Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance
Z.Q. Zhong,
R. Li,
Z. Wang,
S.S. Tian,
X.F. Xie,
Z.Y. Wang,
W. Na,
Q.S. Wang,
Y.C. Pan,
Q. Xiao
Affiliations
Z.Q. Zhong
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
R. Li
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
Z. Wang
Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
S.S. Tian
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
X.F. Xie
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
Z.Y. Wang
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
W. Na
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
Q.S. Wang
Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China; Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
Y.C. Pan
Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China; Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
Q. Xiao
Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China; Corresponding author.
Heat stress is a major problem that constrains pig productivity. Understanding and identifying adaptation to heat stress has been the focus of recent studies, and the identification of genome-wide selection signatures can provide insights into the mechanisms of environmental adaptation. Here, we generated whole-genome re-sequencing data from six Chinese indigenous pig populations to identify genomic regions with selection signatures related to heat tolerance using multiple methods: three methods for intra-population analyses (Integrated Haplotype Score, Runs of Homozygosity and Nucleotide diversity Analysis) and three methods for inter-population analyses (Fixation index (FST), Cross-population Composite Likelihood Ratio and Cross-population Extended Haplotype Homozygosity). In total, 1 966 796 single nucleotide polymorphisms were identified in this study. Genetic structure analyses and FST indicated differentiation among these breeds. Based on information on the location environment, the six breeds were divided into heat and cold groups. By combining two or more approaches for selection signatures, outlier signals in overlapping regions were identified as candidate selection regions. A total of 163 candidate genes were identified, of which, 29 were associated with heat stress injury and anti-inflammatory effects. These candidate genes were further associated with 78 Gene Ontology functional terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways in enrichment analysis (P < 0.05). Some of these have clear relevance to heat resistance, such as the AMPK signalling pathway and the mTOR signalling pathway. The results improve our understanding of the selection mechanisms responsible for heat resistance in pigs and provide new insights of introgression in heat adaptation.
