Genome Data Uncover Conservation Status, Historical Relatedness and Candidate Genes Under Selection in Chinese Indigenous Pigs in the Taihu Lake Region

Chinese indigenous pig breeds in the Taihu Lake (TL) region of Eastern China are well documented by their exceptional prolificacy. There are seven breeds in this region including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI), and Hongdenglong (HDL). At present, these breeds are facing a great threat of population decline, inbreeding depression and lineage admixture since Western commercial pigs have dominated in Chinese pig industry. To provide better conservation strategies and identify candidate genes under selection for these breeds, we explored genome-wide single nucleotide polymorphism (SNP) markers to uncover genetic variability and relatedness, population structure, historical admixture and genomic signature of selection of 440 pigs representing the most comprehensive lineages of these breeds in TL region in a context of 1228 pigs from 45 Eurasian breeds. We showed that these breeds were more closely related to each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two subgroups, one including JXB and FJ, and the other comprising of EHL, MI, HDL, MS, and SWT. In addition, HDL was highly inbred whereas EHL and MS had more abundant genetic diversity owing to their multiple conservation populations. Moreover, we identified a list of candidate genes under selection for body size and prolificacy. Our results would benefit the conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.