Integration of multi-omics resources reveals genetic features associated with environmental adaptation in the Wuzhishan pig genome

Abstract

In light of the challenges posed by global climate change, the environmental adaptability of organisms is becoming increasingly important. The Wuzhishan (WZS) pig, tolerant to high heat and humidity, is an ideal model for genomic study. By characterizing its genome and assessing its genetic diversity and runs of homozygosity (ROH), we can gain insights into its current conservation status and genomic architecture. To this end, we analyzed whole-genome resequencing data from WZS pigs, identifying a comprehensive set of genetic variations: 12,844,858 single nucleotide polymorphisms (SNPs), 4,723,303 insertions and deletions (InDels), 39,311 copy number variations (CNVs), and 70,392 structural variations (SVs). ROH analysis revealed mostly short segments, indicating limited recent admixture and relatively low inbreeding, reflecting high genetic diversity. Linkage disequilibrium decay and effective population size analyses supported these findings, consistent with previous studies. Population genetic analyses of pig populations from Asia, Europe, and the Americas were conducted using SNPs, InDels, and SVs. The results obtained from different variant types were largely concordant, suggesting that the constructed genomic variation database is robust. Notably, the WZS pig displayed relatively unique genetic characteristics compared to other breeds. By intersecting the top 5 % of genes under selection signatures, we identified key pathways and candidate genes associated with important traits in WZS pigs, including reproduction (ABCC9, APC2, CABS1, CSNK1G1), immunity (ARPIN, CMAS, ITPR1, SLC25A13), meat quality (GANC, OBSCN, SLC5A4), environmental adaptability (MAGI1, PHF3), and heat tolerance (GABPB1, LRRC25). Further integrative analyses based on transcriptomic, single-cell transcriptomic, and epigenomic data were conducted to explore the regulatory mechanisms of key genes such as LRRC25 and ITPR1. We identified relevant expression quantitative trait loci (eQTLs), associated tissues, and distal regulatory elements that potentially influence gene expression. These findings suggest that epigenetic modifications may contribute to the enhanced heat tolerance and immune function observed in WZS pigs. In conclusion, WZS pigs represent a valuable genetic resource. Further research on this breed will deepen our understanding of mechanisms underlying environmental adaptability, and provide important insights into evolutionary biology and breeding strategies for improved resilience in livestock.