Genome-Wide Analysis Reveals Copy Number Variation-Mediated Adaptive Evolution in Chickens Under Diverse Environmental and Domestication Pressures

To elucidate the genetic basis underlying chicken adaptation to diverse environmental selection pressures, this study performed a genome-wide analysis of copy number variations (CNVs) using publicly available whole-genome resequencing data from global chicken populations. Population differentiation (FST) and nucleotide diversity (π ratio) were integrated to identify signatures of selection associated with thermal adaptation, domestication, and high-altitude adaptation, followed by the identification of candidate genes and enriched biological pathways. In total, 6862, 9348, and 9384 high-confidence copy number variations (CNVs) were identified in the heat adaptation group, domestication group, and high-altitude adaptation group, respectively. Candidate genes associated with heat adaptation include AQP9, SLC4A8, CAT, SMPD2, and CLOCK, which are mainly enriched in biological processes related to water and ion homeostasis, antioxidant defense, and circadian rhythm regulation. Candidate genes related to domestication, such as IL18R1, HTR2C, GRIN2A, PRKAG2, and FABP1, are mainly involved in neuroactive ligand-receptor interaction, energy metabolism, immune regulation, and melanogenesis. In contrast, candidate genes identified in high-altitude populations include EDNRB, ITPR1, OGDH, PPARA, and ADCY6, which are significantly enriched in vascular smooth muscle contraction, the tricarboxylic acid (TCA) cycle, the PPAR signaling pathway, and pathways related to hypoxic metabolic adaptation. The above findings indicate that distinct environmental selection pressures and artificial selection pressures have shaped population-specific CNV patterns in the chicken genome and promoted the formation of phenotypic adaptation through regulating water–salt balance, neural function, energy metabolism, vascular homeostasis, and hypoxic response pathways.