| Summary: | Shin color diversity is a widespread phenomenon in birds. In this study, ducks were assessed to identify candidate genes for yellow, black, and spotted tibiae. For this purpose, we performed whole-genome resequencing of an F<sub>2</sub> population consisting of 275 ducks crossed between Runzhou crested-white ducks and Cherry Valley ducks. We obtained 12.6 Mb of single nucleotide polymorphism (SNP) data, and the three shin colors were subsequently genotyped. Genome-wide association studies (GWASs) were performed to identify candidate and potential SNPs for the three shin colors. According to the results, 2947 and 3451 significant SNPs were associated with black and yellow shins, respectively, and six potential SNPs were associated with spotted shins. Based on the SNP annotations, the <i>MITF</i>, <i>EDNRB2</i>, POU family members, and the SLC superfamily were the candidate genes regulating pigmentation. In addition, the isoforms of <i>EDNRB2</i>, <i>TYR</i>, <i>TYRP1</i>, and MITF-M were significantly different between the black and yellow tibiae. <i>MITF</i> and <i>EDNRB2</i> may have synergistic roles in the regulation of melanin synthesis, and their mutations may lead to phenotypic differences in the melanin deposition between individuals. This study provides new insights into the genetic factors that may influence tibia color diversity in birds.
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