Abstract
The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.
Highlights
Pigs were independently domesticated in Europe and China approximately 9000 years ago[1,2,3,4]
It is possible to use selection signature detection methods to elucidate the genetic background of the distinct phenotypes of pig breeds, which were influenced by different selection pressures
Except for Duroc pigs, all individuals from the western pig breeds were clustered together. This is consistent with the breed’s history, since Duroc pigs were developed in the United States, while other western pig breeds were originated from the European continent
Summary
Pigs were independently domesticated in Europe and China approximately 9000 years ago[1,2,3,4]. There has been gene flow from Chinese pigs to European pig breeds since the nineteenth century[18] aiming to improve the productivity of local breeds. To obtain the superior characteristics of western pigs, human-mediated hybridization and introgression were performed to improve the productivity and environmental adaptability of Chinese pig breeds. This is similar to the formation of the hybrid nature of Chinese Sutai pigs cultivated from Chinese Erhualian and Duroc pigs[16,22]. We collected samples from western pig breeds and different Chinese pig breeds with distinct phenotypic characteristics in the Yangtze River Delta (YRD) area in China. Some Chinese pig breeds in this region might have gene flow from western breeds
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