating datasets of registered Duroc (n = 88) Landrace (n = 129), and Hampshire (n = 17) breeds. We also developed new methods to evaluate locus-based breed probabilities. Such methods have been applied to multi-locus SNP genotypes flanking the KIT gene known to predominantly control coat color, thereby inferring the probability that an animal has haplotypes in the KIT region that are predominant in white breeds. These methods have been adopted by the National Swine Registry as a means to identify purebred Yorkshire animals.