Genetic Diversity and Differentially Selected Regions Among 5 Common U.S. Sheep Breeds

Worldwide, sheep are an economically important livestock species produced for their meat, wool, milk, and pelt. Genetic diversity and genome selection among U.S. Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds were investigated in this study using the Illumina OvineSNP50 BeadChip.  After quality-control filtering, 48,026 SNPs (single nucleotide polymorphisms) were analyzed, including 46,850 SNPs on all autosomes that were in Hardy-Weinberg equilibrium and 1,176 SNPs on chromosome X.  Phylogenetic analysis of the autosomal SNPs separated the traditional meat breed, Suffolk, from wool or maternal type sheep, Rambouillet, Columbia, Polypay, and Targhee.  Based on pair-wise estimates of F_ST, Rambouillet and Targhee had the closest relationship (F_ST = 0.0681) and significant genetic differentiation appeared between Suffolk and Rambouillet (F_ST = 0.1621).  The analysis revealed 45 and 41 differentially selected regions between Suffolk and Rambouillet and among Rambouillet-related breeds, respectively.  Differentially selected genomic region 24 accurately separated polled Suffolk from horned Rambouillet at the breed level.  Functionally known homologous genes were linked to economically important traits covered by these differentially selected regions using ovine genome v3.1 assembly.  Our data indicated that differentially selected region 13 might be good candidate region for evaluating growth rate differences between breeds. This study provides a genome-wide view on within- and between-breed genetic differentiation and biodiversity among U.S. Suffolk, Rambouillet, Columbia, Polypay, and Targhee sheep breeds.