Identification of Divergently Selected Regions in the Thoroughbred and Jeju Pony by using Equine SNP Chip Array

Allelic differences that are associated with traits suggest evidence for artificial selections.The sliding window approach can identify distinctly selected genomic regions between two breeds.The purpose of this study was to identify divergently selected regions between the Jeju pony (JP) and the Thoroughbred (THB) horse and to confirm the potential candidate genes.After a high-density single nucleotide polymorphism (SNP) array was analyzed for 50 JP and 50 THB, 38,378 SNPs were selected.Observed heterozygosity, expected heterozygosity and polymorphism information content were calculated to evaluate the genetic diversity of both breeds.All values for the JP were lower than those for the THB.An analysis was performed on 38,099 windows to identify the regions with the highest frequency of alleles between JP and THB.The sliding window average difference values were concentrated on 43 windows and were distributed in 10 regions.Furthermore, 19 candidate genes were detected inside the 10 regions.We found that 12 candidate genes mutually interact, and 4 candidate genes are involved in significant biological pathways.Results from this study suggest that the 10 regions are selection signatures with causative genes and mutations that affect certain traits.