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

Pigs from Asia and Europe were independently domesticated from c. 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, particularly for indigenous Chinese pigs. Here, we performed a
genome-wide analysis to screen 196 regions with selective sweep signals in
Tongcheng pigs, which are a typical indigenous Chinese breed. Genes
located in these regions have been found to be involved in lipid
metabolism, melanocyte differentiation, neural development and other
biological processes, which coincide with the evolutionary phenotypic
changes in this breed. A synonymous substitution, c.669T>C, in
ESR1, which colocalizes with a major quantitative trait locus for litter
size, shows extreme differences in allele frequency between Tongcheng pigs
and wild boars. Notably, the variant C allele in this locus exhibits high
allele frequency in most Chinese populations, suggesting a consequence of
positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C)
related to reproductive traits were found to have high haplotype
similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are
implied to shape the two-end black colour trait in Tongcheng pig.
Subsequent SNP microarray studies of five Chinese white-spotted breeds
displayed a concordant signature at both loci, suggesting that these two
genes are responsible for colour variations in Chinese breeds. Utilizing
massively parallel sequencing, we characterized the candidate sites that
adapt to artificial and environmental selections during the Chinese pig
domestication. This study provides fundamental proof for further research
on the evolutionary adaptation of Chinese pigs.