Molecular characterization of coat color gene in Sahiwal versus Karan Fries bovine

Abstract Background Melanocortin-1-receptor gene (MC1R) plays a significant role in signaling cascade of melanin production. In cattle, the coat colors, such as red and black, are an outcome of eumelanin and pheomelanin pigments, respectively. The coat colors have become critical factors in the animal selection process. This study is therefore aimed at the molecular characterization of reddish-brown coat-colored Sahiwal cattle in comparison to the black and white-colored Karan Fries. Results The Sequence length of the MC1R gene was 954 base pairs in Sahiwal cattle. The sequences were examined and submitted to GenBank Acc.No. MG373575 to MG373605. Alignment of both (Sahiwal and Karan Fries) protein sequences by applying ClustalO multiple sequence alignment programs revealed 99.8–96.8% sequence similarity within the bovine. MC1R gene phylogenetic studies were analyzed by MEGA X. The gene MC1R tree, protein confines, and hereditary difference of cattle were derived from Ensemble Asia Cow Genome Browser 97. One unique single-nucleotide polymorphism (c.844C>A) (SNP) was distinguished. Single amino acid changes were detected in the seventh transmembrane structural helix region, with SNP at p.281 T>N of MC1R gene in Karan Fries cattle. Conclusions In this current research, we first distinguished the genomic sequence of the MC1R gene regions that showed evidence of coat variation between Indian indigenous Sahiwal cattle breed correlated with crossbreed Karan Fries. These variations were found in the Melanocortin 1 receptor coding regions of the diverse SNPs. The conclusions of this research provide new insights into understanding the coat color variation in crossbreed compared to the Indian Sahiwal cattle. Graphical abstract

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Genetic characterization of coat color genes in Brazilian Crioula sheep from a conservation nucleus

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2017000800007 ◽

2017 ◽

Vol 52 (8) ◽

pp. 615-622 ◽

Cited By ~ 4

Author(s):

Lilian Cristina Gomes Cavalcanti ◽

José Carlos Ferrugem Moraes ◽

Danielle Assis de Faria ◽

Concepta Margaret McManus ◽

Alcebiades Renato Nepomuceno ◽

...

Keyword(s):

Coat Color ◽

Color Variation ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Epistatic Interactions ◽

Low Frequencies ◽

Melanocortin 1 Receptor ◽

Tyrosinase Related Protein

Abstract: The objective of this work was to identify single nucleotide polymorphisms (SNPs) in resequencing data from MC1R, ASIP, and TYRP1 genes derived from Crioula sheep (Ovis aris) with different coat colors. Polymorphisms in the ASIP (agouti-signaling protein), MC1R (melanocortin 1 receptor), and TRYP1 (tyrosinase-related protein 1) genes were analyzed in 115 sheep from Embrapa’s conservation nucleus of crioula sheep, in Brazil. A total of 7,914 bp were sequenced per animal, and 14 SNPs were identified. Two additional assays were performed to detect duplications and deletions in the ASIP gene. Ninety-five percent of the coat color variation was explained by epistatic interactions observed between specific alleles in the MC1R and ASIP genes. Evidence suggests an important role of TYRP1 variants for wool color, despite their low frequencies. The marker panel was efficient enough in predicting coat color in the studied animals and, therefore, can be used to implement a marker-assisted selection program in the conservation nucleus of sheep of the crioula breed.

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Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation is associated with partial recessive red phenotypes in dog

10.21203/rs.3.rs-36023/v1 ◽

2020 ◽

Author(s):

Heidi Anderson ◽

Leena Honkanen ◽

Päivi Ruotanen ◽

Julia Mathlin ◽

Jonas Donner

Keyword(s):

Citizen Science ◽

Coat Color ◽

Allelic Variation ◽

Wild Type ◽

Melanocortin 1 Receptor ◽

Phenotype Analysis ◽

Genotype Screening ◽

Dominant Black ◽

Novel Allele

Abstract Background The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in dogs and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1–3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs. Results Commercial genotyping of 11,726 dog samples showed the R301C variant of the MC1R gene was present in 34 breeds or breed varieties, at an allele frequency of 1.48% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient”. Phenotype analysis of owner-provided dog pictures reveals eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle. Conclusions This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.

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Sequence Characterization of theMC1RGene in Yak (Poephagus grunniens) Breeds with Different Coat Colors

Journal of Biomedicine and Biotechnology ◽

10.1155/2009/861046 ◽

2009 ◽

Vol 2009 ◽

pp. 1-6 ◽

Cited By ~ 10

Author(s):

Shi-Yi Chen ◽

Yi Huang ◽

Qing Zhu ◽

Luca Fontanesi ◽

Yong-Gang Yao ◽

...

Keyword(s):

Coat Color ◽

Extracellular Loop ◽

Wild Type ◽

Coding Region ◽

Functional Effect ◽

Nucleotide Substitutions ◽

Melanocortin 1 Receptor ◽

Sequence Characterization ◽

Potential Association

Melanocortin 1 receptor (MC1R) gene plays a key role in determining coat color in several species, including the cattle. However, up to now there is no report regarding theMC1Rgene and the potential association of its mutations with coat colors in yak (Poephagus grunniens). In this study, we sequenced the encoding region of theMC1Rgene in three yak breeds with completely white (Tianzhu breed) or black coat color (Jiulong and Maiwa breeds). The predicted coding region of the yakMC1Rgene resulted of 954 bp, the same to that of the wild-type cattle sequence, with >99% identity. None of the mutation events reported in cattle was found. Comparing the yak obtained sequences, five nucleotide substitutions were detected, which defined three haplotypes (EY1,EY2, andEY3). Of the five mutations, two, characterizing theEY1haplotype, were nonsynonymous substitutions (c.340C>A and c.871G>A) causing amino acid changes located in the first extracellular loop (p.Q114K) and in the seventh transmembrane region (p.A291T).In silicoprediction might indicate a functional effect of the latter substitution. However, all three haplotypes were present in the three yak breeds with relatively consistent frequency distribution, despite of their distinguished coat colors, which suggested that there was no across-breed association between haplotypes or genotypes and black/white phenotypes, at least in the investigated breeds. Other genes may be involved in affecting coat color in the analyzed yaks.

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Molecular Characterization of Parvovirus Strain GX-Tu-PV-1, Isolated from a Guangxi Turkey

Microbiology Resource Announcements ◽

10.1128/mra.00152-19 ◽

2019 ◽

Vol 8 (46) ◽

Cited By ~ 1

Author(s):

Yanfang Zhang ◽

Zhixun Xie ◽

Xianwen Deng ◽

Zhiqin Xie ◽

Liji Xie ◽

...

Keyword(s):

Molecular Characterization ◽

Genome Sequence ◽

South China ◽

Genomic Sequence ◽

Molecular Characteristics ◽

Guangxi Province

The aim of the current study was to determine the genomic sequence of parvovirus strain GX-Tu-PV-1, which was isolated from a turkey in Guangxi Province, South China. The analysis showed that the genome sequence of GX-Tu-PV-1 was 81.3% to ∼99.3% similar to those of other turkey parvoviruses (TuPVs) and 79.8% to ∼92.1% related to chicken parvovirus (ChPV). This study will help in understanding the epidemiology and molecular characteristics of parvovirus in turkeys.

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Molecular Characterization of Potato virus V Genomes from Europe Indicates Limited Spatiotemporal Strain Differentiation

Phytopathology ◽

10.1094/phyto.2000.90.4.437 ◽

2000 ◽

Vol 90 (4) ◽

pp. 437-444 ◽

Cited By ~ 22

Author(s):

Igor Oruetxebarria ◽

Tuija Kekarainen ◽

Carl Spetz ◽

Jari P. T. Valkonen

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

Potato Virus ◽

Genomic Sequence ◽

Host Responses ◽

Single Strain ◽

Reading Frame ◽

Solanaceae Species ◽

Nontranslated Region

Because there were no previous reports on the molecular characterization of Potato virus V (PVV, genus Potyvirus, family Potyviridae), the complete genomic sequence of PVV isolate Dv42 was determined. The length of the single-stranded messenger-polarity RNA genome was 9,851 nt (nucleotides), followed by a poly(A) tail. The genome contained a 5′-terminal nontranslated region (5′-NTR; 204 nt), a single open reading frame (nucleotides 205-9406; 3,067 amino acids), and a 3′-NTR that was unusually long (446 nt) compared with that of Potato virus Y (PVY; 331-nt 3′-NTR), Potato virus A (PVA; 207-nt 3′-NTR), and other potyviruses that naturally infect Solanaceae species. Phylogenetic analysis with the cylindrical inclusion protein-encoding and coat protein (CP)-encoding regions indicated that PVV Dv42 was most closely related to Pepper mottle virus and PVY, respectively. Seven PVV isolates (including Dv42) collected from cultivated potatoes in the Netherlands, the United Kingdom, and Norway from 1964 to 1997 were uniform in serological properties and symptomatology in indicator hosts that could distinguish strains of PVY and PVA. The nucleotide sequences of the 5′-NTR, P1, CP, and 3′-NTR regions of the PVV isolates were determined and were 94.6 to 99.5, 96.3 to 98.8, 96.4 to 98.7, and 96.3 to 99.6% identical, respectively. The amino acid similarities for the P1 and CP were 95.8 to 98.6 and 96.0 to 97.8%, respectively. Phylogenetic analysis of the CP sequences of PVV revealed no significant grouping, in contrast to PVY and PVA, which were grouped largely according to the previously recognized strains based on host responses. However, the relatively few differences in the P1 sequences of PVV were correlated with the different countries of origin. Hence, the PVV isolates infecting potatoes in Europe seem to vary little genetically and may belong to a single strain.

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Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation associated with partial recessive red phenotypes in dog

Canine Medicine and Genetics ◽

10.1186/s40575-020-00095-7 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Heidi Anderson ◽

Leena Honkanen ◽

Päivi Ruotanen ◽

Julia Mathlin ◽

Jonas Donner

Keyword(s):

Citizen Science ◽

Coat Color ◽

Allelic Variation ◽

Phenotypic Expression ◽

Wild Type ◽

Melanocortin 1 Receptor ◽

Phenotype Analysis ◽

Genotype Screening ◽

Dominant Black

Abstract Background The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in various species and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1–3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs. Results Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the phenotypic expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle. Conclusions This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.

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Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation is associated with partial recessive red phenotypes in dog

10.21203/rs.3.rs-36023/v2 ◽

2020 ◽

Author(s):

Heidi Anderson ◽

Leena Honkanen ◽

Päivi Ruotanen ◽

Julia Mathlin ◽

Jonas Donner

Keyword(s):

Citizen Science ◽

Coat Color ◽

Allelic Variation ◽

Wild Type ◽

Melanocortin 1 Receptor ◽

Phenotype Analysis ◽

Genotype Screening ◽

Dominant Black ◽

Novel Allele

Abstract Background: The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in dogs and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1-3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs.Results: Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle.Conclusions: This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.

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Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation associated with partial recessive red phenotypes in dog

10.21203/rs.3.rs-36023/v3 ◽

2020 ◽

Author(s):

Heidi Anderson ◽

Leena Honkanen ◽

Päivi Ruotanen ◽

Julia Mathlin ◽

Jonas Donner

Keyword(s):

Citizen Science ◽

Coat Color ◽

Allelic Variation ◽

Phenotypic Expression ◽

Wild Type ◽

Melanocortin 1 Receptor ◽

Phenotype Analysis ◽

Genotype Screening ◽

Dominant Black

Abstract Background: The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in various species and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1-3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs.Results: Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the phenotypic expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle.Conclusions: This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.

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Molecular characterization of two candidate genes associated with coat color in Tibetan sheep (Ovis arise)

Journal of Integrative Agriculture ◽

10.1016/s2095-3119(14)60928-x ◽

2015 ◽

Vol 14 (7) ◽

pp. 1390-1397 ◽

Cited By ~ 5

Author(s):

Ji-long HAN ◽

Min YANG ◽

Ting-ting GUO ◽

Yao-jing YUE ◽

Jian-bin LIU ◽

...

Keyword(s):

Candidate Genes ◽

Molecular Characterization ◽

Coat Color ◽

Tibetan Sheep

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Molecular characterization of A1/A2 Beta-casein Alleles in Vrindavani crossbred and Sahiwal cattle

Indian Journal of Animal Research ◽

10.18805/ijar.b-3493 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sushil Kumar ◽

Ram Vir Singh ◽

Anuj Chauhan

Keyword(s):

Genetic Variability ◽

Molecular Characterization ◽

Allelic Frequency ◽

Genotypic Frequency ◽

Allelic Frequencies ◽

Genotype Frequencies ◽

Sahiwal Cattle ◽

Sahiwal Cows ◽

Beta Casein

In the present investigation Vrindavani cross bred and indigenous Sahiwal cows were genotyped for A1/ A2 b-casein alleles. Present genotypic study on A1/A2 Beta-casein variants was conducted in a population of 660 cattle which comprises of 354 Vrindavani and 306 Sahiwal cows. Out of them 354 Vrindavani cows were maintained at Cattle and Buffalo Farm, IVRI, Izatnagar and 306 Sahiwal cows under study were maintained at Kamdhenu Gaushala, Noormahal, Jalandhar. In Vrindavani cows, all three type of genotype were observed viz., A1A1, A1A2 and A2A2. Genotypic frequencies of A1A1, A1A2 and A2A2 genotypes were 0.11, 0.47 and 0.42 respectively. The frequency of A1 and A2 allelic frequency in this population was 0.35 and 0.65 respectively in Vrindavani cows. In Sahiwal cows, only two types of genotypes were observed viz., A1A2 and A2A2. Genotype frequencies for A1A2 and A2A2 genotypes were 0.13 and 0.87 in Sahiwal cattle. The allelic frequencies for A1 and A2 were 0.06 and 0.94 respectively in Sahiwal cows. The results revealed that maximum genotypic frequency observed was A1A2 (0.47) followed by A2A2 (0.42) and A1A1 (0.11) in Vrindavani cattle while in Sahiwal cattle maximum genotypic frequency of A2A2 (0.87) followed by A1A2 (0.13) respectively. The observed heterozygosity (0.47) and PIC value (0.35) pointed towards the existence of medium genetic variability in the tested population.

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