Genomic regions related to white/black tail feather color in Dwarf chickens detected using a genome-wide association study

Abstract Background: The genetic foundation of chicken tail feather color is not very well studied to date, though that of body feather color is extensively explored. In the present study, we used a synthetic chicken dwarf line (DW), which was originated from the hybrids between a black tail chicken breed, Rhode Island Red (RIR) and a white tail breed, Dwarf Layer (DL), to understand the genetic rules of the white/black tail color. The DW line still contain the individuals with black or white tails, even if the body feather are predominantly red, after more than ten generation of self-crossing and being selected for the body feather color. We firstly performed four crosses using the DW line chickens including black tail male to female, reciprocal crosses between the black and white, and white male to female to elucidate the inheritance pattern of the white/black tail. Furtherly, we performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color by using black tail chickens from the RIR and DW chickens and white individuals from DW lines. Results: In the cross experiment, we found that (i) the white/black tail feather colors are independent of body feather color and (ii) the phenotype are autosomal simple trait and (iii) the white are dominant to the black in the DW lines. The GWA results showed that seven Single-nucleotide polymorphism (SNP) on chromosome 24 were significantly correlated with tail feather color. The significant region (3.97-4.26 Mb) perches nine known genes and five anonymous genes. The nine genes were: NECTIN1, THY1, gga-mir-1466, USP2, C1QTNF5, RNF26, MCAM, CBL and CCDC153. Conclusions: The study has revealed the white/black tail feather trait is autosome-linked in Dwarf chickens. In the genome significant ~0.29 Mb region, fourteen genes were found and some of them could play critical roles in the formation of white/black tail feather color, especially gene MCAM. Taken together, our research is the first study on genetics of tail feather color and could help the more understanding of feather pigmentation in chicken.