OMIA:000374-9031 : Feather colour, extended black in Gallus gallus (chicken)

In other species: Mallard , 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

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 266300 (trait) , 155555 (gene)

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."

Associated gene:

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 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

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:000374-9031: Online Mendelian Inheritance in Animals (OMIA) [dataset].


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 51:842-843, 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 51:235-248, 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 61:382-389, 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 Eur J Biochem 270:1441-9, 2003. Pubmed reference: 12653999. DOI: 10.1046/j.1432-1033.2003.03506.x.
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. DOI: 10.1016/0167-4781(96)00100-5.
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. Poult Sci 72:1405-10, 1993. Pubmed reference: 8378215. DOI: 10.3382/ps.0721405.
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. DOI: 10.1139/g69-015.

Edit History

  • Created by Frank Nicholas on 22 Oct 2008
  • Changed by Frank Nicholas on 12 Oct 2011
  • Changed by Frank Nicholas on 09 Dec 2011
  • Changed by Frank Nicholas on 22 Sep 2012
  • Changed by Frank Nicholas on 07 Dec 2012
  • Changed by Frank Nicholas on 19 Jun 2013
  • Changed by Frank Nicholas on 21 Sep 2019
  • Changed by Frank Nicholas on 26 Jan 2020
  • Changed by Frank Nicholas on 15 May 2020
  • Changed by Imke Tammen2 on 19 Aug 2021
  • Changed by Imke Tammen2 on 27 Sep 2021
  • Changed by Imke Tammen2 on 24 Nov 2022