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

In other species: Coscoroba swan , black swan , helmeted guineafowl , , brown booby , red-footed booby , zebra finch , Lesser snow goose , Bananaquit , gyrfalcon , ,

Possibly relevant human trait(s) and/or gene(s) (MIM number): 266300

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)".

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_006098.5 (18840646..18841590) 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.

Breed(s) Variant Phenotype Gene Allele Type of Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
Feather colour, extended black MC1R regulatory c.-37C>T ss2137510513 2017 28699279
Feather colour, extended black MC1R missense c.212T>C p.Met71Thr ss2727686851 2017 28699279
Feather colour, extended black MC1R missense c.274G>A p.E92K ss2727686852 2003 12873211
Mieā€Jidori Feather colour, wheaten-like MC1R e^m missense 11 c.644A>C p.(His215Pro) 2020 31977074
Feather colour, buttercup MC1R missense c.644A>C p.H215P ss2727686853 2003 12873211


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.
2020 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.
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 :, 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 <i>MC1R</i>, <i>TYR</i> and <i>ASIP</i> 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.

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