OMIA 000374-9031 : Feather colour, extended black in Gallus gallus
In other species: Coscoroba swan , black swan , rock pigeon , helmeted guineafowl , king penguin , Arctic skua , pomarine skua , brown booby , red-footed booby , zebra finch , Lesser snow goose , Bananaquit , gyrfalcon , ruff , Chestnut-bellied monarch , Eleonora's falcon
Category: Pigmentation phene
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal
Considered a defect: no
Key variant known: yes
Year key variant first reported: 2003
Species-specific description: Kerje et al. (2003) provided convincing evidence that this locus is orthologous to the classic mammalian coat-colour E-locus (MC1R; extension).
Mapping: Kerje et al. (2003) showed that the Extension locus and the MC1R gene are one in the same, and that they map to chromosome GGA11, the nearest marker being ADL308 with a recombination fraction of 0.21.
Mao et al. (2019) "conducted a genome scan for signatures of selection for black plumage [in] . . . two contrasting groups (three black-feathered breeds vs. six non-black-feathered breeds) [and] consistently detected 25 putative regions under selection . . . [in which are located] Nine pigmentation-associated genes (DCT, SLC24A5, SLC30A4, MYO5A, CYP19A1, NADK2, SLC45A2, GNAQ and DCP2)".
Markers: Zhang et al. (2020) reported a haplotype of MC1R variants that is associated with, but not directly causal of, tile-grey plumage in Chinese breeds.
Molecular basis: Armed with the mapping information described in the Mapping section above, and by sequencing the MC1R gene, Kerje et al. (2003) showed that the Extended Black allele at the E locus is due to a base substitution leading to an E92K substitution in the MC1R peptide. Interestingly, the authors note that "The same substitution is also associated with dominant black colour (ESO-3J) in mouse and in the bananaquit . . . Previous studies in the mouse have shown that this substitution leads to a constitutively active receptor". Kerje et al. (2003) also showed that the buttercup allele (e_sub_bc) at the Extension locus is due to an H215P substitution in MC1R. Guo et al. (2010) reported "A total of 11 novel variations [in MC1R] were detected in Hebei chickens, of which 8 were non-synonymous".
Kabir et al. (2020) "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."
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|MC1R||melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)||Gallus gallus||11||NC_052542.1 (18487539..18488982)||MC1R||Homologene, Ensembl, NCBI gene|
By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.
WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
|OMIA Variant ID||Breed(s)||Variant Phenotype||Gene||Allele||Type of Variant||Source of Genetic Variant||Reference Sequence||Chr.||g. or m.||c. or n.||p.||Verbal Description||EVA ID||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|817||Feather colour, extended black||MC1R||regulatory||Naturally occurring variant||GRCg6a||11||g.18840609C>T||c.-37C>T||5 prime UTR variant||rs733919322||2017||28699279||ENSGALT00000096195.1:c.-37C>T|
|818||Feather colour, extended black||MC1R||E||missense||Naturally occurring variant||GRCg6a||11||g.18840857T>C||c.212T>C||p.(M71T)||ENSGALT00000096195.1:c.212T>C ENSGALP00000071620.1:p.Met71Thr||rs312264213||2017||28699279|
|6||Feather colour, extended black||MC1R||E||missense||Naturally occurring variant||GRCg6a||11||g.18840919G>A||c.274G>A||p.(E92K)||ENSGALT00000096195.1:c.274G>A ENSGALP00000071620.1:p.Glu92Lys||rs314881228||2003||12873211|
|7||Feather colour, buttercup||MC1R||missense||Naturally occurring variant||GRCg6a||11||g.18841289A>C||c.644A>C||p.(H215P)||ENSGALT00000096195.1:c.644A>C ENSGALP00000071620.1:p.His215Pro||rs735789743||2003||12873211|
|1142||Mie-Jidori, Japan (Chicken)||Feather colour, wheaten-like||MC1R||e^m||missense||Naturally occurring variant||GRCg6a||11||g.18841289A>C||c.644A>C||p.(H215P)||ENSGALT00000096195.1:c.644A>C ENSGALP00000071620.1:p.His215Pro||rs735789743||2020||31977074|
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
|2022||Fan, Y., Wu, X., Li, Y., Han, H., Zhang, Y., Yang, J., Liu, Y. :|
|Effect of polymorphisms in the 5'-flanking sequence of MC1R on feather color in Taihang chickens. Poult Sci 101:102192, 2022. Pubmed reference: 36283141. DOI: 10.1016/j.psj.2022.102192.|
|2021||Hua, G., Chen, J., Wang, J., Li, J., Deng, X. :|
|Genetic basis of chicken plumage color in artificial population of complex epistasis. Anim Genet 52:656-66, 2021. Pubmed reference: 34224160. DOI: 10.1111/age.13094.|
|Nam, I.S., Oh, M.G., Nam, M.S., Kim, W.S. :|
|Specific mutations in the genes of MC1R and TYR have an important influence on the determination of pheomelanin pigmentation in Korean native chickens. J Adv Vet Anim Res 8:266-273, 2021. Pubmed reference: 34395597. DOI: 10.5455/javar.2021.h511.|
|2020||Andersson, L., Bed’hom, B., Chuong, CM., Inaba, M.Inaba, M., Okimoto, R.Okimoto, R., Tixier-Boichard, M. :|
|The genetic basis for pigmentation phenotypes in poultry In S. E. Aggrey, H. Zhou, M. Tixier-Boichard, & D. D. Rhoads (Eds.), Advances in Poultry Genetics and Genomics. Cambridge, UK: Burleigh Dodds Science Publishing. :, 2020.|
|Deng, Y., Li, B., Chen, H., Zhang, J., Yan, Y., Xiang, J., Liu, A., Zhang, G.W. :|
|Haplotypes of three missense mutations in Melanocortin 1 receptor serve as genetic markers for black plumage in Chinese chicken. Anim Genet :, 2020. Pubmed reference: 32627225. DOI: 10.1111/age.12975.|
|Kabir, M.H., Takenouchi, A., Haqani, M.I., Nakamura, Y., Takeuchi, S., Tsudzuki, M. :|
|Discovery of a new nucleotide substitution in the MC1R gene and haplotype distribution in native and non-Japanese chicken breeds. Anim Genet :, 2020. Pubmed reference: 31977074. DOI: 10.1111/age.12906.|
|Zhang, L.Y., Huang, M.Y., Li, Y., Yang, X.D., Luo, Y.S., Shi, X.W. :|
|Molecular characteristics of MC1R gene in tile-grey plumage of domestic chicken. Br Poult Sci :1-8, 2020. Pubmed reference: 32264700. DOI: 10.1080/00071668.2020.1751804.|
|2019||Mao, H., Wang, X., Fan, Y., Cheng, D., Chen, K., Liu, S., Xi, S., Wan, L., Li, X., Ren, J. :|
|Whole-genome SNP data unravel population structure and signatures of selection for black plumage of indigenous chicken breeds from Jiangxi province, China. Anim Genet 50:475-483, 2019. Pubmed reference: 31305959. DOI: 10.1111/age.12827.|
|Yang, C.W., Ran, J.S., Yu, C.L., Qiu, M.H., Zhang, Z.R., Du, H.R., Li, Q.Y., Xiong, X., Song, X.Y., Xia, B., Hu, C.M., Liu, Y.P., Jiang, X.S. :|
|Polymorphism in MC1R, TYR and ASIP genes in different colored feather chickens. 3 Biotech 9:203, 2019. Pubmed reference: 31065503. DOI: 10.1007/s13205-019-1710-z.|
|2017||Zhang, G.W., Liao, Y., Zhang, W.X., Wu, Y., Liu, A. :|
|A new dominant haplotype of MC1R gene in Chinese black plumage chicken. Anim Genet 48:624, 2017. Pubmed reference: 28699279. DOI: 10.1111/age.12576.|
|2012||Chang, C.S., Chen, C.F., Berthouly-Salazar, C., Chazara, O., Lee, Y.P., Chang, C.M., Chang, K.H., Bed'Hom, B., Tixier-Boichard, M. :|
|A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan. Anim Genet 43:172-82, 2012. Pubmed reference: 22404353. DOI: 10.1111/j.1365-2052.2011.02226.x.|
|2010||Guo, X.L., Li, X.L., Li, Y., Gu, Z.L., Zheng, C.S., Wei, Z.H., Wang, J.S., Zhou, R.Y., Li, L.H., Zheng, H.Q. :|
|Genetic variation of chicken MC1R gene in different plumage colour populations. Br Poult Sci 51:734-9, 2010. Pubmed reference: 21161779. DOI: 10.1080/00071668.2010.518408.|
|Liu, W.B., Chen, S.R., Zheng, J.X., Qu, L.J., Xu, G.Y., Yang, N. :|
|Developmental phenotypic-genotypic associations of tyrosinase and melanocortin 1 receptor genes with changing profiles in chicken plumage pigmentation. Poult Sci 89:1110-4, 2010. Pubmed reference: 20460655. DOI: 10.3382/ps.2010-00628.|
|2003||Andersson, L. :|
|Melanocortin receptor variants with phenotypic effects in horse, pig, and chicken Annals of the New York Academy of Sciences 994:313-8, 2003. Pubmed reference: 12851331.|
|Kerje, S., Lind, J., Schutz, K., Jensen, P., Andersson, L. :|
|Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Anim Genet 34:241-8, 2003. Pubmed reference: 12873211.|
|Ling, M.K., Lagerstrom, M.C., Fredriksson, R., Okimoto, R., Mundy, N.I., Takeuchi, S., Schioth, H.B. :|
|Association of feather colour with constitutively active melanocortin 1 receptors in chicken European Journal of Biochemistry 270:1441-9, 2003. Pubmed reference: 12653999.|
|Takeuchi, S., Takahashi, S., Okimoto, R., Schioth, H.B., Boswell, T. :|
|Avian melanocortin system: alpha-MSH may act as an autocrine/paracrine hormone: a minireview Annals of the New York Academy of Sciences 994:366-72, 2003. Pubmed reference: 12851337.|
|1996||Takeuchi, S., Suzuki, H., Yabuuchi, M., Takahashi, S. :|
|A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the chicken. Biochim Biophys Acta 1308:164-8, 1996. Pubmed reference: 8764834.|
|1993||Carefoot, WC. :|
|Further studies of linkage and mappings of the loci of genes in group 3 on chromosome 1 of the domestic fowl. Br Poult Sci 34:205-9, 1993. Pubmed reference: 8467400. DOI: 10.1080/00071669308417576.|
|Shoffner, R.N., Otis, J.S., Garwood, V.A. :|
|Association of dominant marker traits and metric traits in chickens. Poultry Science 72:1405-1410, 1993. Pubmed reference: 8378215.|
|1974||Carver, V.H., Brumbaugh, J.A. :|
|Melanocyte developmental genetics: biophasic control of dopa oxidase activity by the E locus of the fowl. J Exp Zool 190:353-66, 1974. Pubmed reference: 4215861. DOI: 10.1002/jez.1401900312.|
|1969||Brumbaugh, J.A., Moore, J.W. :|
|The effects of the E alleles upon melanocyte differentiation in the fowl. Can J Genet Cytol 11:118-24, 1969. Pubmed reference: 5797802.|
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