Research note: Integration of GWAS and RNA-seq identifies mutations linked to within feather patterning in domestic chickens

Within feather pattern variation is widespread among chicken breeds globally and is primarily characterized by the distributions of eumelanin on a single feather vane. To analyze the genetic basis underlying different within feather patterns, we conducted the GWAS by pairwise comparing the three common patterns observed in Chinese domestic chickens: stippling, pencilling, and arrow. Based on the coding-region variants, a set of candidate genes were sifted out, notably MC1R, CDH1, MYO5C, FOXI2, and RANBP17, which are functionally associated with melanogenesis and pigment transport. From the perspective of regulatory variants, we integrated GWAS signals with RNA-seq data from growing-phase feather follicles to identify candidates driving transcript-level divergence. With putative regulatory variants, RANBP17, MAPK6, and LOC107051763 were identified as overlapping candidates with differentially expressed genes. Overall, by integrating coding-region and regulatory-region variant analysis, this study identified a set of prioritized candidate genes linked to within feather patterning. This study provides the first systematic genetic dissection of within-feather patterns in domestic chickens by integrating GWAS and RNA-seq, offering new insights into the genetic and developmental mechanisms underlying avian within feather pattern formation.