Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

Wenchang chicken, a prized local breed in Hainan Province of China renowned for its exceptional adaptability to tropical environments , good meat quality, is deeply favored by the public. However, an insufficient understanding of its population architecture and the unclear genetic basis that governs its typical attributes have posed challenges in the protection and breeding of this precious breed. To address these gaps, we conducted whole-genome resequencing on 200 Wenchang chicken samples derived from 10 distinct strains , we gathered data on an array of 21 phenotype traits. Popula- tion genomics analysis unveiled distinctive population structures in Wenchang chickens, primarily attributed to strong artificial selection for different feather colors. Selec- tion sweep analysis identified a group of candidate genes, including PCDH9, DPF3, CDIN1, SUGCT, closely linked to adaptations that enhance resilience in tropical island habitats. Genome-wide association studies (GWAS) highlighted potential candidate genes associated with diverse feather color traits, encompassing TYR, RAB38, TRPM1, GABARAPL2, CDH1, ZMIZ1, LYST, MC1R, and SASH1. Through the comprehensive analysis of high-quality genomic and phenotypic data across diverse Wenchang chicken resource groups, this study unveils the intricate genetic backgrounds and population structures of Wenchang chickens. Additionally, it identifies multiple candidate genes linked to environmental adaptation, feather color variations, and production for the purification and breeding of Wenchang chickens of phenotypic diversity in chickens.