A Whole Genomic Scan to Detect Selection Signatures Betweenn Berkshire and Korean Native Pig Breeds

Domestic pig breeds display a wide range of phenotypic variations that have been manipulated and shaped during the course of domestication and breed development for a wide range of traits. Scanning of the genome for selection signatures between breeds may play important role in understanding the underlie causes for observable phenotypic variations. The discovery of high density single nucleotide polymorphisms (SNPs) provide a useful starting point to perform genome–wide scan in pig populations in order to identify loci / candidate genes underlie phenotypic variation in pig breeds and facilitate genetic  improvement programs. However, prior to this study genomic region under selection in commercially selected Berkshire and Korean native pig breeds has never been detected using high density SNP markers.  To this end, we have genotyped 45 animals using Porcine SNP60 chip to detect selection signatures in the genome of the two breeds by using the F_ST approach. We calculated F_ST and heterozygosity at different significance levels as measures of genetic differentiation for each locus between Berkshire and Korean native pigs. We have identified a set of candidate genes under selection and have known to be involved in growth, size and pork quality (CART, AGL, CF7L2, MAP2K5, DLK1, GLI3, CA3 and MC3R), ear morphology and size (HMGA2 and SOX5) stress response (ATF2, MSRB3, TMTC3 and SCAF8) and  immune response ( HCST  and RYR1). Some of the genes may be used to facilitate genetic improvement programs. Our results also provide insights for better understanding of the process and influence of breed development on the pattern of genetic variations.