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

Songbai Yang,Bin Fan,Kui Li,Zhonglin Tang,Xiuling Li

doi:10.1186/1471-2156-15-7

Abstract

BackgroundModern 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.ResultsWe 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.ConclusionsIn 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.

Highlights

Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds
Population structure and genome-wide distribution of Fst To examine the genetic structure of the studied populations, the principle component analysis (PCA) was conducted based on all available SNP information
Taking into account the PCA analysis results, the pairwise Fst between Chinese indigenous and European commercial breeds were calculated by merging Chinese indigenous breeds and commercial breeds into two groups (CHN VS EURO)

Summary

Introduction

Modern breeding and artificial selection play critical roles in pig domestication and shape the genetic variation of different breeds. The development of high-throughput sequencing and genotyping technologies makes it possible to investigate the selective pressures of various domestic animal species at the genomic level and to identify candidate genes associated with economic traits in order to better understand the mechanisms of adaptive evolution. Akey et al [9] identified 155 regions in the canine genome that have likely been subjected to strong artificial selection, including the HAS2 gene, which is involved in skin wrinkling. Akey et al [12] suggested that the loci in the tails of the empirical distribution of Fst be used as candidate targets of selection Another method of identifying loci under selection is the EHH (Extended Haplotype Homozygosity) test [13], which identifies the genome regions that have unusually high LD and allele frequency

Objectives

Methods

Results

Discussion

Conclusion