Genomic analyses identify distinct patterns of selection in game fowl and Nami chicken.

The Xishuangbanna game fowl (GF) and Shangri-La Nami chicken (NF) represent two distinct chicken populations shaped by contrasting selection pressures. However, the genomic basis of their divergent phenotypic and physiological traits remains poorly understood. This study employed a comprehensive genomic approach to decipher their genetic adaptations, including de novo chromosome-level genome assembly for NF, whole-genome resequencing of 40 NFs, and comparative analyses against wild chicken (Gallus gallus) populations alongside our previously published GF genomic data. Our analyses revealed distinct genetic architectures between the two breeds. We identified 75 GF-specific and 76 NF-specific positively selected genes, with only six shared between breeds, indicating largely independent evolutionary trajectories. Selective sweep analysis further identified 794 and 1,102 selected genes in GF and NF, respectively. GF exhibited strong selection signals in genes related to growth regulation (GH, ACADS), immune response (IL18), and pigmentation (BCO2), reflecting artificial selection for fighting ability and ornamental traits. In contrast, NF showed enrichment in high-altitude adaptation genes, including those involved in oxidative phosphorylation (COX7C), cardiovascular function (AGTR1), and skeletal development (ADAMTS7). Pathway analysis revealed divergent adaptive strategies: GF was enriched in MAPK signaling, calcium signaling, and immune-related pathways, supporting enhanced muscular development and injury response. NF showed strong selection in hypoxia-responsive pathways including oxidative phosphorylation, cardiac muscle contraction, and calcium signaling, indicating coordinated adaptation to high-altitude conditions. Population structure analyses confirmed clear genetic differentiation between the breeds, with NF exhibiting larger genomic regions under selection and higher linkage disequilibrium, consistent with stronger directional selection. Our findings demonstrate how distinct selection pressures have shaped the genomic landscapes of GF and NF. The identified candidate genes and pathways provide valuable insights into the genetic mechanisms underlying aggression, muscular development, and high-altitude adaptation in domestic chickens, offering important resources for future breeding and conservation strategies.