Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa

Simple Summary Wild boar (WB) originate in southeastern Asia. With the migration of WBs into the European continent, their domestication started as early as the Neolithic period. With the continuous domestication and considering people's different needs for pork, many local WB breeds with their own characteristics appeared on European land. In this article, the whole genome files of 10 local WB and 38 domestic local breeds (1098 individuals in total) were screened in terms of genetic differences in metabolism, disease, and temperament by genome-wide association scan selection signals. Moreover, the geographical distribution and historical events of the different breeds were combined to confirm the wide genetic contribution of WB to the domestication process. The results of this study will provide a reference on the metabolism and emotionality between European WBs and domestic pigs. The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.