Melanocortin 1-receptor (MC1R) is one of the major genes that controls chicken plumage colour. In this study, we investigated the sequence and haplotype distribution of the MC1R gene in native Japanese chickens, along with non-Japanese chicken breeds. In total, 732 and 155 chickens from 30 Japanese and eight non-Japanese breeds respectively were used. Three synonymous and 11 non-synonymous nucleotide substitutions were detected, resulting in 15 haplotypes (H0-H14). Of these, three were newly found haplotypes (H9, H13 and H14), of which one (H9) was composed of known substitutions C69T, T212C, G274A and G636A. The second one (H13) possessed newly found non-synonymous substitution C919G, apart from the known substitutions C69T, G178A, G274A, G636A and T637C. The third one (H14) comprised a newly discovered substitution C919G in addition to the known C69T, G274A and G409A substitutions. The homozygote for this new haplotype exhibited wt like plumage despite the presence of G274A. In addition to discovering a new nucleotide substitution (C919G) and three new haplotypes, we defined the plumage colour of the bird that was homozygous for the A644C substitution (H5 haplotype) as wheaten-like for the first time; although the substitution has been already reported, its effect was not revealed. Besides detecting the new plumage colour, we also confirmed that the A427G and G274A substitutions contribute in expressing brownish and black plumage colour respectively, as reported by the previous studies. Moreover, we confirmed that the buttercup allele does not express black plumage despite possessing a G274A substitution, under the suppression effect of A644C. In contrast, the birds homozygous for the birchen allele presented solid black plumage, which was contradictory to the previous reports. In conclusion, we revealed a large diversity in the MC1R gene of native Japanese chicken breeds, along with the discovery of a new non-synonymous nucleotide substitution (C919G) and three novel haplotypes (H9, H13 and H14).

中文翻译：

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在本地和非日本鸡品种中发现了MC1R基因的新核苷酸取代和单倍型分布。

黑皮质素1-受体（MC1R）是控制鸡羽毛颜色的主要基因之一。在这项研究中，我们调查了MC1R基因在日本本土鸡和非日本鸡种中的序列和单倍型分布。总共分别使用了30种日本和8种非日本品种的732和155只鸡。检测到三个同义和11个非同义核苷酸取代，产生15个单倍型（H0-H14）。其中，三个新发现的单倍型（H9，H13和H14），其中一个（H9）由已知的取代基C69T，T212C，G274A和G636A组成。第二个（H13）具有新发现的非同义取代C919G，除了已知的取代C69T，G178A，G274A，G636A和T637C。第三个（H14）除已知的C69T，G274A和G409A替代物外，还包含新发现的替代物C919G。尽管存在G274A，该新单倍型的纯合子仍显示出wt状的羽毛。除了发现一个新的核苷酸取代（C919G）和三个新的单倍型，我们还首次将与A644C取代（H5单倍型）纯合的禽类的羽毛颜色首次定为小麦样。尽管已经报道了这种替代作用，但尚未揭示其作用。除了检测新的羽毛颜色外，我们还证实了A427G和G274A取代分别有助于表达棕色和黑色的羽毛颜色，如先前的研究报道。此外，我们确认，在A644C的抑制作用下，毛all等位基因尽管具有G274A取代基，但并未表达黑色羽毛。相比之下，桦木等位基因纯合的鸟类呈现黑色实心羽毛，这与以前的报道相矛盾。总之，我们发现了日本本土鸡品种的MC1R基因具有很大的多样性，同时发现了一个新的非同义核苷酸取代（C919G）和三个新的单体型（H9，H13和H14）。