Genomeic and transcriptomic analysis suggests potential regulatory relationships among MC1R, TUBB3, and PMEL associated with black-flecked plumage in chickens

Abstract The Dominant white ( I ) allele in chickens suppresses the expression of black eumelanin, resulting in white plumage. However, both previous reports and our observations showed that some heterozygous ( I / i + ) individuals exhibited black-flecked plumage rather than completely white plumage, unlike homozygous dominant white chickens. This phenomenon suggests incomplete penetrance and incomplete dominance of the I allele. The genetic mechanisms underlying the phenotypic divergences in I / i + individuals remain unclear. In this study, through integrated genomic and transcriptomic analyses of chickens with different I locus genotypes and feather color phenotypes, we identified candidate variants in MC1R (p.T143A) and TUBB3 (p.R202R) that may be associated with phenotypic variation in pigmentation. Notably, PMEL serves as the primary causal gene underlying the Dominant white phenotype, while the identified loci may act as modifying factors influencing residual melanin deposition in heterozygous individuals. Furthermore, our data suggest that biological processes such as glial cell formation and development, as well as responses to organic cyclic compounds, may participate in regulating the spatiotemporal distribution of melanin, thereby influencing the formation of black-flecked feathers. This finding provides a new perspective on the molecular mechanisms of incomplete penetrance and incomplete dominance of I and reveals the complexity of the melanin deposition regulatory network.