羽色是家禽品种鉴定的关键表型特征之一，解析其遗传基础对种质资源的保护与可持续利用具有重要意义。本研究对127只广东黑鸽和12只塔里木鸽进行全基因组重测序（whole genome sequencing，WGS），并整合其他4个鸽种已有的重测序数据（共40只），通过主成分分析、群体结构分析和系统进化树构建发现，广东黑鸽遗传背景独特，与白羽及灰羽鸽群存在明显分化。进一步利用全基因组关联分析（genome-wide association study，GWAS），经过过滤筛选后共得到1,598个单核苷酸多态性（single-nucleotide polymorphism，SNP）位点和97个插入/缺失（insertion/deletion，InDel）位点，这些位点集中分布于4号染色体内皮素B型受体亚型（endothelin receptor type B2，EDNRB2）基因及其邻近区域。本研究从该区域挑选显著性较高的3个SNP位点和2个InDel位点进行Sanger测序验证，结果显示：白羽鸽所有位点均为野生型，广东黑鸽全部位点均为突变纯合型或杂合型，说明这些变异位点的基因型与黑羽表型高度一致。本研究结果为解析广东黑鸽羽色形成的分子机制、开展分子标记辅助育种提供了可靠的候选标记。

Plumage color is one of the key phenotypic traits for breed identification in poultry, and deciphering its genetic basis is of great significance for the conservation and sustainable utilization of germplasm resources. In this study, we performed whole-genome sequencing (WGS) on 127 Guangdong Black pigeons and 12 Tarim pigeons, and integrated existing WGS data from four other pigeon breeds (40 individuals in total). Principal component analysis, population structure analysis, and phylogenetic tree construction revealed that Guangdong Black pigeons have a unique genetic background and are clearly differentiated from white- and gray-feathered pigeon populations. We further conducted a genome-wide association study (GWAS), and after filtering and screening, identified a total of 1,598 single-nucleotide polymorphisms (SNPs) and 97 insertions/deletions (InDel). These loci were predominantly clustered in the endothelin receptor type B2 (EDNRB2) gene on chromosome 4 and in its flanking regions. From this region, we selected three highly significant SNPs and two InDels for Sanger sequencing validation. The results showed that all tested loci in white-feathered pigeons were wild-type, whereas in Guangdong Black pigeons they were either homozygous mutant or heterozygous, indicating that the genotypes at these variant loci are highly consistent with the black plumage phenotype. Our results provide reliable candidate markers for elucidating the molecular mechanism underlying plumage color formation in Guangdong Black pigeons and for implementing molecular marker-assisted breeding.