Development of a comprehensive GWAS atlas for chicken breeds

Abstract Modern poultry breeding requires integrated genomic and phenotypic data to optimize production traits, yet comprehensive resources remain fragmented and often inaccessible. We developed a comprehensive electronic Genome-Wide Association Studies (GWAS) Atlas for chicken breeds that consolidates genomic data with phenotypic information from both commercial and heritage breeds. This web-based platform addresses critical gaps in existing databases through a unified, cross-referenced system linking more than 2,500 SNPs and other DNA alterations to 454 documented traits across diverse chicken breeds. The Atlas features four integrated portals: breed profiles with visual catalogs, trait-based breed searches using hierarchical classification, genomic information with DNA alterations and affected genes linked to specific traits, and advanced search functionality. A key innovation is the platform’s ability to reveal previously hidden cross-source genetic associations, such as connecting the GJA5 gene’s roles in both egg production and feather coloration. This publicly accessible resource provides breeders and researchers worldwide with comprehensive tools for informed decision-making in poultry breeding programs.