A ∼18 kb upstream deletion of H2AFY is associated with the feathered leg trait in Yanying chickens

Feather-related traits in poultry give rise to a vibrant array of visually striking characteristics. Among these, the Yanying chickens, an indigenous breed, displays a variably expressed feathered-leg phenotype. However, the underlying genetic mechanisms remain largely unexplored, making this breed a valuable model for investigation. In present study, we performed Genome-wide association studies (GWAS) based on whole-genome resequencing data (average depth: 10 ×) of 123 chickens, and found a locus on chromosome 13 (chr13: 14.97-15.05 Mb) that is significantly associated with leg feather trait. By gene annotation, we found a coding gene for H2A-histone-family, member-Y (H2AFY), which encodes a histone variant crucial for chromatin architecture and the regulation of developmental genes, was located in this region. We then identified an approximately 18-kb deletion up-stream of H2AFY. Through PCR validation, we confirmed that this structural variation is significantly associated with the feathered-leg trait. The segregation pattern suggests it is a major genetic determinant, though with incomplete penetrance. This study not only deepens our understanding of the genetic mechanisms underlying feather-related traits but also provides a reliable genetic marker, offering a potential target for molecular-assisted selection of external characteristics in chickens.