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.