Figure 4.

Genome-wide association analysis and selection sweep of white feather traits in Wenchang chickens. (A) Manhattan plot and (B) quantile-quantile plot (QQ plot) showing the observed P values of the genome-wide association analysis for white feather and nonwhite feather traits in Wenchang chickens. The Manhattan plot indicates the red dashed line depicts the genome-wide significant threshold (2.88 × 10⁻⁹), and the green loci represent 2 missense mutations. In the QQ plot (B), the red loci represent the genome-wide significant associations. (C) Fst, (D) XP-CLR, and (E) Pi-ratio analyses were conducted with the white feather strain as the target population and yellow feather strain as the reference population. (F) SweeD analysis was performed based on the white feather strain. The orange shadows denote regions of candidate genes. The TYR gene is a candidate gene for white plumage, and GRM5 may be linked to the TYR gene.