Data from: Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs

Pigs from Asian and European were independently domesticated from ~9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, especially in the Chinese indigenous pigs. We performed genome-wide sequencing and searched for regions with selective sweep signals in the indigenous Chinese breed, Tongcheng pigs. Genes located in 180 selected regions were significantly associated with lipid metabolism, melanocyte differentiation, neural development, and other biological processes, which coincided with the evolutionary phenotypic changes in this breed. Two selected genes, MITF and EDNRB, are crucial for melanocyte development and are most likely associated with the two-end black colour of Tongcheng pigs. Additionally, studies of other white spotted pigs from China revealed coordinated signatures at both loci. Moreover, a synonymous substitution c.669T>C was identified in ESR1 that co-localised with a major quantitative trait locus of litter size, and the variant C allele exhibited high allele frequency in most Chinese pig populations. Furthermore, high haplotype similarity was found at genes from three other genetic loci associated with reproductive traits among Chinese pig populations. Utilizing the high-throughput sequencing, we characterized the genomic changes that adapt to artificial and environmental selections during the Chinese pigs domestication. Moreover, the high density SNPs data revealed from this work could be utilized as genomic resources in further studies to help us better understand evolutionary process of Chinese indigenous pigs’ domestication.