Effects of MTAP and PMEL gene Polymorphisms on Plumage Color Variation in Chickens

Plumage color is an important economic trait in chickens and is mainly affected by genetic factors than environmental factors. This study aimed to detect the single-nucleotide polymorphisms (SNPs) in <italic>CDKN2A</italic>, <italic>MTAP</italic>, and <italic>PMEL</italic> genes and explore their influence on plumage color variation in chickens. We used 428 chicken blood samples, consisting of all-black: 62, all-white: 246, and black and white barred: 120 chickens of F2 population produced from crossing the F1 progenies. The F1 population was produced by crossing Yeonsan Ogye (YO) and White Leghorn (WL). The SNPs in the <italic>CDKN2A</italic>, <italic>MTAP</italic>, and <italic>PMEL</italic> genes were initially detected by sequencing. PACE Genotyping technology was used for genotyping and results were observed for a synonymous SNP, rs316391660C/T of the <italic>MTAP</italic> gene, missense SNPs, rs312616138A/G and rs14684281T/C of the <italic>PMEL</italic> gene. The association test between the genotypes in <italic>MTAP</italic> (SNP: rs316391660C/T) and <italic>PMEL</italic> (SNP: rs14684281T/C) genes was performed by Chi-square test while Fisher’s exact test to evaluate association the genotypes of PMEL gene (SNP: rs312616138A/G) with plumage color variations. The missense SNP, rs1058656732C/T in <italic>CDKN2A</italic> gene was monomorphic and could not be used for the association test. There was a significant (p&lt;0.05) association between genotypes of MTAP and PMEL genes with the three plumage color variations: all-black, all-white, and black and white barred. Our results confirm the genotype effects of the PMEL gene on the dominant white plumage color, and suggest that the synonymous SNP (rs316391660C/T) of the MTAP gene could be used as a genetic marker for the breeding of chickens with black-and-white barred plumage.