Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses
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{"title"=>"Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses", "type"=>"journal", "authors"=>[{"first_name"=>"Deborah", "last_name"=>"Cook", "scopus_author_id"=>"36177099700"}, {"first_name"=>"Samantha", "last_name"=>"Brooks", "scopus_author_id"=>"7401651238"}, {"first_name"=>"Rebecca", "last_name"=>"Bellone", "scopus_author_id"=>"25631986100"}, {"first_name"=>"Ernest", "last_name"=>"Bailey", "scopus_author_id"=>"35584810500"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"352440604", "isbn"=>"1553-7404; 1553-7390", "pmid"=>"18802473", "doi"=>"10.1371/journal.pgen.1000195", "sgr"=>"52949086463", "scopus"=>"2-s2.0-52949086463", "issn"=>"15537390"}, "id"=>"47eac799-4641-3b41-861b-0b2665a71264", "abstract"=>"The purpose of this study was to uncover the molecular basis for the champagne hair color dilution phenotype in horses. Here, we report a DNA base substitution in the second exon of the horse gene SLC36A1 that changes an amino acid in the transmembrane domain of the protein from threonine to arginine. The phenotypic effect of this base change is a diminution of hair and skin color intensity for both red and black pigment in horses, and the resulting dilution has become known as champagne. This is the first genetic variant reported for SLC36A1 and the first evidence for its effect on eye, skin, and hair pigmentation. So far, no other phenotypic effects have been attributed to this gene. This discovery of the base substitution provides a molecular test for horse breeders to test their animals for the Champagne gene (CH).", "link"=>"http://www.mendeley.com/research/missense-mutation-exon-2-slc36a1-responsible-champagne-dilution-horses", "reader_count"=>41, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>30, "Medicine and Dentistry"=>4, "Veterinary Science and Veterinary Medicine"=>3, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>30}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1, "United Kingdom"=>1, "Australia"=>1, "Iceland"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/921678"], "description"=>"<p>N = the number of informative meiosis.</p><p>Θ = recombination frequency between that microsatelite and the <i>champagne gene</i> for all families combined.</p><p>Σ = LOD score for which 1/10<sup>Σ</sup> = the odds the association between the phenotype and the marker is due to chance.</p>", "links"=>[], "tags"=>["champagne", "dilution", "microsatellite"], "article_id"=>592130, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.t001", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linkage_Analysis_between_the_Champagne_Dilution_and_Microsatellite_Markers_UM010_COOK007_TKY329_and_VHL209_/592130", "title"=>"Linkage Analysis between the Champagne Dilution and Microsatellite Markers; <i>UM010</i>, <i>COOK007</i>, <i>TKY329</i> and <i>VHL209</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-09-19 00:35:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/921297"], "description"=>"<p>Linear relationship from top to bottom between the microsatellites, phenotype, and genotype of recombinant offspring for study sire #3. Phenotype is noted in top row with offspring's ID #.</p>", "links"=>[], "tags"=>["recombinant"], "article_id"=>591747, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_Recombinant_Haplotypes_/591747", "title"=>"Example of Recombinant Haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:29:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/921617"], "description"=>"<p>The R highlighted in red is the amino acid replacement associated with the champagne phenotype.</p>", "links"=>[], "tags"=>["alignment", "exons"], "article_id"=>592070, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g006", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seven_Species_Protein_Sequence_Alignment_for_SLC36A1_exons_1_and_2_/592070", "title"=>"Seven Species Protein Sequence Alignment for <i>SLC36A1</i> exons 1 and 2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:34:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/921401"], "description"=>"<p>A) RT-PCR results for <i>SLC36A1</i>. B) RT-PCR results for <i>SLC36A2</i>. C) RT-PCR results for <i>SLC36A3</i>. (Faint bands observed above 400 bp on gel C were sequenced and did not show homology to <i>SLC36A3</i>.)</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/comparative genomics", "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "genetics and genomics/gene function"], "article_id"=>591850, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RT_PCR_product_results_for_SLC36A1_A2_and_A3_/591850", "title"=>"RT-PCR product results for <i>SLC36A1</i>, <i>A2</i> and <i>A3</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:30:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/921503"], "description"=>"<p>Alignment is between homozygous champagne, non-dilute, and horse genome assembly. Reading frame is marked by alternating colors of codons. Bottom is diagram of <i>SLC36A1</i> with the identified SNP in exon 2. Sequence and gene layout have been verified on Ensembl genome browser equine assembly v2. Blue blocks of gene layout are exons and red boxes are the 5′ and 3′ UTRs.</p>", "links"=>[], "tags"=>["alignment"], "article_id"=>591952, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_Alignment_and_Gene_Diagram_/591952", "title"=>"Sequence Alignment and Gene Diagram.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:32:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/921712"], "description"=>"<p>Genotyping Results for c.188(C/G) locus.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/comparative genomics", "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "genetics and genomics/gene function"], "article_id"=>592158, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotyping_Results_for_c_188_C_G_locus_/592158", "title"=>"Genotyping Results for c.188(C/G) locus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-09-19 00:35:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/454670", "https://ndownloader.figshare.com/files/454725", "https://ndownloader.figshare.com/files/454821", "https://ndownloader.figshare.com/files/454909", "https://ndownloader.figshare.com/files/454990"], "description"=>"<div><p>Champagne coat color in horses is controlled by a single, autosomal-dominant gene (<em>CH</em>). The phenotype produced by this gene is valued by many horse breeders, but can be difficult to distinguish from the effect produced by the <em>Cream</em> coat color dilution gene (<em>CR</em>). Three sires and their families segregating for <em>CH</em> were tested by genome scanning with microsatellite markers. The <em>CH</em> gene was mapped within a 6 cM region on horse chromosome 14 (LOD = 11.74 for θ = 0.00). Four candidate genes were identified within the region, namely <em>SPARC</em> [<em>Secreted protein</em>, <em>acidic</em>, <em>cysteine-rich (osteonectin)</em>], <em>SLC36A1</em> (<em>Solute Carrier 36 family A1</em>), <em>SLC36A2 (Solute Carrier 36 family A2)</em>, and <em>SLC36A3 (Solute Carrier 36 family A3)</em>. <em>SLC36A3</em> was not expressed in skin tissue and therefore not considered further. The other three genes were sequenced in homozygotes for <em>CH</em> and homozygotes for the absence of the dilution allele (<em>ch</em>). <em>SLC36A1</em> had a nucleotide substitution in exon 2 for horses with the champagne phenotype, which resulted in a transition from a threonine amino acid to an arginine amino acid (T63R). The association of the single nucleotide polymorphism (SNP) with the champagne dilution phenotype was complete, as determined by the presence of the nucleotide variant among all 85 horses with the champagne dilution phenotype and its absence among all 97 horses without the champagne phenotype. This is the first description of a phenotype associated with the <em>SLC36A1</em> gene.</p></div>", "links"=>[], "tags"=>["missense", "mutation", "exon", "slc36a1", "champagne", "dilution", "horses"], "article_id"=>149592, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000195.s001", "https://dx.doi.org/10.1371/journal.pgen.1000195.s002", "https://dx.doi.org/10.1371/journal.pgen.1000195.s003", "https://dx.doi.org/10.1371/journal.pgen.1000195.s004", "https://dx.doi.org/10.1371/journal.pgen.1000195.s005"], "stats"=>{"downloads"=>6, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Missense_Mutation_in_Exon_2_of_SLC36A1_Responsible_for_Champagne_Dilution_in_Horses/149592", "title"=>"Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-09-19 02:39:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/921139"], "description"=>"<p>A, B and C) Eye and skin color of foals. D and E) Eye color and skin mottling of adult horse.</p>", "links"=>[], "tags"=>["genetics and genomics", "genetics and genomics/comparative genomics", "genetics and genomics/gene discovery", "genetics and genomics/gene expression", "genetics and genomics/gene function"], "article_id"=>591582, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Champagne_Eye_and_Skin_traits_/591582", "title"=>"Champagne Eye and Skin traits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:26:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/920944"], "description"=>"<p>A) Chestnut – horse only produces red pigment. B) Chestnut diluted by <i>Champagne</i> = Gold Champagne. C) Bay – black pigment is limited to the points (e.g. mane, tail, and legs) allowing red pigment produced on the body to show. D) Bay diluted by <i>Champagne</i> = Amber Champagne. E) Black – red and black pigment produced, red masked by black. F) Black diluted by <i>Champagne</i> = Classic Champagne.</p>", "links"=>[], "tags"=>["colors", "horses"], "article_id"=>591391, "categories"=>["Genetics"], "users"=>["Deborah Cook", "Samantha Brooks", "Rebecca Bellone", "Ernest Bailey"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000195.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_Champagne_gene_action_on_base_coat_colors_of_horses_chestnut_bay_and_black_/591391", "title"=>"Effect of <i>Champagne</i> gene action on base coat colors of horses (chestnut, bay, and black).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-09-19 00:23:11"}

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