Year: 2025
Type: article
Abstract: Local adaptation allows animal populations to persist in diverse and changing environments, yet its genomic underpinnings remain poorly characterized in livestock. Chinese indigenous pigs, renowned for their rich phenotypic and ecological diversity, offer a powerful model for investigating environmental adaptation. Here, we integrated whole-genome resequencing data, environmental variables, genotype-environment association (GEA) analyses, and functional annotation to explore the adaptive genomic landscape of 46 native pig breeds across China. Based on 578 individuals and 17.7 million SNPs, we performed genome-wide GEA using latent factor mixed models (LFMMs), identifying 8644 SNPs significantly associated with environmental factors, including 310 linked to precipitation in the wettest quarter (BIO16). Redundancy analysis (RDA) and gradient forest modeling identified BIO16 as a major environmental driver of genomic variation. Functional annotation of BIO16-associated SNPs revealed significant enrichment in regulatory elements and genes highly expressed in the lung, spleen, hypothalamus, and intestine, implicating immune and metabolic pathways in local adaptation. Among the candidate loci, MS4A7 exhibited strong association signals, population differentiation, and tissue-specific regulation, suggesting a role in precipitation-mediated adaptation. This work enhances our understanding of livestock adaptation and informs climate-resilient conservation and breeding strategies.
Source: Animals
DOI: 10.3390/ani15162412
Institution: South China Agricultural University
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $2,896
Awards: G1947737455, G8066125006
OpenAlex ID: W4413292792