Signatures of Selection and Interspecies Introgression in the Genome of Chinese Domestic Pigs

Chinese domestic pigs have experienced strong artificial selection for thousands of years. However, the molecular mechanisms underlying the selection-causing phenotypic changes in Chinese domestic pigs are still largely unknown. Here we used whole-genome resequencing data of 54 pigs from 9 Chinese diverse breeds and 16 wild boars from 7 localities across China to identify genes that show evidence of positive selection in the process of domestication. A total of 14 candidate domestication regions were detected by selective sweep analyses of genetic differentiation and variability, and a set of genes in these candidate domestication regions were found to be related to metabolic process, development, reproduction, olfactory, behavior, and nervous system. The most promising candidate gene under selection - TBX19 - probably underlies the metabolic alteration and developmental traits, and may also associate with timidity of Chinese domestic pigs. Intriguingly, we found that the haplotype at TBX19 locus shared by nearly all Chinese domestic pigs was possibly introgressed from another Sus species. We also revealed the AHR gene associated with female reproduction is under strong positive selection. These results advance our understanding of the evolutionary history of Chinese domestic pigs and shed insights into identifying functionally important genes/mutations contributing to the phenotypic diversity in pigs.