The SOX10 Upstream Deletion CausesCause Light Yellow Plumage Color in Chicken

Chicken plumage color is a complex trait that is controlled by several genes, shows great differences, and has a great significance for chicken breeding. In this study, through Rhode Island Red (RIR) and White Leghorn (WL) cross populations, the segregation of plumage color was observed to be dark red (DR) and light yellow (LY), respectively. To obtain the SNP set of all chickens, 40 DR and 39 LY chickens were randomly selected for paired-end sequencing. The association analysis suggested that SOX10 was the only candidate gene. However, a significant SNP was observed to be located on the flank of SOX10, while those in SOX10 were not significant. Furthermore, it was noted that the sequencing depth of RD chickens upstream of SOX10 was significantly higher than that of LY chickens. The PCR test showed that there was a 7.6 Kb deletion in LY chickens, and all LY chickens were homozygous deletions.