Integrated Analysis of mRNA Expression, CpG Island Methylation, and Polymorphisms in the Gene in Ducks ().

Microphthalmia-associated transcription factor () is a key regulator for the development and function of melanocytes in skin, eye, and plumage pigmentations. Thus, the was selected as a candidate gene associated with plumage coloration in ducks. This study analyzed the mRNA expression, promoter methylation, and polymorphisms in the gene in ducks with different plumage colors (Putian Black, Putian White, Liancheng White, and Longsheng Jade-green). No expression of the melanin-specific isoform () was detected in white feather bulbs. By contrast, the mRNA expression levels of were high in black feather bulbs. Bioinformatics analysis showed that two CpG islands were present in the promoter region of the gene. The methylation level of the second CpG island was significantly lower in black feather bulbs than in white feather bulbs. However, the methylation level of the first CpG island was not different among the feather bulbs with various colors except Liancheng White feather bulbs. The methylation status of the whole CpG island significantly and negatively correlated with the mRNA expression of ( < 0.05). Furthermore, four novel SNPs (single nucleotide polymorphisms) were identified in the 5'UTR, exon 4, intron 7, and intron 8 of the gene. Allele T in g.39807T>G and allele G in g.40862G>A were the predominant alleles only found in Putian White, whereas the variant A allele in g.32813G>A exhibited a high allele frequency in Liancheng White. Collectively, these results contributed to the understanding of the function of the gene in duck plumage coloration.