Identification of InDels in MITF associated with beak color of Duck

As a pigment-related trait, beak color is an important feature for duck breeds. Nowadays, several studies have been conducted on the genetic mechanisms and candidate markers of duck beak color. However, related loci which were mostly single base mutations could hardly explain the phenotype. To select greater structural mutations associated with beak color, all 308 birds of the F₂ population of the Runzhou white crested ducks were selected to perform the genome-wide association studies to select key genes and differential InDels related to the formation of beak color in ducks. To verify the accuracy of the GWAS and to further select the candidate variants of beak colors, Line H (H1, H2, H3 and HF) was selected as black-beaked ducks along with yellow-beaked ducks which consist of CV ducks and Line E for genomic selection signatures by integrated analysis of F_ST and θπ. Genotyping was performed to verify the functions of the candidate sites. As the result, 2 InDels in the intronic region were selected as candidate variants by GWAS. Furthermore, eight genes were selected according to a standard FDR of <0.05 and MITF was finally selected based on a comparison of the F_ST values by genomic selection signature. After the selection of the loci, 1 bp insertion (InDel-4, at the position of 17829988 on chromosome 10 of ASM874695v1) in intron regions of MITF were selected as candidate sites. As the result of the genotyping, all yellow-beaked ducks were homozygous mutated individuals, while all individuals in Line H (black-beaked ducks) were found to have the RR (ref / ref) genotype. In addition, the relative expression of MITF from beak tissue of the H2 ducks was significantly higher than that of CV ducks(p < 0.001). Thus, MITF plays a critical role in melanogenesis and melanin deposition in duck beaks, which can affect beak color, and InDel-4 were significantly different in the yellow- and black-beaked individuals and could be used as markers to identify the beak colors of ducks.