In other species: lorises , coyote , dog , red fox , American black bear , domestic cat , jaguar , ass (donkey) , horse , Przewalski's horse , pig , Arabian camel , reindeer , indicine cattle (zebu) , 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: yes

Mode of inheritance: Autosomal

Disease-related: no

Key variant known: yes

Year key variant first reported: 1995

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.

Species-specific name: Black/red coat colour; Haplotype HBR; Haplotype HHR

Species-specific symbol: MC1-R, MSH; HBR; HHR

Species-specific description: For information relating to Bos indicus cattle see: OMIA 001199-9915 : Coat colour, extension in Bos indicus

Inheritance: As summarised by Lawlor et al. (2014), "Dominant inheritance of black over red hair color was suggested by Barrington and Pearson (1906), and later proven through a designed experiment by Lloyd-Jones and Evvard (1916) at Iowa State University". As summarised by Hauser et al. (2002), "The order of dominance is ED > E + > e (Lawlor et al., 2014; Olson, 1999). Cattle that are e/e are red and ED /− are typically black, as ED is the dominant allele and eumelanin is permanently produced. Individuals with the genotypes E +/E + and E +/e can be of any colour as E + acts as a neutral allele and normal activity of the melanocortin‐1 receptor is assumed so that both types of pigment are produced simultaneously in different parts of the body ... (Klungland et al., 1995)".

Mapping: Klungland et al. (1995) reported close linkage (theta = 0.08) between the classic bovine E locus and RFLPs in the bovine MSHR gene.

Molecular basis: By cloning and sequencing the most likely comparative candidate gene (based on similar phenotypes in mice), Klungland et al. (1995) obtained molecular evidence for three alleles at the MSHR locus in Norwegian and Icelandic cattle. The wild-type allele (E+) encodes the normal functional receptor for MSH. The E^D allele contains a missense mutation, changing the 99th amino acid from leucine to proline (p.Leu99Pro). The resultant MSHR molecule is constitutively expressed, i.e. it is expressed without the need for MSH binding. This results in continuously high levels of tyrosinase, and hence production of eumelanin (black coat colour). The e allele contains a single base deletion (a frameshift mutation; c.772delG; p.Tyr155X) which gives rise to a non-functional receptor, and hence to low levels of tyrosinase, resulting in production of phaeomelanin (red coat colour). Because one copy of the E^D allele is sufficient to produce functional MSHR molecules and hence to produce black coat colour, this allele is dominant, while the e allele is recessive. Thus black is dominant to red. As expected, the coat colour associated with wild-type (E+) allele varies, depending, among other things, on the level of MSH produced. Joerg et al. (1996) extended these results by showing that red coat colour in Friesians is due to the same deletion (c.772delG; p.Tyr155X) in the MSHR gene, which is now known as MC1R. Olsen (1999) reports that the ancestral MC1R allele designated as E+ has been reported in various breeds of cattle. Rouzaud et al. (2000): "A new allele, named E1, was found in either homozygous (E1/E1) or heterozygous (E1/E) individuals in Aubrac and Gasconne breeds. This allele displayed a 4 amino acid duplication (12 nucleotides) located within the third cytoplasmic loop of the receptor, a region known to interact with G proteins." Hauser et al. (2022) summarise that "in addition to the three bovine E alleles mentioned above, two further protein‐changing MC1R variants, denoted Ed1 and Ed2 , have been identified in cattle, but neither for the p.Arg223Trp nor for the p.Gly220_Arg223dup variant can a clear influence on the base colour be demonstrated so far (Graphodatskaya et al., 2002; Kriegesmann et al., 2001; Rouzaud et al., 2000)." Matsumoto et al. (2020) reported a (missense) variant (c.871G>A; p.(A291T)) that may account for the red coat colour of the Kumamoto sub‐breed of Japanese Brown cattle. More investigation is required before this variant can be added to the OMIA list. Hauser et al. (2022) “performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. [The authors] … searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. [The authors] … propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds ... as well. [The authors] … observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour.”

Prevalence: In a project involving the whole-genome sequencing (WGS) of 43 Fleckvieh cattle with average coverage 7.46X (range 4.17X to 24.98X), Jansen et al. (2013) showed that all but one of the animals was homozygous for the recessive red (deletion; c.772delG; p.Tyr155X) allele, consistent with the typical red and white colour of this breed. The other animal was heterozygous for the recessive red allele and the wild-type allele, but was also red and white.

Breeds: Abondance (Cattle) (VBO_0000091), Angus (Cattle) (VBO_0000104), Brown Swiss (Cattle) (VBO_0000166), Evolèner, Switzerland (Cattle) (VBO_0004498), Fries Roodbont, Netherlands (Cattle) (VBO_0005141), Holstein Friesian (Cattle) (VBO_0000239), Icelandic Cattle (Cattle) (VBO_0000242), Itäsuomenkarja, Finland (Cattle) (VBO_0004749), Limousin (Cattle) (VBO_0000274), Normande (Cattle) (VBO_0000322), Original Schweizer Braunvieh, Switzerland (Cattle) (VBO_0003764), Rotes Höhenvieh, Germany (Cattle) (VBO_0004642), Simmental (Cattle) (VBO_0000380), Witrood Ras van Belgie, Belgium (Cattle) (VBO_0003281).
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: