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

2009 ◽  
Vol 2009 ◽  
pp. 1-6 ◽  
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.

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

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.

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

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.

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

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.

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

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.

Association of genetic variants of the prolactin gene with milk production traits in Russian Red Pied cattle

2007 ◽  
Vol 2007 ◽  
pp. 156-156 ◽  
Author(s):  
Masoud Alipanah ◽  
Lobov Kalashnikova ◽  
Genadi Rodionov
Keyword(s):  
Genetic Marker ◽  
Regulatory Function ◽  
Cdna Clones ◽  
Production Traits ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Prolactin Gene ◽  
Pcr Rflp ◽  
Rsai Polymorphism

Prolactin plays an important regulatory function in mammary gland development, milk secretion, and expression of milk protein genes. Hence the PRL gene is a potential genetic marker of production traits in dairy cattle. The gene was mapped on chromosome 23 by Hallerman et al. (1988). It consists of 5 exons and four introns (Camper et al. 1984) encoding the 199-amino-acid mature protein (Wallis 1974). On the basis of sequence analysis of four different cDNA clones, seven possible nucleotide substitutions were described by Sasavage et al. (1982). One of them, recognized by RsaI endonuclease, has become a popular genetic marker used for genetic characterization of cattle populations by means of PCR-RFLP (Mitra et al., 1995). Two allelic variants (B and b) have been distinguished at the DNA level, based on RsaI polymorphism in the third exon of the coding region. It has been suggested that prolactin alleles correlate with milk yield (Lewin et al., 1992).

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

2017 ◽  
Vol 52 (8) ◽  
pp. 615-622 ◽  
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.

Molecular Characterization of the TLR2 Gene in Datong Yak

2019 ◽  
Author(s):  
Shuai Peng ◽  
Lang Chen ◽  
Tian Yu Zheng ◽  
Li Zhang ◽  
Zhuo Li ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Amino Acid Sequences ◽  
Regulation Mechanism ◽  
Coding Region ◽  
Sequence Characterization ◽  
Tir Domain ◽  
Tlr2 Gene ◽  
Nucleotide Mutation ◽  
Leucine Rich Repeats

The coding region of Datong yak’s TLR2 gene was amplified and subjected to sequence characterization. The coding region of the Datong yak TLR2 gene comprised a single ORF of 2355 nucleotides that coded for 784 amino acids with translatable products. The coding region of the TLR2 gene of the Datong yak contained two nucleotide mutation sites, namely, G677A and G1587A. G677A exhibited a missense mutation. After comparing nucleotide and amino acid sequences among related species and constructing the phylogenetic relationships, Datong yak sequences were shown to be highly similar to those of Bos taurus. The Datong yak TLR2 protein simultaneously possessed leucine-rich repeats, a TIR domain and an aldehyde dehydrogenase active site. Results showed that the protein plays an important role in the body’s immune regulation mechanism.

Regulation of Hoxc-8 during mouse embryonic development: identification and characterization of critical elements involved in early neural tube expression

Development ◽  
1995 ◽  
Vol 121 (12) ◽  
pp. 4339-4347 ◽  
Author(s):  
C.S. Shashikant ◽  
C.J. Bieberich ◽  
H.G. Belting ◽  
J.C. Wang ◽  
M.A. Borbely ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Neural Tube ◽  
Small Region ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Cis Acting ◽  
Critical Elements ◽  
Reporter Gene Analysis ◽  
Combinatorial Interactions

We have characterized cis-acting elements that direct the early phase of Hoxc-8 expression using reporter gene analysis in transgenic mice. By deletion we show that a 135 bp DNA fragment, located approximately 3 kb upstream of the coding region of Hoxc-8, is capable of directing posterior neural tube expression. This early neural tube (ENT) enhancer consists of four separate elements, designated A, B, C and D, whose nucleotide sequences are similar to binding sites of known transcription factors. Nucleotide substitutions suggest that element A is an essential component of the ENT enhancer. However element A by itself is incapable of directing neural tube expression. This element requires interactions at any two of the other three elements, B, C or D. Thus, the components of the ENT enhancer direct neural tube expression in an interdependent manner. We propose that Hoxc-8 is activated in the neural tube by combinatorial interactions among several proteins acting within a small region. Our transgenic analyses provide a means to identify transcription factors that regulate Hoxc-8 expression during embryogenesis.

scholarly journals Characterization of Recombinant Dengue-2 Virus Derived from a Single Nucleotide Substitution in the 5′ Noncoding Region

2010 ◽  
Vol 2010 ◽  
pp. 1-8 ◽  
Author(s):  
Vijittra Leardkamolkarn ◽  
Wipawan Sirigulpanit ◽  
Richard M. Kinney
Keyword(s):  
Single Point ◽  
Life Cycles ◽  
Site Directed Mutagenesis ◽  
Mosquito Vector ◽  
Wild Type ◽  
Nucleotide Substitutions ◽  
Newborn Mice ◽  
Adult Mice ◽  
Cell Culture Assay

Variants of wild-type dengue serotype 2 (DEN-2) virus containing nucleotide substitutions at positions 14, 15, or 57 in the5′NCR were constructed by PCR-mediated site-directed mutagenesis. All three viruses containing a single point substitution demonstrated attenuation phenotype as evidenced by decreases replication and plaque size in cell culture assay. All three variants were less neurovirulent in newborn mice compared to the wild type. The mutants were immunogenic in adult mice immunogenicity and maintained stable replication characteristics following passage in mice. The variant viruses were competent for replication inAedes aegypimosquito vector, albeit at lower levels of infection and dissemination in the mosquito than the wild-type Den-2 16681 virus. Although all of the viruses, including the wild type, were found transmissible in mosquito life cycles, they were found subsequentially decreased in efficiency of infection, transmission, and dissemination rates along the mosquito generations and all of them remained genetically stable.

scholarly journals Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum)

2019 ◽  
Vol 20 (9) ◽  
pp. 2204 ◽  
Author(s):  
Xiaorong Sun ◽  
Jinshuai Shu ◽  
Ali Mohamed Ali Mohamed ◽  
Xuebin Deng ◽  
Xiaona Zhi ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Bulked Segregant Analysis ◽  
Chromosome 2 ◽  
Internode Elongation ◽  
Wild Type ◽  
Coding Region ◽  
Tomato Cultivar ◽  
Expression Levels ◽  
The Difference

Internode length is an important agronomic trait affecting plant architecture and crop yield. However, few genes for internode elongation have been identified in tomato. In this study, we characterized an elongated internode inbred line P502, which is a natural mutant of the tomato cultivar 05T606. The mutant P502 exhibits longer internode and higher bioactive GA concentration compared with wild-type 05T606. Genetic analysis suggested that the elongated internode trait is controlled by quantitative trait loci (QTL). Then, we identified a major QTL on chromosome 2 based on molecular markers and bulked segregant analysis (BSA). The locus was designated as EI (Elongated Internode), which explained 73.6% genetic variance. The EI was further mapped to a 75.8-kb region containing 10 genes in the reference Heinz 1706 genome. One single nucleotide polymorphism (SNP) in the coding region of solyc02g080120.1 was identified, which encodes gibberellin 2-beta-dioxygenase 7 (SlGA2ox7). SlGA2ox7, orthologous to AtGA2ox7 and AtGA2ox8, is involved in the regulation of GA degradation. Overexpression of the wild EI gene in mutant P502 caused a dwarf phenotype with a shortened internode. The difference of EI expression levels was not significant in the P502 and wild-type, but the expression levels of GA biosynthetic genes including CPS, KO, KAO, GA20ox1, GA20ox2, GA20ox4, GA3ox1, GA2ox1, GA2ox2, GA2ox4, and GA2ox5, were upregulated in mutant P502. Our results may provide a better understanding of the genetics underlying the internode elongation and valuable information to improve plant architecture of the tomato.

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