Historical introgression from commercial meat-type ducks constitutes the common genetic basis of white plumage in egg-type duck breeds.

White plumage is an important economic trait in duck, but the genetic mechanism underlying white plumage in egg-type ducks remains unclear. In this study, white plumage individuals were obtained from a naturally segregating population of the grey plumage line of Shaoxing ducks. Cross families were constructed through reciprocal mating between white and grey-plumage lines for genetic mapping. Genome-wide association analysis mapped the white plumage trait to chromosome 13 and identified MITF as the sole candidate gene. Structural variation detection revealed an approximately 6.6 kb Gypsy insertion between exon 1M and exon 2 of MITF (the variant underlying white plumage in meat-type ducks), homozygous in all white individuals. Across 1,192 individuals from 38 populations, this insertion was fixed in all commercial meat-type ducks and in the indigenous white-plumage lines of Jinding, Putian black and Shaoxing ducks (but absent in Liancheng white duck), establishing the MITF insertion as the common genetic basis for white plumage across these lines. Population genetic structure analysis showed that each indigenous white-plumage line clustered closely with its corresponding colored-plumage population, with no detectable signals of large-scale hybridization from commercial meat-type ducks. Although indigenous white-plumage lines have considerably shorter breeding history than commercial meat-type ducks, the positive selection signature at the MITF locus in these lines is highly similar to that in the latter, with both sharing a nearly homozygous haplotype block of approximately 31.6 kb located in a genomic interval of markedly reduced recombination rate. Haplotype network analysis placed the insertion-carrying haplotypes of indigenous white-plumage lines in a haplogroup shared with commercial meat-type ducks. Collectively, these results support the interpretation that the MITF insertion was historically introgressed from commercial meat-type ducks, persisted at low frequency in indigenous populations, and was subsequently driven to rapid fixation under recent market-driven selection, thereby generating selection signatures highly consistent with those in commercial meat ducks within a short period.