Genetic Diversity, Admixture and LD Analyses in Korean Native and Western Pig Breeds Using High Density SNP Panel

Korean native pig breed has been under genetic dilution from European pig breeds as result of crossbreeding to improve growth related traits. Despite the concerns of genetic introgression of Western pig breeds, yet the level of admixture is not well known. Here, we analyzed Porcine 60K SNP chip to assess genetic diversity, level of admixture and estimate LD in four Western and Korean native pig (KNP) breeds. Expected heterozygosity (H_E) was the lowest in Berkshire (0.31 ± 0.15) and the highest in Landrace (0.39 ± 0.12). KNP had comparable genetic diversity with Western pig breeds. Total inbreeding (F_IT) value of 0.265 was also significantly different from 0 (p< 0.00001). Population differentiation (F_ST) estimates were significantly different (p <0.0001) with an overall value of 0.24. KNP had the largest divergent with Duroc and Yorkshire (0.26). PC1 and PC2 results explained about (32.30%) and (22.69%) of the variations and revealed that KNP breed was closer to Western pig breeds (Berkshire and Landrace). At K = 2, with the exception of Duroc Korean native pig breed has been under genetic dilution from European pig breeds as result of crossbreeding to improve growth related traits. Surprisingly, with assumed K= 3 over 87% the Korean native pg breed shared the same cluster with Berkshire. Based up on our PCA and STRUCTURE anayses, potentiatlly Western pig breeds are introgressing into KNP, therfore KNP breed should be conserved with a proper breeding strategy for its sustainable utilization.