Missense SNP of the MC1R gene is associated with plumage variation in the Gyrfalcon (Falco rusticolus)

A single nucleotide polymorphism (MC1R: c.376A>G) in the MC1R gene was found to be highly correlated with pigment phenotype in the Gyrfalcon. Homozygous genotypes c.376GG and c.376AA were found to dominate the extreme white and dark plumage types respectively, and heterozygotes occurred mainly in intermediate phenotypes. However, some heterozygotes were associated with extreme phenotypes, indicating that melanism/albinism might also involve other loci.     

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.     

Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domestic rabbit (Oryctolagus cuniculus)

We sequenced almost the complete coding region of the MC1R gene in several domestic rabbits (Oryctolagus cuniculus) and identified four alleles: two wild-type alleles differing by two synonymous single nucleotide polymorphisms (c.333A>G;c.555T>C), one allele with a 30-nucleotide in-frame deletion (c.304_333del30) and one allele with a 6-nucleotide in-frame deletion (c.280_285del6). A polymerase chain reaction-based protocol was used to distinguish the wild-type alleles from the other two alleles in 263 rabbits belonging to 37 breeds or strains. All red/fawn/yellow rabbits were homozygous for the c.304_333del30 allele. This allele represents the recessive e allele at the extension locus identified through pioneering genetic studies in this species. All Californian, Checkered, Giant White and New Zealand White rabbits were homozygous for allele c.280_285del6, which was also observed in the heterozygous condition in a few other breeds. Black coat colour is part of the standard colour in Californian and Checkered breeds, in contrast to the two albino breeds, Giant White and New Zealand White. Following the nomenclature established for the rabbit extension locus, the c.280_285del6 allele, which is dominant over c.304_333del30, may be allele E(D) or allele E(S).     

Discovery of a new nucleotide substitution in the MC1R gene and haplotype distribution in native and non-Japanese chicken breeds

Melanocortin 1-receptor (MC1R) is one of the major genes that controls chicken plumage colour. In this study, we investigated the sequence and haplotype distribution of the MC1R gene in native Japanese chickens, along with non-Japanese chicken breeds. In total, 732 and 155 chickens from 30 Japanese and eight non-Japanese breeds respectively were used. Three synonymous and 11 non-synonymous nucleotide substitutions were detected, resulting in 15 haplotypes (H0–H14). Of these, three were newly found haplotypes (H9, H13 and H14), of which one (H9) was composed of known substitutions C69T, T212C, G274A and G636A. The second one (H13) possessed newly found non-synonymous substitution C919G, apart from the known substitutions C69T, G178A, G274A, G636A and T637C. The third one (H14) comprised a newly discovered substitution C919G in addition to the known C69T, G274A and G409A substitutions. The homozygote for this new haplotype exhibited wt like plumage despite the presence of G274A. In addition to discovering a new nucleotide substitution (C919G) and three new haplotypes, we 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. In conclusion, we revealed a large diversity in the MC1R gene of native Japanese chicken breeds, along with the discovery of a new non-synonymous nucleotide substitution (C919G) and three novel haplotypes (H9, H13 and H14).     

Single nucleotide polymorphisms in the Melanocortin 1 Receptor gene are linked with lightness of fibre colour in Peruvian Alpaca (Vicugna pacos)

Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) (MC1R) is a gene‐controlling melanogenesis in mammals. However, it is not well characterized in alpacas and its association with colour is not known. The aim of this study was to look for polymorphisms in the MC1R gene in Peruvian Huacaya alpacas and to analyse the relationship between MC1R single nucleotide polymorphisms (SNPs) and the variations in the instrumental measurement of colour of alpaca fibre. Sixty alpaca fibre samples from black, brown, cream and white animals (15 for each colour) were used to extract DNA from hair bulbs. Colour was measured with a spectrophotometer to obtain quantitative values (CieL*a*b*). Sixteen samples, four of each colour group, were sequenced. Eighteen SNP mutations, 10 not previously described, were found in these 16 sequences. Three of them were chosen (c.82A>G, c.865C>T, c.901C>T) to analyse genotypes by PCR‐RFLP in the other 44 fibre samples and to determine the association of mutations with instrumental colour. These three polymorphisms showed association with fibre lightness (P < 0.05), although there was no correlation with colour groups.     

3个猪品种黑素皮质素受体1(MC1R)基因变异研究

利用测序、PCR-RFLP和PCR-SSCP等技术对杜洛克、长白、大白猪MC1R基因进行研究发现了5个多态位点。其中,668位点G→C突变发生在5′UTR,其余4个多态位点nt894insCC(894位点CC插入),1318C→T,1554G→A和1197G→A发生在编码区。nt894insCC导致编码蛋白过早终止。1318C→T,1554G→A和1197G→A突变分别导致a164Val,Ala243Thr和Asp124Asn氨基酸的改变。所有长白、大白猪个体在894位点均存在CC插入,其余多态位点基因型分别为668GG,1197AA,1318CC,1554GG。所有杜洛克个体在894位点均不存在CC插入,其余多态位点基因型分别为668CC,1197GG,1318TT,1554AA。所有突变位点无杂合子出现。由此可以推测,668G→C,1318C→T和1554G→A可能与杜洛克的红毛色存在相关,导致1197G→A突变无意义的894位点CC插入可能与长白、大白猪白毛色存在相关。     

黑素皮质激素受体1（MC1R）基因系统发育树与犬的毛色

犬的驯养迄今约有1万多年,由于不同环境和不同目的人工选择形成了犬品种间或品种内极丰富的毛色多样性,经证实,这些犬的很多毛色类型与MC1R相关 ,MC1R在一些物种中有同源基因 本文阐述了犬MC1R多态性研究进展,并选择其它9个有代表性的哺乳动物物种与犬MC1R同源基因进行了比较,以此建立系统发育树。结果显示,10个物种的MC1R基因的分子进化关系与物种的经典分类学地位基本相符。      

猪黑素皮质素受体1(MC1R)基因与毛色表型的研究

猪的毛色表型虽然与经济性状没有直接相关,但它却对经济效益产生重要影响,在猪育种实践、商品猪生产等方面都有应用。结合PCR—AccⅡ—RFIP、PCR—BspH I—RFLP及PCR-SSCP技术,分析了16个全同胞家系和金华猪、嘉兴黑猪、玉山黑猪、乐平花猪、上高两头乌猪及嵊县花猪等6个地方猪种随机采样个体的黑素皮质素受体1(MCIR)基因型。结果显示,地方猪种在MCIR位点携带高频率的显性黑等位基因E^DI,表明我国地方猪种的黑毛色可能主要由显性黑等位基因E^DI调控。通过对嵊县花猪MCIR位点的分析,首次发现PCR-SSCP证据的新序列,与已知的其他5个等位基因带型不同。家系个体的分析结果进一步验证了E^DI对E^p、e为完全显性,E^p对e为不完全显性。     

Non‐synonymous SNPs in MC1R gene are associated with the extended black variant in domestic ducks (Anas platyrhynchos)

In this study, we performed a sequence characterization of the duck melanocortin 1 receptor (alpha‐melanocyte stimulating hormone receptor) (MC1R) gene to analyze the relationship between MC1R polymorphism and the extended black variant in domestic ducks based on the extended black (E) and non‐extended black (e⁺) allele hypothesis of the duck MC1R gene. Both c.52G>A and c.376G>A substitutions are highly associated with the duck extended black variant (P < 0.01), but the novel c.52G>A substitution is more of a fit for the allele hypothesis of the duck MC1R gene.     

棕背伯劳羽色多态与MC1R基因的相关性

黑素皮质素受体1 (melanocortin-1 receptor, MC1R)基因是控制动物黑色素合成的重要基因, 鸟类羽色的变异与MC1R基因的变异有密切关系。棕背伯劳(Lanius schach)在我国东部沿海多地存在羽色多态现象, 有棕色型、黑色型和黑色白边型的分化。为了探究MC1R基因与棕背伯劳色型分化的关系, 本研究对分布于广东省的3种色型共计11只棕背伯劳的MC1R基因编码区进行单核苷酸多态性(SNPs)分析和氨基酸多态性分析。结果表明: (1) 11个实验个体的MC1R基因序列共有4种单倍型, 其中黑色型和黑色白边型共享单倍型H3。(2) 3种色型棕背伯劳MC1R基因编码区的第34-931位的899个碱基中共有47个碱基变异位点, 相对应的氨基酸序列共有18个变异位点, 这些变异位点与黑色表型无对应关系。(3)黑色型与黑色白边型个体基因型在第268-303位编码区出现了36个碱基的缺失, 对应着12个氨基酸的缺失, 该缺失与黑色表型相对应。因此推测棕背伯劳的黑化与MC1R基因碱基片段的缺失密切相关。     

Melanocortin 1 receptor (MC1R) polymorphisms’ influence on size and dermoscopic features of nevi

The melanocortin 1 receptor (MC1R) is a highly polymorphic gene. The loss‐of‐function MC1R variants (“R”) have been strongly associated with red hair color phenotype and an increased melanoma risk. We sequenced the MC1R gene in 175 healthy individuals to assess the influence of MC1R on nevus phenotype. We identified that MC1R variant carriers had larger nevi both on the back [p‐value = .016, adjusted for multiple parameters (adj. p‐value)] and on the upper limbs (adj. p‐value = .007). Specifically, we identified a positive association between the “R” MC1R variants and visible vessels in nevi [p‐value = .033, corrected using the FDR method for multiple comparisons (corrected p‐value)], dots and globules in nevi (corrected p‐value = .033), nevi with eccentric hyperpigmentation (corrected p‐value = .033), a high degree of freckling (adj. p‐value = .019), and an associative trend with presence of blue nevi (corrected p‐value = .120). In conclusion, the MC1R gene appears to influence the nevus phenotype.     

Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine‐256 in the MC1R gene

We have characterized a deletion in the MC1R gene causing the loss of one amino acid (p.Phe256del), which is perfectly associated with melanism in guinea fowl (Numida meleagris). Co‐segregation of the p.Phe256del with melanism was confirmed in 25 offspring born from a cross of two heterozygote birds; therefore we suggest that this mutation is responsible for the black phenotype. Interestingly, this is the first case of recessive melanism linked to MC1R.     

Coat colours in the Massese sheep breed are associated with mutations in the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes

Massese is an Italian dairy sheep breed characterized by animals with black skin and horns and black or apparent grey hairs. Owing to the presence of these two coat colour types, this breed can be considered an interesting model to evaluate the effects of coat colour gene polymorphisms on this phenotypic trait. Two main loci have been already shown to affect coat colour in sheep: Agouti and Extension coding for the agouti signalling protein (ASIP) and melanocortin 1 receptor (MC1R) genes, respectively. The Agouti locus is affected by a large duplication including the ASIP gene that may determine the Agouti white and tan allele (A(Wt)). Other disrupting or partially inactivating mutations have been identified in exon 2 (a deletion of 5 bp, D(5); and a deletion of 9 bp, D(9)) and in exon 4 (g.5172T>A, p.C126S) of the ASIP gene. Three missense mutations in the sheep MC1R gene cause the dominant black E(D) allele (p.M73K and p.D121N) and the putative recessive e allele (p.R67C). Here, we analysed these ASIP and MC1R mutations in 161 Massese sheep collected from four flocks. The presence of one duplicated copy allele including the ASIP gene was associated with grey coat colour (P = 9.4E-30). Almost all animals with a duplicated copy allele (37 out of 41) showed uniform apparent grey hair and almost all animals without a duplicated allele (117 out of 120) were completely black. Different forms of duplicated alleles were identified in Massese sheep including, in almost all cases, copies with exon 2 disrupting or partially inactivating mutations making these alleles different from the A(Wt) allele. A few exceptions were observed in the association between ASIP polymorphisms and coat colour: three grey sheep did not carry any duplicated copy allele and four black animals carried a duplicated copy allele. Of the latter four sheep, two carried the E(D) allele of the MC1R gene that may be the cause of their black coat colour. The coat colour of all other black animals may be determined by non-functional ASIP alleles (non-agouti alleles, A(a)) and in a few cases by the E(D) Extension allele. At least three frequent ASIP haplotypes ([D(5):g.5172T], [N:g.5172A] and [D(5):g.5172A]) were detected (organized into six different diplotypes). In conclusion, the results indicated that coat colours in the Massese sheep breed are mainly derived by combining ASIP and MC1R mutations.     

Association of a Glu92Lys substitution in MC1R with extended brown in Japanese quail (Coturnix japonica)

We investigated melanocortin 1 receptor (MC1R) as a candidate locus for the Extended brown phenotype in quail, in which there is a general darkening throughout the plumage. An initial screen of variation in MC1R in Extended brown and in wild-type quails revealed two polymorphic non-synonymous sites. One of these sites, a G-to-A substitution leading to a Glu92Lys mutation, was perfectly associated with plumage phenotype; all Extended brown birds were homozygous for Lys92. Co-segregation of the Glu92Lys mutation with the Extended brown phenotype was confirmed in 24 progeny of an E/e(+) x E/e(+) cross. Glu92Lys is likely to be the causative mutation for the increased melanism in Extended brown, given that the same mutation is associated with melanic plumage in many breeds of domestic chicken, as well as in a wild passerine bird (the bananaquit, Coereba flaveola) and laboratory mice. Interestingly, the increase in melanization with the Glu92Lys mutation is less marked in quails than in most other birds and mammals. Phylogenetic results indicate that the Glu92Lys mutation has independently occurred in quail and chicken lineages.     

The role of MC1R gene in buffalo coat color

Melanocortin-1 receptor (MC1R) plays a major role in pigmentation in many species. To investigate if the MC1R gene is associated with coat color in water buffalo, the coding region of MC1R gene of 216 buffalo samples was sequenced, which included 49 black river buffalo (Murrah and Nili-Ravi), 136 swamp buffalo (Dehong, Diandongnan, Dechang, Guizhou, and Xilin) with white and gray body, and 31 hybrid offspring of river buffalo Nili-Ravi (or Murrah) and swamp buffalo. Among the three variation sites found, SNP684 was synonymous, while SNP310 and SNP384 were nonsynonymous, leading to p.S104G and p.I128M changes, respectively. Only Individuals carrying homozygote EBR/EBR were black. The genotype and phenotype analysis of the hybrid offspring of black river buffalo and gray swamp buffalo further revealed that the river buffalo type allele EBR or the allele carrying the amino acid p.104S was important for the full function of MC1R. The in silico functional analysis showed that the amino acid substitutions p.G104S and p.M128I had significant impact on the function of MC1R. Above results indicate that the allele EBR or the allele carrying the amino acid p.104S was associated with the black coat color in buffalo.     

MC1R CpG island regulates MC1R expression and is methylated in a subset of melanoma tumours

Melanocortin 1 receptor (MC1R) is a G protein‐coupled receptor expressed in melanocytes where it plays an important role in skin pigmentation and in the UV response, and has implications in melanoma development. Here we show that methylation of a CpG island (CGI) within the MC1R gene can control expression of MC1R in melanoma. This CGI overlaps with a potential enhancer region, and is unmethylated in normal melanocytes but highly methylated in other skin cells, suggesting a melanocyte specific function. Analysis showed that MC1R was the only gene significantly differentially expressed by methylation of this region. Within several data sets, this region is methylated in a subset of melanoma tumours (55%–74% of tumours) and results in reduced MC1R expression and significantly longer overall survival.     

Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.

The melanocortin receptor 1 (MC1R) plays a central role in regulation of eumelanin (black/brown) and phaeomelanin (red/yellow) synthesis within the mammalian melanocyte and is encoded by the classical Extension (E) coat color locus. Sequence analysis of MC1R from seven porcine breeds revealed a total of four allelic variants corresponding to five different E alleles. The European wild boar possessed a unique MC1R allele that we believe is required for the expression of a wild-type coat color. Two different MC1R alleles were associated with the dominant black color in pigs. MC1R*2 was found in European Large Black and Chinese Meishan pigs and exhibited two missense mutations compared with the wild-type sequence. Comparative data strongly suggest that one of these, L99P, may form a constitutively active receptor. MC1R*3 was associated with the black color in the Hampshire breed and involved a single missense mutation D121N. This same MC1R variant was also associated with EP, which results in black spots on a white or red background. Two different missense mutations were identified in recessive red (e/e) animals. One of these, A240T, occurs at a highly conserved position, making it a strong candidate for disruption of receptor function.     

Mutation load in melanoma is affected by MC1R genotype

Whole‐genome sequencing of matched germline and tumour pairs in a well‐characterized cohort of melanoma patients allowed investigation of associations between melanoma body site, age at melanoma onset and MC1R variant status with overall mutation burden and specific base pair changes observed in the corresponding melanoma. We observed statistically significant associations between mutation burden in melanoma and body site, age at onset and MC1R genotype, for both ultraviolet radiation (UVR) signature changes (C>T and CC>TT) and non‐UVR base pair substitutions, as well as with overall variant load.     

CDKN2A mutations and MC1R variants in Italian patients with single or multiple primary melanoma

We evaluated the contribution of germline CDKN2A mutations and MC1R variants to the development of melanoma in a hospital-based study of single (SPM, n = 398) and multiple primary melanoma (MPM, n = 95). The overall frequency of CDKN2A mutations was 15.2%, and four-fold higher in MPM than in SPM cases (OR = 4.27; 95% CI 2.43-7.53). The likelihood of identifying a CDKN2A mutation increased with family history of melanoma and younger age at diagnosis in MPM cases. Compared to SPM patients, the risk of harboring a CDKN2A mutation rose as the number of primary melanomas increased and was not influenced by family history. The G101W and E27X founder mutations were the most common. Several other mutations (W15X, Q50X, R58X, A68L, A127P and H142R) were detected for the first time in Italian patients. One novel mutation, T77A, was identified. Several non-coding variants with unknown functional significance were also found (5'UTR -25C > T, -21C > T, -67G > C, IVS1 +37G > C); the novel 5'UTR -21C > T variant was not detected in controls. The CDKN2A A148T polymorphism was more frequent in MPM patients than in the control population (15.7% versus 6.6%). Compared to the SPM patients, MPM cases had a 2-fold increased probability of being MC1R variant carriers and a higher probability of carrying two or more variants. No specific association was observed between the type of variant and the number of melanomas, suggesting that the number rather than the type of MC1R variant increases the risk of MPM. We observed no interaction between CDKN2A status and the presence of MC1R variants. The high frequency of CDKN2A mutations in our MPM cases, independent of their family history, is of relevance to genetic counseling and testing in our population.