SOX10 Upstream Deletion

Chicken plumage color is a complex trait controlled by many genes. Herein, through Rhode Island Red (RIR) and White Leghorn (WL) cross populations, the segregation of plumage color was observed in females, showed white, dark red (DR) and light yellow (LY), respectively. The white has been found to be caused by dominant white alleles (<i>I</i>)<i> </i>and the DR phenotype is attributed to a sex-linked recessive silver allele (<i>s</i>). LY is a derived feather color phenotype and the genetic mechanism of this is unclear. In order to explore genetic basis for LY, we randomly selected 40 DR and 39 LY chickens for paired-end sequencing to obtain the SNP set of all chickens. Then the case-control genome wide association study (GWAS) was performed to identify the phenotype related mutations. The association analysis showed that only one region harboring the SOX10 gene was significantly associated to LY. We furtherly discovered that the sequencing depth of DR chickens upstream of SOX10 is significantly higher than LY chickens. Subsequent diagnostic PCR tests showed that there is a ~7.6 kb deletion in LY chickens and that all LY chickens are homozygous for this deletion, indicating the deletion is causative for LY phenotype.

鸡的羽毛颜色是受多基因调控的复杂性状。本研究以罗德岛红鸡（Rhode Island Red, RIR）与白来航鸡（White Leghorn, WL）的杂交群体为材料，观察到雌性个体出现羽毛颜色分离现象，分别表现为白色、深红（DR）和浅黄（LY）三种表型。其中白羽表型已被证实由显性白羽等位基因（*I*）导致，深红羽表型则归因于性连锁隐性银等位基因（*s*）。浅黄羽是一种衍生羽毛颜色表型，其遗传机制尚未明确。为探究浅黄羽表型的遗传基础，本研究随机选取40只深红羽鸡与39只浅黄羽鸡进行双端测序（paired-end sequencing），获取所有受试鸡的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点集；随后开展病例对照全基因组关联分析（Genome Wide Association Study, GWAS），以鉴定与该表型相关的突变位点。关联分析结果显示，仅包含SOX10基因的一个基因组区域与浅黄羽表型显著关联。进一步研究发现，深红羽鸡SOX10基因上游区域的测序深度显著高于浅黄羽鸡。后续诊断聚合酶链式反应（Polymerase Chain Reaction, PCR）检测结果表明，浅黄羽鸡中存在一段约7.6 kb的缺失片段，且所有浅黄羽鸡均为该缺失的纯合子，证实该缺失是导致浅黄羽表型的致因突变。