Melanocortin-1 Receptor Locus Research Articles

Polymorphism of the Melanocortin 1 Receptor (MC1R) Gene and its Role in Determining the Coat Colour of Central European Cattle Breeds.

Simple SummaryAnimal coat colour has been the subject of numerous studies for many years. While most phenotypic features of animals result from the interaction of genetic and environmental factors, coat colour is considered to be almost exclusively genetically determined. Differences in coat colour underscore the distinct character of a given breed or group of animals, testify to its uniqueness, and sometimes serve as selection criteria. Observations of changes in cattle coat colour are an important source of information used to track domestication processes and discover how animals were selected for breeding. One of the genes responsible for variation in coat colour is the melanocortin receptor (MC1R) gene locus, which controls the production of black and red pigments that determine basic colours. Other interacting genes also influence cattle phenotypes. In view of the complexity of the genetic factors influencing cattle coat colour, this study investigated the genetic basis of different coat colours of Central European cattle breeds.There are many genes responsible for the appearance of different coat colours, among which the melanocortin 1 receptor gene (MC1R) plays an important role. The aim of the study was to characterize genetic variation in Central European cattle breeds based on polymorphism of the MC1R gene and factors determining their coat colour. The study was conducted on 290 individuals of the following breeds: Polish White-Backed (PW), Lithuanian White-Backed (LW), Polish Red (PR), Lithuanian Red (LR), Carpathian Brown (CB), Ukrainian Grey (UG), and Slovak Pinzgau (SP). Polymorphism at the MC1R gene locus was analysed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using two restriction enzymes: Cfr10I and SsiI. The proportions of alleles and genotypes in the MC1R locus indicates a strong relationship between polymorphism and the coat colour of cattle: The ED allele proved to be characteristic for the breeds with a white-backed coat (PW and LW), while the dominant allele in the red breeds (PR and LR) was E+. It is noteworthy that coat colour in the SP population was determined only by the recessive e allele, which resulted in the formation of a separate clade in the phylogenetic tree.

Detangling red hair from pain: phenotype-specific contributions from different genetic variants in melanocortin-1 receptor.

Genetic variation in melanocortin-1 receptor (MC1R) has a known role in red hair. Studies on responses to noxious stimuli in red-haired individuals have also been conducted, with mixed findings. To investigate a possible divergence between variants responsible for red hair and pain sensitivity, we performed a genewide association analysis in the Orofacial Pain: Prospective Evaluation and Risk Assessment cohort. All genotyped (17) MC1R variants were tested for association with heat pain temporal summation and sensitivity. Our analyses showed an association for pain sensitivity with the 5'-UTR, tagged by rs3212361, and 1 missense variant, rs885479 (R163Q), previously shown to be weakly associated with red hair. For both variants, the minor allele was protective. These results were validated in the 500,000-person UK Biobank cohort, where the minor alleles of rs3212361 and rs885479 were associated with a reduced count of persistent pain conditions as well as individual pain conditions. Haplotype association analysis revealed a possible joint effect from the 2 individual variants. The 5'-UTR variant rs3212361 was further identified as an expression quantitative trait locus, associated with reduced transcript levels of MC1R in the brain and in the peripheral tibial nerve. Hair colour association analysis of the loss-of-function 5'-UTR rs3212361 allele identified association with red hair, and red hair colour itself was associated with a reduced count of persistent pain conditions. Together, our results suggest that primarily different mechanisms-affecting expression levels vs protein activity-mediated by different genetic variants in the MC1R locus contribute to red hair and pain.

Evolution of dark colour in toucans (Ramphastidae): a case of molecular adaptation?

In the last decades, researchers have been able to determine the molecular basis of some phenotypes, to test for evidence of natural selection upon them, and to demonstrate that the same genes or genetic pathways can be associated with convergent traits. Colour traits are often subject to natural selection because even small changes in these traits can have a large effect on fitness via camouflage, sexual selection or other mechanisms. The melanocortin-1 receptor locus (MC1R) is frequently associated with intraspecific coat colour variation in vertebrates, but it has been far harder to demonstrate that this locus is involved in adaptive interspecific colour differences. Here, we investigate the contribution of the MC1R gene to the colour diversity found in toucans (Ramphastidae). We found divergent selection on MC1R in the clade represented by the genus Ramphastos and that this coincided with the evolution of darker plumage in members of this genus. Using phylogenetically corrected correlations, we show significant and specific relationships between the rate of nonsynonymous change in MC1R (dN) and plumage darkness across Ramphastidae, and also between the rate of functionally significant amino acid changes in MC1R and plumage darkness. Furthermore, three of the seven amino acid changes in MC1R that occurred in the ancestral Ramphastos branch are associated with melanism in other birds. Taken together, our results suggest that the dark colour of Ramphastos toucans was related to nonsynonymous substitutions in MC1R that may have been subject to positive selection or to a relaxation of selective pressure. These results also demonstrate a quantitative relationship between gene and phenotype evolution, representing an example of how MC1R molecular evolution may affect macroevolution of plumage phenotypes.

Major breeding plumage color differences of male ruffs (Philomachus pugnax) are not associated with coding sequence variation in the MC1R gene.

Sequence variation in the melanocortin-1 receptor (MC1R) gene explains color morph variation in several species of birds and mammals. Ruffs (Philomachus pugnax) exhibit major dark/light color differences in melanin-based male breeding plumage which is closely associated with alternative reproductive behavior. A previous study identified a microsatellite marker (Ppu020) near the MC1R locus associated with the presence/absence of ornamental plumage. We investigated whether coding sequence variation in the MC1R gene explains major dark/light plumage color variation and/or the presence/absence of ornamental plumage in ruffs. Among 821bp of the MC1R coding region from 44 male ruffs we found 3 single nucleotide polymorphisms, representing 1 nonsynonymous and 2 synonymous amino acid substitutions. None were associated with major dark/light color differences or the presence/absence of ornamental plumage. At all amino acid sites known to be functionally important in other avian species with dark/light plumage color variation, ruffs were either monomorphic or the shared polymorphism did not coincide with color morph. Neither ornamental plumage color differences nor the presence/absence of ornamental plumage in ruffs are likely to be caused entirely by amino acid variation within the coding regions of the MC1R locus. Regulatory elements and structural variation at other loci may be involved in melanin expression and contribute to the extreme plumage polymorphism observed in this species.

Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)

BackgroundGenetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons.FindingsWe sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene.ConclusionsOur results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.

The evolution of black plumage from blue in Australian fairy‐wrens (Maluridae): genetic and structural evidence

Genetic variation in the melanocortin‐1 receptor (MC1R) locus is responsible for color variation, particularly melanism, in many groups of vertebrates. Fairy‐wrens, Maluridae, are a family of Australian and New Guinean passerines with several instances of dramatic shifts in plumage coloration, both intra‐ and inter‐specifically. A number of these color changes are from bright blue to black plumage. In this study, we examined sequence variation at the MC1R locus in most genera and species of fairy‐wrens. Our primary focus was subspecies of the white‐winged fairy‐wren Malurus leucopterus in which two subspecies, each endemic to islands off the western Australian coast, are black while the mainland subspecies is blue. We found fourteen variable amino acid residues within M. leucopterus, but at only one position were alleles perfectly correlated with plumage color. Comparison with other fairy‐wren species showed that the blue mainland subspecies, not the black island subspecies, had a unique genotype. Examination of MC1R protein sequence variation across our sample of fairy‐wrens revealed no correlation between plumage color and sequence in this group. We thus conclude that amino acid changes in the MC1R locus are not directly responsible for the black plumage of the island subspecies of M. leucopterus. Our examination of the nanostructure of feathers from both black and blue subspecies of M. leucopterus and other black and blue fairy‐wren species clarifies the evolution of black plumage in this family. Our data indicate that the black white‐winged fairy‐wrens evolved from blue ancestors because vestiges of the nanostructure required for the production of blue coloration exist within their black feathers. Based on our phylogeographic analysis of M. leucopterus, in which the two black subspecies do not appear to be each other's closest relatives, we infer that there have been two independent evolutionary transitions from blue to black plumage. A third potential transition from blue to black appears to have occurred in a sister clade.

Conservation and Convergence of Colour Genetics: MC1R Mutations in brown Cavefish

Conservation and Convergence of Colour Genetics: MC1R Mutations in brown Cavefish

Characterization of the effect of Melanocortin 1 Receptor, a member of the hair color genetic locus, in alpaca ( Lama pacos) fleece color differentiation

Little is known about the inheritance and influence of the fleece color gene Melanocortin 1 Receptor (MC1R). Melanocortin 1 Receptor (MC1R) is a well-known gene responsible for red versus black fleece pigmentation and is hypothesized to be a candidate gene for variation in alpaca coloration patterns. Inheritance of red versus black pigmentation in the context of genetic mutation is well understood in many domesticated mammals. We characterized the MC1R gene in a population of multi-colored alpacas in order to better understand its effect on coat color in the alpaca. Our characterization of the alpaca MC1R gene revealed 11 mutations. Of these one is a 4 bp deletion, four are silent mutations and six are single nucleotide polymorphisms (SNPs) that alter the amino acid sequence (T28V, M87V, S126G, T128I, S196F, R301C). No mutation correlated completely with fleece color in alpacas at the MC1R locus. This may be due to the epistatic relationship of MC1R with other coat color genes especially agouti signaling protein (ASIP).

Testing whether macroevolution follows microevolution: Are colour differences among swans (Cygnus) attributable to variation at the MC1R locus?

BackgroundThe MC1R (melanocortin-1 receptor) locus underlies intraspecific variation in melanin-based dark plumage coloration in several unrelated birds with plumage polymorphisms. There is far less evidence for functional variants of MC1R being involved in interspecific variation, in which spurious genotype-phenotype associations arising through population history are a far greater problem than in intraspecific studies. We investigated the relationship between MC1R variation and plumage coloration in swans (Cygnus), which show extreme variation in melanic plumage phenotypes among species (white to black).ResultsThe two species with melanic plumage, C. atratus and C. melanocoryphus (black and black-necked swans respectively), both have amino acid changes at important functional sites in MC1R that are consistent with increased MC1R activity and melanism. Reconstruction of MC1R evolution over a newly generated independent molecular phylogeny of Cygnus and related genera shows that these putative melanizing mutations were independently derived in the two melanic lineages. However, interpretation is complicated by the fact that one of the outgroup genera, Coscoroba, also has a putative melanizing mutation at MC1R that has arisen independently but has nearly pure white plumage. Epistasis at other loci seems the most likely explanation for this discrepancy. Unexpectedly, the phylogeny shows that the genus Cygnus may not be monophyletic, with C. melanocoryphus placed as a sister group to true geese (Anser), but further data will be needed to confirm this.ConclusionOur study highlights the difficulty of extrapolating from intraspecific studies to understand the genetic basis of interspecific adaptive phenotypic evolution, even with a gene whose structure-function relationships are as well understood as MC1R as confounding variation make clear genotype/phenotype associations difficult at the macroevolutionary scale. However, the identification of substitutions in the black and black-necked swan that are known to be associated with melanic phenotypes, suggests Cygnus may be another example where there appears to be convergent evolution at MC1R. This study therefore provides a novel example where previously described intraspecific genotype/phenotype associations occur at the macroevolutionary level.

The Genetics of Adaptive Coat Color in Gophers: Coding Variation at Mc1r Is Not Responsible for Dorsal Color Differences

The genetics of adaptation is a key problem in evolutionary biology. Pocket gophers of the species Thomomys bottae provide one of the most striking examples of coat color variation in mammals. Dorsal pelage color is strongly correlated with soil color across the range of the species, presumably reflecting the selective pressure exerted by predation. To investigate the genetic basis of coat color variation in T. bottae, we cloned and sequenced the melanocortin-1 receptor locus (Mc1r), a candidate pigmentation gene, in 5 dark and 5 light populations of the species. Our results show that, in contrast to many other species of mammals and other vertebrates, coding variation at Mc1r is not the main determinant of coat color variation in T. bottae. These results demonstrate that similar phenotypic variation may have a different genetic basis among different mammalian species.

The Genetic Basis of the Plumage Polymorphism in Red-Footed Boobies (Sula sula): a Melanocortin-1 Receptor (MC1R) Analysis

The red-footed booby (Sula sula) is considered one of the most polymorphic seabirds, with 3 recognized major adult plumage types: 1) white, 2) white-tailed brown, and 3) brown and several degrees of intermediates. Here we show that the white/melanic polymorphism observed in this species is perfectly associated with 2 point substitutions, Val85Met and His207Arg, at the melanocortin-1 receptor (MC1R) gene. Among the melanic plumage variants, we also found a strong association between the degree of melanism and the number of copies of variant MC1R alleles. Furthermore, the Val85Met point substitution has been previously shown to be associated with melanic phenotypes in the lesser snow goose (Anser c. caerulescens), suggesting parallel evolution of the melanic allele, and hence, melanism, between these 2 distantly related species. We also compared the MC1R locus in red-footed boobies with a nonpolymorphic congener, the Nazca booby (Sula granti), in which all adults are white. We found that Nazca boobies present the same genotype at sites 85 and 207 as white morph red-footed boobies.

Analysis of melanocortin 1 receptor (MC1R) gene polymorphisms in some cattle breeds: their usefulness and application for breed traceability and authentication ofParmigiano Reggiano cheese

In cattle, the MC1R gene has been the subject of several studies with the aim to elucidate the biology of coat colour. Then, polymorphisms of this gene have been proposed as tools for breed identification and animal products authentication. As a first step to identify breed specific DNA markers that can be used for the traceability of mono-breed dairy cattle products we investigated, using PCR-RFLP and PCR-APLP protocols, the presence and distribution of some alleles at the MC1R locus in 18 cattle breeds for a total of 1360 animals. For each of seven breeds (Italian Holstein, Italian Brown, Italian Simmental, Rendena, Jersey, Reggiana and Modenese) a large number of animals (>70) was genotyped so the obtained results can be considered with more confidence. Allele Ed was identified only in black pied cattle (Italian Holstein and Black Pied Valdostana). Allele E (this nomenclature includes all alleles except Ed, E1 and e) was observed in Italian Brown, Rendena, Jersey, Modenese, Italian Simmental, Grigio Alpina, Piedmontese, Chianina, Romagnola, Marchigiana, Swedish Red and White and Danish Red. Allele E1 was identified in Italian Brown, Rendena, Grigio Alpina, Piedmontese, Swedish Red and White and Danish Red. The recessive allele e, known to cause red coat colour, was fixed in Reggiana and almost fixed in Italian Simmental. This allele was observed also in Italian Holstein, Italian Brown, Rendena, Jersey and Modenese albeit with low frequency. Moreover, this allele was detected in Valdostana, Pezzata Rossa d’Oropa, Piedmontese, Romagnola, Swedish Red and White, Danish Red, Charoleis and Salers. In the case of the Reggiana breed, which is fixed for allele e, the MC1R locus is highly informative with respect to breeds that carry other alleles or in which allele e is at very low frequency. In theory, using the MC1R locus it is possible to identify the presence of milk from some other breeds in Parmigiano Reggiano cheese labelled as exclusively from the Reggiana breed. This possibility was practically tested by setting up protocols to extract and analyse polymorphisms of the MC1R locus in several dairy products, including Parmigiano Reggiano cheese cured for 30 months. The lower detection limit was estimated to be 5% of non expected DNA. This test can represent a first deterrent against fraud and an important tool for the valorisation and authentication of Parmigiano Reggiano cheese obtained from only Reggiana milk.

Nero Siciliano pig: analysis of coat colour affecting genes and perspectives for breed traceability

Nero Siciliano is an autochthonous pig breed reared in the internal areas of Sicily region mainly in the Nebrodi mountains. The animals are usually completely black with a dorsal stripe but a few present white portions mainly in the face or in the fore legs. According to the increased requests of the consumers for local and typical products, meat and cured products of Nero Siciliano pigs are sold at a higher price compared to other pig products. Thus there is the need to guarantee both consumers and the whole Nero Siciliano production chain from possible frauds. The identification and/or use of DNA markers that may be breed specific could make it possible to establish breed traceability and authenticity systems for the products obtained with this local pig breed. Mutations in coat colour genes have been already described and utilized for porcine breed traceability. In this trial we analysed mutations identified in two coat colour affecting genes, the melanocortin 1 receptor (MC1R) and the v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene (KIT), with the aim to characterize the Nero Siciliano pig at these loci and provide useful information to establish authenticity systems for the meat products. Fragment analysis of PCR products and PCR-RFLP methods were used to identify the polymorphic sites that can distinguish known alleles at these two loci in 104 Nero Siciliano pigs. Four alleles were identified at the MC1R locus: the two dominant black alleles (Ed2, frequency of 0.673; Ed1, 0.187), allele Ep (0.106) and the recessive e allele (0.034). The results showed that different alleles were observed at this locus, polymorphisms at the MC1R gene cannot be used for product traceability and authentication of this breed. As regards the KIT locus, all the animals were negative for the splice site mutation of exon/intron 17. Thus, meat of Nero Siciliano pigs can be distinguished from meat of white pigs that are positive for this polymorphic site. Moreover, at this locus only 4 pigs showed the 3’-5’ duplication breakpoint suggesting that they carried the Ip allele. Studies are in progress to evaluate the effect of this allele on coat colour phenotypes in Nero Siciliano pig.

Activation of the cAMP pathway by variant human MC1R alleles expressed in HEK and in melanoma cells

α-Melanocyte-stimulating hormone (α-MSH) activates the melanocortin-1 receptor (MC1R) on melanocytes to promote a switch from red/yellow pheomelanin synthesis to darker eumelanins via positive coupling to adenylate cyclase. The human MC1R locus is highly polymorphic with the specific variants associated with red hair and fair skin (RHC phenotype) postulated to be loss-of-function receptors. We have examined the ability of MC1R variants to activate the cAMP pathway in stably transfected HEK293 cells. The RHC associated variants, Arg151Cys, Arg160Trp and Asp294His, demonstrated agonist-mediated increases in cAMP and phosphorylation of cAMP-responsive element-binding protein (CREB). Whereas the Asp294His variant showed severely impaired functional responses, the Arg151Cys and Arg160Trp variants retained considerable signaling capacity. Melanoma cells homozygous for either the Arg151Cys variant or consensus sequence both elicited CREB phosphorylation in response to α-MSH in the presence of IBMX. The common RHC alleles, Arg151Cys, Arg160Trp and Asp294His, are neither complete loss-of-function receptors nor are they functionally equivalent.

Unmelanized plumage patterns in Old World leaf warblers do not correspond to sequence variation at the melanocortin-1 receptor locus (MC1R).

Evolutionary changes in patterns and coloration of plumage are likely to represent a major mechanism for speciation among birds, yet the molecular basis for such changes remains poorly understood. Recently much attention has focused on the melanocortin-1 receptor (MC1R) as a candidate locus for determining the level and extent of epidermal melanin deposition. We tested the hypothesis that MC1R sequence variation is associated with interspecific variation in unmelanized plumage pattern elements in Old World leaf warblers (genus Phylloscopus). This genus is characterized by a variety of plumage patterns that nonetheless vary along similar lines. Species vary in the presence or absence of pale (unmelanized) pattern elements against a dark background, and these patterns are used in species recognition and courtship. We sequenced most of the MC1R coding region for eight Phylloscopus species, representing the full range of plumage patterns found in this genus. Although MC1R sequence varied among species, this variation was not related to melanin-based plumage variation. Rather, evolution of this locus in these birds appears to be conservative. Ratios of nonsynonymous to synonymous substitutions (dN/dS) were consistently low, suggesting that strong purifying selection has operated at this locus, and likelihood ratio testing revealed no evidence of variable selective pressures among lineages or across codons. Adaptive evolution at MC1R may be constrained by the adaptive importance of plumage pattern elements in this genus.

DNA polymorphism and selection at the melanocortin-1 receptor gene in normally pigmented southern African individuals.

Skin pigmentation is a polygenic multifactorial trait determined by the cumulative effects of multiple genetic variants and environmental factors. Melanocortin-1 receptor (MC1R) is one of the genes involved in pigmentation, and has been implicated in the red hair and pale skin phenotype in human Caucasoid individuals. The present study was undertaken to identify variation at the MC1R locus in normally pigmented individuals in two African populations, sub-Saharan Negroids (22 unrelated individuals) and the San (17 unrelated individuals). The study showed considerable MC1R gene sequence variation with the detection of eight synonymous and three nonsynonymous mutations. This is the first report of nonsynonymous mutations in African individuals in the MC1R gene: L99I was found in a single San individual, S47I was detected in a single Negroid individual, and F196L was detected in five Negroid individuals (5/44; 0.11). The functional significance of these mutations is not known. Three of the eight synonymous mutations found, L106L (CTG --> CTA), F300F (TTC --> TTT), and T314T (ACA --> ACG) (also known as A942G), have been reported previously. T314T was the only variant that showed a significant difference between the Negroid and San populations (0.477 and 0.059, respectively; P = 1.6 x 10(-5)). Its low frequency in the San may be the result of random genetic drift in a population of small size, or selection. Several tests of neutrality of the MC1R coding region in these and other African populations were significant, suggesting that purifying selection (functional constraint) had occurred at this gene locus in Africans. This demonstrates that although some nonsynonymous MC1R mutations are tolerated in individuals with dark skin, this gene has likely played a significant role in the maintenance of dark pigmentation in Africans and normal pigment variation in non-African populations.

High Polymorphism at the Human Melanocortin 1 Receptor Locus

Variation in human skin/hair pigmentation is due to varied amounts of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eu- and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many mammals. We have sequenced the MC1R gene in 121 individuals sampled from world populations with an emphasis on Asian populations. We found variation at five nonsynonymous sites (resulting in the variants Arg67Gln, Asp84Glu, Val92Met, Arg151Cys, and Arg163Gln), but at only one synonymous site (A942G). Interestingly, the human consensus protein sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency (7%) in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. The MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon was sequenced to study the evolution of MC1R. The ancestral human MC1R sequence is identical to the human consensus protein sequence, while MC1R varies considerably among higher primates. A comparison of the rates of substitution in genes in the melanocortin receptor family indicates that MC1R has evolved the fastest. In addition, the nucleotide diversity at the MC1R locus is shown to be several times higher than the average nucleotide diversity in human populations, possibly due to diversifying selection.