Abstract
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.