Whole-genome resequencing identifies adaptive variation associated with complex terrain in southwestern Chinese ducks

The complex and diverse ecological environment of southwestern China has exerted significant influences on the domestication and genetic adaptation of local duck breeds. Although ducks exhibit extensive genetic variation in heterogeneous environments, the genomic mechanisms underlying their adaptation to the complex topography and high-altitude conditions of southwestern China remain unclear. To elucidate the evolutionary processes of genetic differentiation and environmental adaptation in regional duck populations, this study analyzed the genetic diversity, population structure, and selection characteristics based on the whole-genome resequencing data from a total of 500 individuals, encompassing 7 local duck breeds from the southwest region, 2 wild duck breeds, and 6 duck breeds from other regional. Analysis of nucleotide diversity (π) revealed that 2 wild duck breeds exhibited the highest genetic diversity (π = 0.0047-0.0052), Jianchang duck (JC) has the lowest (π = 0.0026). Among domestic breeds, those from plains areas-Sichuan Shelduck (SC), Hanzhong duck (HZ), Kaijiang duck (KJ), and Jianshui yellow-brown duck (JS) (π = 0.00360-0.00377)-showed significantly higher genetic diversity than those from topographically complex regions-Yunnan Sheldrake (YN), Sansui duck (SS), and Jianchang duck (π = 0.00259-0.00311). Populations from complex terrain (JC, YN, and SS) also displayed a high abundance of long runs of homozygosity (ROH). Analysis of the fixation index (Fst) demonstrated low genetic differentiation among YN, SS, and JC, as well as among SC, HZ, and KJ. Genomic scans comparing zFst and the log2(π ratio) identified regions in the top 5% as candidate regions, revealing 20 domestication-related genes, which are functionally associated with nervous system remodeling, angiogenesis, cell adhesion, mitochondrial metabolism, growth and reproduction; 15 regional adaptation-related genes, primarily involved in cell signal transduction, protein synthesis, hormone production, gene expression and DNA damage repair; and 15 candidate genes related to adaptation to the complex high-altitude terrain, participating in nervous system development, immune adaptation, synaptic transmission, sensory systems, cytoskeletal remodeling, and endocrine functions. Collectively, these findings enhance our understanding of evolutionary processes in southwestern Chinese ducks and provide actionable insights for their conservation and breeding programs.