Abstract

Plumage color is an economically important trait in chickens, and barred chickens are characterized by a distinct feather pattern in which variation in pigmentation (yellow-barred vs. white-barred) is frequently observed. Although the genetic basis of barred patterning has been partially elucidated, the mechanisms underlying pigmentation differences within barred feathers remain unclear. In this study, genome-wide association study (GWAS) and selection signature (FST) analyses based on 47 individuals (20 yellow-barred and 27 white-barred) identified several candidate genomic regions and genes, including BRINP2, SLC22A4, SLC22A5, and ACTN1, potentially associated with pigment variation. Transcriptomic analysis of feather follicles further revealed substantial gene expression divergence between the two phenotypes, with 739 differentially expressed genes identified, among which SLC45A2, BCO2, EDAR, KRT75, and KRT14 were notable candidates. Functional enrichment analysis indicated that these genes are primarily involved in skin development, epidermal differentiation, keratinization, and intermediate filament organization. Integrated analyses suggest that coordinated regulation of melanin synthesis, carotenoid metabolism, and feather follicle structural development contributes to the observed pigmentation differences. Overall, this study provides genomic and transcriptomic insights into the molecular basis of pigmentation variation in barred chickens and offers a foundation for future functional validation and molecular breeding.