A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds

Abstract

Background: Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. China has many indigenous pig breeds with various characteristics in morphology and production performance that differ from those of foreign commercial pig breeds. However, the signatures of selection on genes implying for economic traits between Chinese indigenous and commercial pigs have been poorly understood.

Results: We identified footprints of positive selection at the whole genome level, comprising 44,652 SNPs genotyped in six Chinese indigenous pig breeds, one developed breed and two commercial breeds. An empirical genome-wide distribution of Fst (F-statistics) was constructed based on estimations of Fst for each SNP across these nine breeds. We detected selection at the genome level using the High-Fst outlier method and found that 81 candidate genes show high evidence of positive selection. Furthermore, the results of network analyses showed that the genes that displayed evidence of positive selection were mainly involved in the development of tissues and organs, and the immune response. In addition, we calculated the pairwise Fst between Chinese indigenous and commercial breeds (CHN VS EURO) and between Northern and Southern Chinese indigenous breeds (Northern VS Southern). The IGF1R and ESR1 genes showed evidence of positive selection in the CHN VS EURO and Northern VS Southern groups, respectively.

Conclusions: In this study, we first identified the genomic regions that showed evidences of selection between Chinese indigenous and commercial pig breeds using the High-Fst outlier method. These regions were found to be involved in the development of tissues and organs, the immune response, growth and litter size. The results of this study provide new insights into understanding the genetic variation and domestication in pigs.

Figure 1

Principal component analysis results based on whole genome SNP data. (235 individuals, 44,652 SNPs). Individuals are plotted according to their coordinates on the biplot of PC1 versus PC2. Breed abbreviations are described in Materials and Methods.

Figure 2

Genome-wide distribution of Fst in ALLPOP group.

Figure 3

Fst for each SNP as a function of chromosome position in Mb in the ALLPOP group. The red dashed line corresponds to the 99% threshold on the corresponding empirical distributions, and the blue indicates the 97.5% threshold.

Figure 4

Representation of the gene network N. Symbols corresponding to genes under selection are colored in grey.

Figure 5

Representation of the gene network N1. Symbols corresponding to genes under selection are colored in grey.