Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Colfeete of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
J Anim Sci. 2024 Jan 3;102. doi: 10.1093/jas/skae252.
Chickens are the most thoroughly domesticated vertebrate species, and after long-continued natural and artificial selection, they now show rich phenotypic diversity. In particular, feathered legs present in domestic chickens are a characteristic that is carefully selected by advanced breeders. Previous studies have identified the key mutations responsible for feathered legs on chromosomes 13 and 15; however, not all chickens can be easily distinguished based on these two markers. In this study, whole-genome resequencing of 29 Bamaxiaogu chickens (BXCs) yielded 12,201,978 valid single-nucleotide polymorphisms (SNPs) and 2,792,426 valid insertions and deletions (InDels). Population structure analysis based on SNPs revealed that the test samples came from the same natural population. Based on these findings, we used an SNP- and InDel-based genome-wide association study (GWAS) to investigate the genetic basis of feathered legs in chickens. GWAS results revealed that 2 SNPs located in the introns of cubilin (CUBN; SNP1, chr2:19885382T>A) and recombinant Ras suppressor protein 1 (RSU1) genes (SNP2, chr2:20002551G>A), as well as an InDel (InDel1, chr2:19884383TG>T) on CUBN, were all significantly associated with the presence of feathered legs. Diagnostic testing demonstrated that SNP1 effectively differentiated between chickens with feathered legs and those with clean legs (leg without feathers) within the BXC population and may thus be considered an effective marker of feathered legs in BXC. In contrast, other loci did not show the same discriminatory power. This study not only presents a new variant of feathered legs but also provides valuable novel insights into the underlying mechanisms of variation in the feathered-legs trait among chickens.
鸡是最彻底的驯化脊椎动物物种，经过长期的自然和人工选择，它们现在表现出丰富的表型多样性。特别是在肉用鸡中出现的羽毛腿是先进饲养者精心选择的特征。以前的研究已经确定了导致 13 号和 15 号染色体上羽毛腿的关键突变；然而，并非所有的鸡都可以根据这两个标记轻易区分。在这项研究中，对 29 只巴山乌鸡（BXCs）进行全基因组重测序，得到了 12,201,978 个有效单核苷酸多态性（SNP）和 2,792,426 个有效插入和缺失（InDel）。基于 SNP 的群体结构分析表明，测试样本来自同一自然群体。基于这些发现，我们使用 SNP 和 InDel 为基础的全基因组关联研究（GWAS）来研究鸡羽毛腿的遗传基础。GWAS 结果表明，位于 Cubilin（CUBN）基因内含子中的 2 个 SNP（SNP1，chr2:19885382T>A）和 Recombinant Ras Suppressor Protein 1（RSU1）基因（SNP2，chr2:20002551G>A）以及 CUBN 上的一个 InDel（InDel1，chr2:19884383TG>T）都与羽毛腿的存在显著相关。诊断测试表明，SNP1 可有效区分 BXC 群体中带有羽毛腿和不带羽毛腿（无羽毛的腿）的鸡，因此可被视为 BXC 中羽毛腿的有效标记。相比之下，其他位点没有表现出相同的区分能力。这项研究不仅提出了羽毛腿的一个新变体，还为鸡羽毛腿特征的变异的潜在机制提供了有价值的新见解。
