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

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 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.

Figure 1

Sample location of Chinese indigenous pig populations within the Yangtze River Delta used in this study. For abbreviations, see Table 1.

Figure 2

Scatter plot for the first and second principal components. The x-axis represents the first principal component, and the y-axis represents the second principal component. Points of individuals from the same region (Table 1) are the same shape but different colours.

Figure 3

Admixture plot comprising ancestry numbers (K) from 2 to 25 of all the individuals analysed in this study. The estimated K is 25.

Figure 4

Manhattan plot of EigenGWAS. The x-axis represents the locations of SNPs, and the y-axis represents the negative logarithm of the p-values for the EigenGWAS that used PC1 (A) and PC3 (B) as the phenotype, respectively. The red line represents the threshold for statistical significance.

Figure 5

Manhattan plot of F_st for Chinese indigenous pigs. The x-axis represents the locations of SNPs, and the y-axis represents the negative log q-values for the F_st values. The red line represents the threshold for statistical significance.