Research note: Pool sequencing nominates MITF as a key candidate gene for white-belted feathers in chickens

A rare variant of the Wuhua yellow chicken rooster exhibits a distinct plumage phenotype characterized by a white belt across the dorsal region and wing shoulder. This variant provides a valuable model for studying regional pigmentation genetics. Using pool sequencing, we identified candidate genes via high-depth sequencing (average 52 × coverage) of DNA pools from 35 brown-belted and 35 white-belted roosters. Integrated analysis of allele frequency differences, Fisher's exact test, and population differentiation revealed 49 shared candidate genes, with 23 concentrated in a 3.83 Mb region on chromosome 12 (13.12-16.95 Mb). Notably, MITF and two adjacent genes exhibited strong selection signals across all methods. Functional enrichment analyses highlighted significant terms related to melanocyte differentiation and the melanogenesis pathway, with MITF serving as a core regulator. Comparative genomic evidence further supported the conserved role of MITF in pigment deposition across vertebrates. We propose MITF as the primary genetic regulator of the white-belted phenotype, potentially modified by other genes such as PRICKLE2. This study provides insights into the genetic architecture of regional depigmentation and underscores the role of MITF in avian plumage patterning.