Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance

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) (iHS, ROH, and Pi) and three methods for inter-population analyses (Fixation index, Cross-population Composite Likelihood Ratio and Cross-population Extended Haplotype Homozygosity) (FST, XP-CLR, and XPEHH). In total, 1 966 796 single nucleotide polymorphisms (SNPs) 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 (GO) functional terms and 30 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in enrichment analysis (P < 0.05). Some of these have clear relevance to heat resistance, such as the AMPK signaling pathway and the mTOR signaling 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.