Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

TY - JOUR

T1 - Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds

AU - Zhang, Zhe

AU - Xiao, Qian

AU - Zhang, Qian qian

AU - Sun, Hao

AU - Chen, Jiu cheng

AU - Li, Zheng cao

AU - Xue, Ming

AU - Ma, Pei pei

AU - Yang, Hong jie

AU - Xu, Ning ying

AU - Wang, Qi-shan

AU - Pan, Yu chun

PY - 2018

Y1 - 2018

N2 - 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 F st 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.

AB - 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 F st 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.

UR - http://www.scopus.com/inward/record.url?scp=85052997029&partnerID=8YFLogxK

U2 - 10.1038/s41598-018-31802-x

DO - 10.1038/s41598-018-31802-x

M3 - Journal article

C2 - 30190566

AN - SCOPUS:85052997029

SN - 2045-2322

VL - 8

SP - 1

EP - 12

JO - Scientific Reports

JF - Scientific Reports

M1 - 13352

ER -