Genetic structure and plumage color candidate genes of Yunnan Partridge duck revealed by whole genome resequencing

Feather color is an important economic trait and genetic marker in domestic ducks, and its genetic architecture is critical for selective breeding. The Yunnan Partridge duck is an important conserved population in Yunnan Province, China, comprising three plumage color types: spotted, gray, and yellow partridge. However, research on its genetic basis remains limited. This study aimed to elucidate the genetic diversity, population structure, and the genetic basis of hatchling plumage color in the Yunnan Partridge duck. Based on whole-genome sequencing data, the genetic diversity, population structure, and selection signals of the Yunnan Partridge duck population were analyzed, with results as follows: the highest proportion (29.6%) exhibited a minor allele frequency between 0.1 and 0.2. The mean observed heterozygosity (Ho = 0.1993) was lower than the expected (He = 0.2909). IBS and NJ tree supported three genetic clusters. Analysis of runs of homozygosity detected 3,474 fragments, yielding a low mean genomic inbreeding coefficient (F ROH ) of 0.05493. Based on genome-wide association study (GWAS) analysis, a significant genetic signal associated with plumage color was identified on chromosome 21 within the 2.25–2.4 Mb region, with ASIP determined as the key candidate gene. LD analysis revealed a strong haplotype structure in this region, with the high-frequency haplotypes H1 and H2 (chr21:2334307-2337146) showing highly significant differentiation between speckled and gray-feathered populations, indicating they are the primary genetic determinants of plumage color. In summary, Yunnan Partridge duck exhibits moderate genetic diversity and a low level of inbreeding, with ASIP is the major gene, haplotypes H1 and H2 can distinguish spotted and gray plumage. These findings provide effective molecular markers and a genetic basis for the conservation and targeted breeding of plumage color in the Yunnan Partridge duck.