Genetic Diversity and Ancestral Study for Korean Native Pigs Using 60K SNP Chip

SIMPLE SUMMARY: Assessing and understanding the genetic resources of indigenous livestock populations is necessary to address issues associated with conservation and domestic supply, etc. This study examined the Korean native pig (KNP; Sus scrofa coreanus), which is among the native porcine breeds in South Korea, in terms of its overall genetic diversity and ancestry. According to 60K single-nucleotide polymorphism (SNP) BeadChip analyses, the KNP pig showed similarity to Western breeds than to Chinese breeds. This conclusion runs contrary to popular belief as a Chinese origin of KNP pigs, as suggested by previous historical and genetic studies. We also describe the possibility of potential biases in the analysis results. ABSTRACT: The Korean native pig (KNP; Sus scrofa coreanus) is an indigenous porcine breed in South Korea considered as a valuable but dwindling genetic resource. Studies using diverse methodologies and genetic markers suggest that this population originated from the Manchu province of Northeastern China and migrated approximately 3000 years ago into the Korean peninsula. This study aimed to verify those findings by performing diversity and ancestral analyses using the 60K single-nucleotide polymorphism (SNP) BeadChip on 891 pigs of 47 breeds worldwide. We also performed principal component analysis (PCA), ancestry analyses, phylogenetic tree analysis using SNPhylo, and linkage disequilibrium analysis. Furthermore, we generated heatmap, obtained Nei’s genetic distance and F(ST) values, and explored the heterozygosity of commercial and native Korean pigs. The results demonstrated that KNP pigs are more closely related to European breeds than to Chinese breeds. In addition, as previous studies have suggested, our admixture analyses indicated that KNP pigs showed distinguishable genetic structure.