Integrated SNP and SV Analyses Reveal Genetic Mechanisms Underlying High-Altitude Adaptation in Goats

High-altitude environments, characterized by hypoxia, intense ultraviolet radiation, and low temperatures, pose major challenges to livestock survival. In recent years, researchers have gradually uncovered adaptive mechanisms in livestock across different altitudes using whole-genome resequencing. Previous studies of goat altitude adaptation have been limited by small breed numbers and low sequencing depth, hindering comprehensive exploration of adaptive mechanisms across different altitudes. This study analyzed whole-genome resequencing data from 151 individuals across 17 goat breeds representing three distinct altitude gradients (high, middle, and low). Using both SNPs and structural variations (SVs), we characterized population relationships, gene flow, and the SV landscape, including QTL–SV associations and transposable element interactions. Selective sweep analyses using FST, θπ ratio, XP-CLR, XP-EHH, and LFMM identified several candidate genes associated with altitude adaptation, including ABCC4, RPS6, DSG4, and LY9, which were significantly enriched in pathways related to hypoxia response, oxidative stress, energy metabolism, angiogenesis, and nervous system regulation. Notably, ABCC4 showed ABCC4 showed recurrent candidate selection signals in both SNP and SV analyses, suggesting its potential involvement in altitude adaptation. These findings provide multi-level genomic evidence for goat adaptation to high-altitude stress and provide important insights into the adaptive evolution of goats.