Integrating whole-genome resequencing data reveals adaptive selection signatures in sheep populations under extreme environments

Adaptation to extreme environments has shaped the genetic architecture of sheep, yet the genomic signatures remain insufficiently understood. This study aimed to uncover genomic regions and candidate genes mediating ovine adaptation to high-altitude, thermal, and arid environments. This study integrated whole-genome resequencing data from 444 individuals representing 91 native sheep populations with high-resolution climatic data encompassing nine ecological regions and eleven environmental variables. Distinct environmental clusters aligned with genomic structure, supporting ecological selection as a driver of population differentiation. Integrating Fst, LFMM, and Samβada analyses for genome–environment association, we identified a stringent set of 178 candidate genes. After screening populations from extreme environments using environmental data, we applied three selection signal analysis methods (Fst, XP-EHH, and θπ), identifying 2, 21, 10, and 13 candidate genes associated with high elevation, hot, cold, and arid environments, respectively. These results indicate that sheep adaptation to extreme environments involves coordinated, multi-system mechanisms integrating metabolism, water balance, immunity, and morphology. Key genes such as MVD and GHR support energy metabolism and thermogenesis, SLC26A4 and KCNMA1 regulate fluid and electrolyte homeostasis, FBXL3 modulates circadian rhythm, and BNC2, RXFP2, and PAPPA2 contribute to pigmentation, skeletal morphology, and fat deposition. Together, these polygenic adaptations enable sheep to maintain survival under complex ecological pressures. This study provides new insights into the mechanisms of sheep adaptation to extreme environments and offers a basis for improving breeds and enhancing stress resilience.