Accumulating Mutations in Series of Haplotypes at the KIT and MITF Loci Are Major Determinants of White Markings in Franches-Montagnes Horses
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{"title"=>"Accumulating Mutations in Series of Haplotypes at the KIT and MITF Loci Are Major Determinants of White Markings in Franches-Montagnes Horses", "type"=>"journal", "authors"=>[{"first_name"=>"Bianca", "last_name"=>"Haase", "scopus_author_id"=>"14323203200"}, {"first_name"=>"Heidi", "last_name"=>"Signer-Hasler", "scopus_author_id"=>"55221869800"}, {"first_name"=>"Matthew M.", "last_name"=>"Binns", "scopus_author_id"=>"7005230972"}, {"first_name"=>"Gabriela", "last_name"=>"Obexer-Ruff", "scopus_author_id"=>"6603482917"}, {"first_name"=>"Regula", "last_name"=>"Hauswirth", "scopus_author_id"=>"55207174200"}, {"first_name"=>"Rebecca R.", "last_name"=>"Bellone", "scopus_author_id"=>"25631986100"}, {"first_name"=>"Dominik", "last_name"=>"Burger", "scopus_author_id"=>"7203040738"}, {"first_name"=>"Stefan", "last_name"=>"Rieder", "scopus_author_id"=>"6701509161"}, {"first_name"=>"Claire M.", "last_name"=>"Wade", "scopus_author_id"=>"7102531600"}, {"first_name"=>"Tosso", "last_name"=>"Leeb", "scopus_author_id"=>"7006758115"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84884750482", "sgr"=>"84884750482", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0075071", "pmid"=>"24098679", "pui"=>"369919115"}, "id"=>"3ae0f6ae-f968-32f3-bb06-2301807c0550", "abstract"=>"Coat color and pattern variations in domestic animals are frequently inherited as simple monogenic traits, but a number are known to have a complex genetic basis. While the analysis of complex trait data remains a challenge in all species, we can use the reduced haplotypic diversity in domestic animal populations to gain insight into the genomic interactions underlying complex phenotypes. White face and leg markings are examples of complex traits in horses where little is known of the underlying genetics. In this study, Franches-Montagnes (FM) horses were scored for the occurrence of white facial and leg markings using a standardized scoring system. A genome-wide association study (GWAS) was performed for several white patterning traits in 1,077 FM horses. Seven quantitative trait loci (QTL) affecting the white marking score with p-values p≤10−4 were identified. Three loci, MC1R and the known white spotting genes, KIT and MITF, were identified as the major loci underlying the extent of white patterning in this breed. Together, the seven loci explain 54% of the genetic variance in total white marking score, while MITF and KIT alone account for 26%. Although MITF and KIT are the major loci controlling white patterning, their influence varies according to the basic coat color of the horse and the specific body location of the white patterning. Fine mapping across the MITF and KIT loci was used to characterize haplotypes present. Phylogenetic relationships among haplotypes were calculated to assess their selective and evolutionary influences on the extent of white patterning. This novel approach shows that KIT and MITF act in an additive manner and that accumulating mutations at these loci progressively increase the extent of white markings.", "link"=>"http://www.mendeley.com/research/accumulating-mutations-series-haplotypes-kit-mitf-loci-major-determinants-white-markings-franchesmon", "reader_count"=>20, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>7, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Student > Master"=>5, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Japan"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1220453", "https://ndownloader.figshare.com/files/1220454", "https://ndownloader.figshare.com/files/1220455", "https://ndownloader.figshare.com/files/1220456", "https://ndownloader.figshare.com/files/1220457", "https://ndownloader.figshare.com/files/1220458"], "description"=>"<div><p>Coat color and pattern variations in domestic animals are frequently inherited as simple monogenic traits, but a number are known to have a complex genetic basis. While the analysis of complex trait data remains a challenge in all species, we can use the reduced haplotypic diversity in domestic animal populations to gain insight into the genomic interactions underlying complex phenotypes. White face and leg markings are examples of complex traits in horses where little is known of the underlying genetics. In this study, Franches-Montagnes (FM) horses were scored for the occurrence of white facial and leg markings using a standardized scoring system. A genome-wide association study (GWAS) was performed for several white patterning traits in 1,077 FM horses. Seven quantitative trait loci (QTL) affecting the white marking score with p-values <i>p</i>≤10<sup>−4</sup> were identified. Three loci, <i>MC1R</i> and the known white spotting genes, <i>KIT</i> and <i>MITF</i>, were identified as the major loci underlying the extent of white patterning in this breed. Together, the seven loci explain 54% of the genetic variance in total white marking score, while <i>MITF</i> and <i>KIT</i> alone account for 26%. Although <i>MITF</i> and <i>KIT</i> are the major loci controlling white patterning, their influence varies according to the basic coat color of the horse and the specific body location of the white patterning. Fine mapping across the <i>MITF</i> and <i>KIT</i> loci was used to characterize haplotypes present. Phylogenetic relationships among haplotypes were calculated to assess their selective and evolutionary influences on the extent of white patterning. This novel approach shows that <i>KIT</i> and <i>MITF</i> act in an additive manner and that accumulating mutations at these loci progressively increase the extent of white markings.</p></div>", "links"=>[], "tags"=>["accumulating", "mutations", "haplotypes", "loci", "determinants", "markings", "franches-montagnes", "horses"], "article_id"=>811674, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0075071.s001", "https://dx.doi.org/10.1371/journal.pone.0075071.s002", "https://dx.doi.org/10.1371/journal.pone.0075071.s003", "https://dx.doi.org/10.1371/journal.pone.0075071.s004", "https://dx.doi.org/10.1371/journal.pone.0075071.s005", "https://dx.doi.org/10.1371/journal.pone.0075071.s006"], "stats"=>{"downloads"=>6, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Accumulating_Mutations_in_Series_of_Haplotypes_at_the_KIT_and_MITF_Loci_Are_Major_Determinants_of_White_Markings_in_Franches_Montagnes_Horses/811674", "title"=>"Accumulating Mutations in Series of Haplotypes at the <i>KIT</i> and <i>MITF</i> Loci Are Major Determinants of White Markings in Franches-Montagnes Horses", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220448"], "description"=>"<p>Phylogenetic relationships between haplotypes at <i>MITF</i> (M1–M6) and <i>KIT</i> (K1–K7). Haplotype combinations (hap1 = haplotype 1, hap2 = haplotype 2) and individuals average total white markings score (aTSC = average Total Score) are shown on the right.</p>", "links"=>[], "tags"=>["haplotypes"], "article_id"=>811669, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationship_between_haplotypes_at_MITF_and_KIT_/811669", "title"=>"Phylogenetic relationship between haplotypes at <i>MITF</i> and <i>KIT</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220447"], "description"=>"<p>Fine–scale quantitative association between total white markings score and linkage disequilibrium (LD) in r<sup>2</sup> between SNPs across 2 Mb regions in (A) the <i>KIT</i> and (B) the <i>MITF</i> region including all horses. The darker shading represents higher LD, black diamond’s represents an r<sup>2</sup> of 1.</p>", "links"=>[], "tags"=>["quantitative", "linkage", "disequilibrium"], "article_id"=>811668, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fine_scale_quantitative_association_mapping_and_linkage_disequilibrium_across_MITF_and_KIT_/811668", "title"=>"Fine-scale quantitative association mapping and linkage disequilibrium across <i>MITF</i> and <i>KIT</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220452"], "description"=>"<p>Results of the haplotype-based quantitative association analysis within the major haplotype block of <i>MITF</i> (M1–M6) and <i>KIT</i> (K1–K7). The analysis includes all horses used for fine mapping. Haplotype frequency, beta coefficient, p-value and empirical p-value are indicated for every investigated haplotype.</p>", "links"=>[], "tags"=>["quantitative", "haplotype"], "article_id"=>811673, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.t002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_quantitative_association_analysis_within_the_major_haplotype_block_/811673", "title"=>"Results of the quantitative association analysis within the major haplotype block.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220450"], "description"=>"<p>Results of the logistic regression model analysis for the relationship between <i>MITF</i> haplotypes, SNPs across the 2 Mb <i>KIT</i> region <i>and KIT</i> haplotypes.</p>", "links"=>[], "tags"=>["logistic", "regression"], "article_id"=>811671, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g006", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_logistic_regression_model_analysis_/811671", "title"=>"Results of the logistic regression model analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220451"], "description"=>"<p>The contributions of <i>MC1R</i>, <i>KIT</i> and <i>MITF</i> were calculated separately for each locus across a 2 Mb interval.</p>", "links"=>[], "tags"=>["variance", "explained"], "article_id"=>811672, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_variance_explained_by_the_three_major_candidate_loci_/811672", "title"=>"Genetic variance (%) explained by the three major candidate loci.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220449"], "description"=>"<p>Average total white markings score and standard deviation for <i>MITF-KIT</i> haplotype combinations. Adjacent squares represent haplotypes (red = <i>MITF</i>; blue = <i>KIT</i>); color shades represent haplotypes of the phylogenetic relationship trees (<i>MITF</i>: M1–M6; <i>KIT</i>: K1–K7).</p>", "links"=>[], "tags"=>["markings", "haplotype"], "article_id"=>811670, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g005", "stats"=>{"downloads"=>1, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_total_white_markings_score_for_MITF_KIT_haplotype_combinations_/811670", "title"=>"Average total white markings score for <i>MITF-KIT</i> haplotype combinations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220446"], "description"=>"<p>A Manhattan plot showing the negative log of the probability of association (p-value) between individual marker and total white marking score. (A) Analysis included horses of all colors, (B) bay horses only, (C) chestnut horses only. Markers are represented in different colors according to their chromosome. Significance level of p≤1×10<sup>−8</sup> is indicated with a dashed red line; a dashed black line represents association with p≤10<sup>−4</sup>.</p>", "links"=>[], "tags"=>["identifies", "loci", "marking"], "article_id"=>811667, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GWAS_identifies_two_major_loci_associated_with_total_white_marking_scores_/811667", "title"=>"GWAS identifies two major loci associated with total white marking scores.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/1220445"], "description"=>"<p>Example of phenotypes. Horse (A) has a total score of white markings of 1 (head = 0; foreleg = 0; hind leg = 1); horse (B) has a total score of white markings of 19 (head = 9; foreleg = 2; hind leg = 8).</p>", "links"=>[], "tags"=>[], "article_id"=>811666, "categories"=>["Uncategorised"], "users"=>["Bianca Haase", "Heidi Signer-Hasler", "Matthew M. Binns", "Gabriela Obexer-Ruff", "Regula Hauswirth", "Rebecca R. Bellone", "Dominik Burger", "Stefan Rieder", "Claire M. Wade", "Tosso Leeb"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0075071.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phenotypic_variation_in_the_expression_of_white_markings_/811666", "title"=>"Phenotypic variation in the expression of white markings.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-09-30 02:56:18"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"10", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"11", "full-text"=>"17", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"12", "full-text"=>"18", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Anatomy and physiology", "average_usage"=>[256, 428]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[272, 472, 600, 713, 815, 911, 1004, 1094, 1185, 1273, 1358, 1441]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[272, 466, 589, 702, 806, 903, 995, 1086, 1176, 1258, 1347, 1422, 1493]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}, {"subject_area"=>"/Biology and life sciences/Population biology", "average_usage"=>[269, 448, 558, 658, 744, 830, 914, 995, 1068, 1139, 1214, 1284, 1349]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}]}
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