PMEL governs autosomal dominant inheritance of white-tail independent of yellow body plumage in chickens (Gallus gallus domesticus)

Region-specific feather pigmentation is widespread in birds, yet the genetic mechanisms enabling independent control of body and tail plumage remain poorly understood. The white-tailed (WT) phenotype in Wuhua yellow chickens, which exhibit yellow body plumage but pure white tail feathers, provides an ideal model for dissecting such modular genetic regulation. Genetic analysis of F₁ and F₂ populations (n = 137) derived from a cross with Huaixiang (black-tailed, BT) chickens revealed an autosomal dominant inheritance pattern for the WT trait, with a 3:1 segregation ratio (105 WT: 32 BT; χ² = 0.20, P = 0.66) in the F₂ generation-independent of the yellow body plumage locus. Integrating genome-wide association study of 47 F₂ roosters with population resequencing (n = 50), we identified a highly significant locus on chromosome 33 (P = 1.35E-8) harboring PMEL as the sole credible candidate. Tail follicle transcriptome profiling (4 WT vs. 4 BT) uncovered 1,712 differentially expressed genes, with coordinated downregulation of the entire melanogenesis pathway (normalized enrichment score = -1.914, FDR = 0.003). PMEL ranked among the most strongly suppressed genes (log₂FC = -2.18, FDR = 5.58E-06). Furthermore, genome-wide alternative splicing analysis identified 2,764 significant events among 30,473 detected, indicating widespread post-transcriptional regulation. Consistent with this global pattern, the PMEL locus exhibited markedly reduced splicing complexity in WT chickens, characterized by a systematic shift toward simpler isoforms. Thus, four orthogonal lines of evidence-genomic association, transcriptional repression, pathway-level melanogenesis shutdown, and splicing simplification-converge on PMEL as the causal gene underlying this autosomal dominant, tail-specific depigmentation. Our findings establish PMEL as the primary regulator underlying this autosomal dominant trait, paving the way for understanding modular avian coloration and enabling its application in precision breeding programs.