Identification of the e allele at the Extension locus (MC1R) in Brazilian Creole sheep and its role in wool color variation

MC1R Gene Variants and Their Relationship with Coat Color in South American Camelids

In domestic camelids, fleece color is an essential characteristic because it defines the direction of production. Variants were determined in the MC1R gene that showed a relationship with coat color in alpacas and llamas at the level of the coding region. This report sequenced the MC1R gene from 290 alpacas (142 white, 84 black, 50 brown, and 14 light fawn), five brown llamas, nine vicuñas, and three guanacos to analyze the association between coat color and the MC1R gene among South American camelids. A total of nineteen polymorphisms were identified. Seven polymorphisms were significant; three of them were of nonsynonymous type (c.82A > G, c.376G > A, and c.901C > T), two were of synonymous type (c.126 T > C and c.933G > A), one was in the promoter region (-42C > G), and one was in the 3' UTR (+5T > C). More polymorphisms were found in domestic camelids than in wild camelids. Besides polymorphism, the association of polymorphisms might cause white and dark pigmentation in the fleece of South American camelids. In addition, the MC1R protein would answer the pigmentation in alpacas.

Melanocortin-1 receptor mutations and pigmentation: Insights from large animals

The melanocortin-1 receptor (MC1R) is a G protein-coupled receptor expressed in cutaneous and hair follicle melanocytes, and plays a central role in coat color determination in vertebrates. Numerous MC1R variants have been identified in diverse species. Some of these variants have been associated with specific hair and skin color phenotypes in humans as well as coat color in animals. Gain-of-function mutations of the MC1R gene cause dominant or partially dominant black/dark coat color, and loss-of-function mutations of the MC1R gene cause recessive or partially recessive red/yellow/pale coat color phenotypes. These have been well documented in a large number of mammals, including human, dog, cattle, horse, sheep, pig, and fox. Higher similarities between large mammals and humans makes them better models to understand pathogenesis of human diseases caused by MC1R mutations. High identities in MC1Rs and similar variants identified in both humans and large mammals also provide an opportunity for receptor structure and function study. In this review, we aim to summarize the naturally occurring mutations of MC1R in humans and large animals.

Genomic mapping identifies two genetic variants in the MC1R gene for coat colour variation in Chinese Tan sheep

Coat colour is one of the most important economic traits of sheep and is mainly used for breed identification and characterization. This trait is determined by the biochemical function, availability and distribution of phaeomelanin and eumelanin pigments. In our study, we conducted a genome-wide association study to identify candidate genes and genetic variants associated with coat colour in 75 Chinese Tan sheep using the ovine 600K SNP BeadChip. Accordingly, we identified two significant SNPs (rs409651063 at 14.232 Mb and rs408511664 at 14.228 Mb) associated with coat colour in the MC1R gene on chromosome 14 with −log10(P) = 2.47E-14 and 1.00E-13, respectively. The consequence of rs409651063 was a missense variant (g.14231948 G>A) that caused an amino acid change (Asp105Asn); however, the second SNP (rs408511664) was a synonymous substitution and is an upstream variant (g.14228343G>A). Moreover, our PCR analysis revealed that the genotype of white sheep was exclusively homozygous (GG), whereas the genotypes of black-head sheep were mainly heterozygous (GA). Interestingly, allele-specific expression analysis (using the missense variant for the skin cDNA samples from black-head sheep) revealed that only the G allele was expressed in the skin covered with white hair, while both the G and A alleles were expressed in the skin covered with black hair. This finding indicated that the missense mutation that we identified is probably responsible for white coat colour in Tan sheep. Furthermore, qPCR analysis of MC1R mRNA level in the skin samples was significantly higher in black-head than white sheep and very significantly higher in GA than GG individuals. Taken together, these results help to elucidate the genetic mechanism underlying coat colour variation in Chinese indigenous sheep.

Review on Genomic Regions and Candidate Genes Associated with Economically Important Production and Reproduction Traits in Sheep (Ovies aries)

Sheep (Ovis aries) is one of the most economically, culturally, and socially important domestic animals. They are reared primarily for meat, milk, wool, and fur production. Sheep were reared using natural selection for a long period of time to offer these traits. In fact, this production system has been slowing the productivity and production potential of the sheep. To improve production efficiency and productivity of this animal through genetic improvement technologies, understanding the genetic background of traits such as body growth, weight, carcass quality, fat percent, fertility, milk yield, wool quality, horn type, and coat color is essential. With the development and utilization of animal genotyping technologies and gene identification methods, many functional genes and genetic variants associated with economically important phenotypic traits have been identified and annotated. This is useful and presented an opportunity to increase the pace of animal genetic gain. Quantitative trait loci and genome wide association study have been playing an important role in identifying candidate genes and animal characterization. This review provides comprehensive information on the identified genomic regions and candidate genes associated with production and reproduction traits, and gene function in sheep.

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

Background

Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia.

Results

Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions.

Conclusions

Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.

Sequence characterization and polymorphism of melanocortin 1 receptor gene in some goat breeds with different coat color of Mongolia

Objective

Extension and Agouti loci play a key role for proportions of eumelanin and pheomelanin in determining coat color in several species, including goat. Mongolian goats exhibit diverse types of coat color phenotypes. In this study, investigation of the melanocortin 1 receptor (MC1R) coding region in different coat colors in Mongolian goats was performed to ascertain the presence of the extension allele.

Methods

A total of 105 goat samples representing three goat breeds were collected for this study from middle Mongolia. A 938 base pair (bp) long coding region of the MC1R gene was sequenced for three different breeds with different coat colors (Gobi Gurwan Saikhan: complete black, Zalaa Jinstiin Tsagaan: complete white, Mongolian native goat: admixture of different of coat colors). The genotypes of these goats were obtained from analyzing and comparing the sequencing results.

Results

A total of seven haplotypes defined by five substitution were identified. The five single nucleotide polymorphisms included two synonymous mutations (c.183C>T and c.489G>A) and three missense (non-synonymous) mutations (c.676A>G, c.748T>G, and c.770T>A). Comparison of genotypes frequencies of two common missense mutions using chi-sqaure (x²) test revealed significant differences between coat color groups (p<0.001). A logistic regression analysis additionally suggested highly significant association between genotypes and variation of black versus white uniform combination. Alternatively, most investigated goats (60.4%) belonged to H2 (TGAGT) haplotype.

Conclusion

According to the findings obtained in this study on the investigated coat colors, mutations in MC1R gene may have the crucial role for determining eumelanin and pheomelanin phenotypes. Due to the complication of coat color phenotype, more detailed investigation needed.

Allelic variation of melanocortin-1 receptor locus in Saudi indigenous sheep exhibiting different color coats

Objective

This study was designed to characterize the DNA polymorphisms of the melanocortin-1 receptor (MC1R) gene in indigenous Saudi Arabian sheep breeds exhibiting different color coats, along with individuals of the Sawaknee breed, an exotic sheep imported from Sudan.

Methods

The complete coding region of MC1R gene including parts of 3′ and 5′ untranslated regions was amplified and sequenced from three the indigenous Saudi sheep; Najdi (generally black, n = 41), Naeimi (generally white with brown faces, n = 36) and Herri (generally white, n = 18), in addition to 13 Sawaknee sheep.

Results

Five single nucleotide polymorphisms (SNPs) were detected in the MC1R gene: two led to nonsynonymous mutations (c.218 T>A, p.73 Met>Lys and c.361 G>A, p.121 Asp>Asn) and three led to synonymous mutations (c.429 C>T, p.143 Tyr>Tyr; c.600 T>G, p.200 Leu>Leu, and c.735 C>T, p.245 Ile>Ile). Based on these five SNPs, eight haplotypes representing MC1R E^d and E⁺ alleles were identified among the studied sheep breeds. The most common haplotype (H3) of the dominant E^d allele was associated with either black or brown coat color in Najdi and Sawaknee sheep, respectively. Two other haplotypes (H6 and H7) of E^d allele, with only the nonsynonymous mutation A218T, were detected for the first time in Saudi indigenous sheep.

Conclusion

In addition to investigating the MC1R allelic variation in Saudi indigenous sheep populations, the present study supports the assumption that the two independent nonsynonymous Met73Lys and Asp121Asn mutations in MC1R gene are associated with black or red coat colors in sheep breeds.

Epistatic Interaction of the Melanocortin 1 Receptor and Agouti Signaling Protein Genes Modulates Wool Color in the Brazilian Creole Sheep

Different pigmentation genes have been associated with color diversity in domestic animal species. The melanocortin 1 receptor (MC1R), agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), and v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (KIT) genes are candidate genes responsible for variation in wool color among breeds of sheep. Although the influence of these genes has been described in some breeds, in many others the effect of interactions among genes underlying wool color has not been investigated. The Brazilian Creole sheep is a local breed with a wide variety of wool color, ranging from black to white with several intermediate hues. We analyzed in this study the influence of the genes MC1R, ASIP, TYRP1, and KIT on the control of wool color in this breed. A total of 410 samples were analyzed, including 148 white and 262 colored individuals. The MC1R and ASIP polymorphisms were significantly associated with the segregation of either white or colored wool. The dominant MC1R allele (E(D) p.M73K and p.D121N) was present only in colored animals. All white individuals were homozygous for the MC1R recessive allele (E(+)) and carriers of the duplicated copy of ASIP A gene expression assay showed that only the carrier of the duplicated copy of ASIP produces increased levels in skin, not detectable in the single homozygous copy. These results demonstrate that the epistatic interaction of the genotypes in the MC1R and ASIP gene is responsible for the striking color variation in the Creole breed.

Genetic variations of the coding region of the melanocortin receptor 1 (MC1R) gene in the fox

BACKGROUND

The melanocortin 1 receptor (MC1R) gene plays an important role in the control of coat colour in mammals. Genetic variation of the MC1R gene and the relationship between genotype and coat colour are not well understood. Studies in the fox may improve our understanding of gene influence on coat colour in dogs and cats.

HYPOTHESIS/OBJECTIVES

To investigate coat colour associated mutations in the coding region of MC1R gene in foxes.

ANIMALS

A total of 118 foxes, comprising 70 red foxes (Vulpes vulpes) (19 red, 10 white silver, 29 silver and 12 chocolate foxes) and 48 arctic foxes (Vulpes lagopus) (9 dominant white blue foxes and 39 normal blue foxes) were included in the study.

METHODS

Evaluation of the DNA sequence of the coding region of MC1R gene and its polymorphisms.

RESULTS

Eight polymorphic sites (single nucleotide polymorphisms, SNPs) distributed throughout the 954-bp coding region of the fox MC1R gene were detected. Among them, c.13G>T, c.124A>G, c.289G>A, c.373T>C and c.839 T>G were mis-sense mutations, which resulted in codon change of p.G5C, p.N42D, p.V97I, p.C125R and p.F280C, respectively. Mutation and haplotype analysis indicated that c.373T>C was associated with black and brown pigmented phenotypes in foxes, and c.13G>T and c.839T>G were important in distinguishing V. lagopus and V. vulpes.

CONCLUSIONS AND CLINICAL IMPORTANCE

SNP c.373T>C in the coding region of the MC1R gene is probably associated with the brown phenotype of chocolate foxes.