OMIA:001199-9915 : Coat colour, extension in Bos indicus (indicine cattle (zebu))

In other species: lorises , coyote , dog , red fox , American black bear , domestic cat , jaguar , ass (donkey) , horse , Przewalski's horse , pig , Arabian camel , reindeer , taurine cattle , goat , sheep , rabbit , Mongolian gerbil , domestic guinea pig , domestic yak , fallow deer , alpaca , gray squirrel , raccoon dog , antarctic fur seal , woolly mammoth , rock pocket mouse , oldfield mouse , lesser earless lizard , Geoffroy's cat , jaguarundi , Colocolo , little striped whiptail , water buffalo , Arctic fox

Categories: Pigmentation phene

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

Mendelian trait/disorder: unknown

Considered a defect: no

Year key variant first reported: 2021

Cross-species summary: The extension locus encodes the melanocyte-stimulating hormone receptor (MSHR; now known as MC1R). This receptor controls the level of tyrosinase within melanocytes. Tyrosinase is the limiting enzyme involved in synthesis of melanins: high levels of tyrosinase result in the production of eumelanin (dark colour, e.g. brown or black), while low levels result in the production of phaeomelanin (light colour, e.g. red or yellow). When melanocyte-stimulating hormone (MSH) binds to its receptor, the level of tyrosinase is increased, leading to production of eumelanin. The wild-type allele at the extension locus corresponds to a functional MSHR, and hence to dark pigmentation in the presence of MSH. As explained by Schneider et al. (PLoS Genet 10(2): e1004892; 2015), "The most common causes of melanism (black coat) mutations are gain-of-function alterations in MC1R, or loss-of function alterations in ASIP, which encodes Agouti signaling protein, a paracrine signaling molecule that inhibits MC1R signaling". Mutations in MC1R have been associated with white colouring in several species.

Molecular basis: Goud et al. (2021) analysed the Sahiwal MC1R gene and proposed that a missense SNP (c.844C>A; p.(T281N) might be the possible reason for the red coat colour in Sahiwal cattle when compared to black and white-coloured Karan Fries (Bos taurus x Bos indicus) cattle. The authors acknowledged that further molecular studies need to be conducted to validate an association of the variant with red coat colour. Santana et al. (2021): Gray coat is one of the breed qualifications in Guzerat cattle. The authors report “the birth of a single red individual … as a result of the mating of two gray Guzerat animals. … The primer pair described by Goud et al. (2021) was used for PCR, which amplifies the single exon of the MC1R gene. Sequence analysis permitted the detection of a deletion of one nucleotide whose nitrogenated base is a thymine, at position 311 of the MC1R gene. This deletion causes a change in the reading frame from this point onwards (amino acid 104) and creates a premature stop codon. The predicted protein is smaller, with 155 amino acids compared with the original protein …. "

Breeds: Guzerat (Cattle) (VBO_0000228), Nelore (Cattle) (VBO_0000318), Sahiwal (Cattle) (VBO_0000365).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
MC1R Bos indicus 18 NC_032667.1 (13780416..13782247) 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
1350 Guzerat (Cattle) Red MC1R deletion, small (<=20) Naturally occurring variant c.311delT p.(G104Vfs*) 2021 34555208
1351 Sahiwal (Cattle) Red MC1R missense Naturally occurring variant c.844C>A p.(T281 N) 2021 33512595

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001199-9915: 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.

2021 Goud, T.S., Upadhyay, R.C., Pichili, V.B.R., Onteru, S.K., Chadipiralla, K. :
Molecular characterization of coat color gene in Sahiwal versus Karan Fries bovine. J Genet Eng Biotechnol 19:22, 2021. Pubmed reference: 33512595. DOI: 10.1186/s43141-021-00117-2.
Jiang, L., Kon, T., Chen, C., Ichikawa, R., Zheng, Q., Pei, L., Takemura, I., Nsobi, L.H., Tabata, H., Pan, H., Omori, Y., Ogura, A. :
Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour. Sci Rep 11:17359, 2021. Pubmed reference: 34462508. DOI: 10.1038/s41598-021-96896-2.
Santana, C.J.S., Alves, J.S., Pinto, L.F.B., Costa, R.B., de Camargo, G.M.F. :
A deletion in the MC1R gene alters coat color in Guzerat cattle. Anim Genet 52:896-897, 2021. Pubmed reference: 34555208. DOI: 10.1111/age.13143.
2020 Goud, T.S., Upadhyay, R.C., Onteru, S.K., Pichili, V.B.R., Chadipiralla, K. :
Identification and sequence characterization of melanocortin 1 receptor gene (MC1R) in Bos indicus versus (Bos taurus X Bos indicus). Anim Biotechnol 31:283-294, 2020. Pubmed reference: 30890019. DOI: 10.1080/10495398.2019.1585866.
2014 Hanna, L.L., Sanders, J.O., Riley, D.G., Abbey, C.A., Gill, C.A. :
Identification of a major locus interacting with MC1R and modifying black coat color in an F₂ Nellore-Angus population. Genet Sel Evol 46:4, 2014. Pubmed reference: 24460986. DOI: 10.1186/1297-9686-46-4.
Zhang, Y., Li, Q., Ye, S., Faruque, M.O., Yu, Y., Sun, D., Zhang, S., Wang, Y. :
New variants in the melanocortin 1 receptor gene (MC1R) in Asian cattle. Anim Genet 45:609-10, 2014. Pubmed reference: 24702190. DOI: 10.1111/age.12160.

Edit History

  • Created by Imke Tammen2 on 11 Feb 2021
  • Changed by Imke Tammen2 on 11 Feb 2021
  • Changed by Imke Tammen2 on 26 Sep 2021
  • Changed by Imke Tammen2 on 15 Jun 2023