Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken
Publication Date
February 29, 2008
Journal
PLOS Genetics
Authors
Jonas Eriksson, Greger Larson, Ulrika Gunnarsson, Bertrand Bed'hom, et al
Volume
4
Issue
2
Pages
e1000010
DOI
https://dx.plos.org/10.1371/journal.pgen.1000010
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000010
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/18454198
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265484
Europe PMC
http://europepmc.org/abstract/MED/18454198
Web of Science
000255386100011
Scopus
40149109370
Mendeley
http://www.mendeley.com/research/identification-yellow-skin-gene-reveals-hybrid-origin-domestic-chicken
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Mendeley | Further Information

{"title"=>"Identification of the Yellow skin gene reveals a hybrid origin of the domestic chicken", "type"=>"journal", "authors"=>[{"first_name"=>"Jonas", "last_name"=>"Eriksson", "scopus_author_id"=>"55310852900"}, {"first_name"=>"Greger", "last_name"=>"Larson", "scopus_author_id"=>"8280762100"}, {"first_name"=>"Ulrika", "last_name"=>"Gunnarsson", "scopus_author_id"=>"7003835061"}, {"first_name"=>"Bertrand", "last_name"=>"Bed'hom", "scopus_author_id"=>"23570344600"}, {"first_name"=>"Michele", "last_name"=>"Tixier-Boichard", "scopus_author_id"=>"7004728208"}, {"first_name"=>"Lina", "last_name"=>"Strömstedt", "scopus_author_id"=>"24344981700"}, {"first_name"=>"Dominic", "last_name"=>"Wright", "scopus_author_id"=>"55471267800"}, {"first_name"=>"Annemieke", "last_name"=>"Jungerius", "scopus_author_id"=>"23768000100"}, {"first_name"=>"Addie", "last_name"=>"Vereijken", "scopus_author_id"=>"6603353952"}, {"first_name"=>"Ettore", "last_name"=>"Randi", "scopus_author_id"=>"7004109837"}, {"first_name"=>"Per", "last_name"=>"Jensen", "scopus_author_id"=>"7402088701"}, {"first_name"=>"Leif", "last_name"=>"Andersson", "scopus_author_id"=>"7403057299"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"40149109370", "doi"=>"10.1371/journal.pgen.1000010", "pui"=>"351328527", "issn"=>"15537390", "pmid"=>"18454198", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "scopus"=>"2-s2.0-40149109370"}, "id"=>"89ce4375-2e3f-3946-8493-0918819b35e2", "abstract"=>"Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele (W*Y) that allows deposition of yellow carotenoids in the skin. Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation(s) that inhibit expression of BCDO2 (beta-carotene dioxygenase 2) in skin. Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the white skin allele (W*W). Surprisingly, our results demonstrate that yellow skin does not originate from the red junglefowl (Gallus gallus), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (Gallus sonneratii). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process.", "link"=>"http://www.mendeley.com/research/identification-yellow-skin-gene-reveals-hybrid-origin-domestic-chicken", "reader_count"=>215, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>25, "Librarian"=>1, "Researcher"=>57, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>10, "Student > Master"=>27, "Other"=>8, "Student > Bachelor"=>12, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>18}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>25, "Librarian"=>1, "Researcher"=>57, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>10, "Student > Master"=>27, "Other"=>8, "Student > Bachelor"=>12, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>18}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Agricultural and Biological Sciences"=>161, "Arts and Humanities"=>6, "Philosophy"=>1, "Veterinary Science and Veterinary Medicine"=>2, "Chemistry"=>3, "Computer Science"=>1, "Engineering"=>2, "Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>19, "Mathematics"=>1, "Medicine and Dentistry"=>4, "Social Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>6}, "Arts and Humanities"=>{"Arts and Humanities"=>6}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>161}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Philosophy"=>{"Philosophy"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>8, "Japan"=>1, "United Kingdom"=>3, "Bolivia"=>1, "Portugal"=>1, "Iceland"=>1, "Spain"=>2, "Netherlands"=>1, "Austria"=>1, "Taiwan"=>1, "Finland"=>2, "Poland"=>1, "Italy"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/936667"], "description"=>"<p>Panel A depicts a map of South Asia onto which the ranges of four species of junglefowl are drawn. Panel B depicts a European domestic chicken with yellow legs. Red, grey, blue, and green regions represent the respective ranges of red, grey, Ceylon, and green junglefowls. Images of these birds are presented in panels C through F respectively, within colored borders that correspond to the colors on the map. (Photo: <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000010#pgen-1000010-g001\" target=\"_blank\">Figures 1B:</a> Björn Jacobsson; 1C: Erik Bongcam-Rudloff; 1D: John Corder, World Pheasant Association; 1E: Jean Howman, World Pheasant Association; 1F: Kenneth W Fink, World Pheasant Association).</p>", "links"=>[], "tags"=>["evolutionary biology/evolutionary and comparative genetics", "genetics and genomics/animal genetics", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/gene function"], "article_id"=>607091, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jonas Eriksson", "Greger Larson", "Ulrika Gunnarsson", "Bertrand Bed'hom", "Michele Tixier-Boichard", "Lina Strömstedt", "Dominic Wright", "Annemieke Jungerius", "Addie Vereijken", "Ettore Randi", "Per Jensen", "Leif Andersson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000010.g001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Adapted_from_2_17_/607091", "title"=>"Adapted from [2],[17].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-29 01:58:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/936799"], "description"=>"<p>(A) Gene content of the <i>yellow skin</i> interval. The 23.8 kb region showing complete association with <i>yellow skin</i> is indicated by a box. The annotation is based on the chicken genome assembly as presented on the UCSC server (<a href=\"http://genome.ucsc.edu\" target=\"_blank\">http://genome.ucsc.edu</a>; Build May2006). (B) Differential expression of the <i>BCDO2</i> transcript in skin but not liver from <i>yellow skin</i> heterozygotes using genomic DNA (gDNA) as control. The polymorphic position chr24:6,268,434 bp was used to monitor differential expression using pyrosequencing. T and C at this position correspond to the <i>white</i> and <i>yellow skin</i> alleles respectively. (C) Summary of the examination of differential expression in skin and liver from six heterozygous (<i>W/Y</i>) birds. Genomic DNA from the three different genotypes were used as controls.</p>", "links"=>[], "tags"=>["evolutionary biology/evolutionary and comparative genetics", "genetics and genomics/animal genetics", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/gene function"], "article_id"=>607233, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jonas Eriksson", "Greger Larson", "Ulrika Gunnarsson", "Bertrand Bed'hom", "Michele Tixier-Boichard", "Lina Strömstedt", "Dominic Wright", "Annemieke Jungerius", "Addie Vereijken", "Ettore Randi", "Per Jensen", "Leif Andersson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000010.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_2_/607233", "title"=>"Figure 2", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-29 02:00:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/936972"], "description"=>"<p>n = number of individuals</p>1<p>SNP A = nucleotide position 6,264,085, G/<b><u>A</u></b>; SNP B = nucleotide position 6,273,428, A/<b><u>G</u></b>; SNP C = nucleotide position 6,287,900, G/<b><u>A</u></b>; bold, underlined nucleotides are those associated with the <i>yellow skin</i> haplotype. The <i>BCDO2</i> gene spans from nucleotide position 6,262,596 to 6,282,641 bp.</p>2<p>These samples were collected by the AvianDiv project <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000010#pgen.1000010-Hillel1\" target=\"_blank\">[28]</a></p>3<p>The red junglefowl data include the genotype deduced from the genome assembly as presented on the UCSC server (<a href=\"http://genome.ucsc.edu\" target=\"_blank\">http://genome.ucsc.edu</a>; Build May2006)</p>4<p>One sample was heterozygous at SNP B and apparently carried the <i>yellow skin</i> allele.</p>", "links"=>[], "tags"=>["frequencies", "snps", "chromosome", "24", "birds"], "article_id"=>607410, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jonas Eriksson", "Greger Larson", "Ulrika Gunnarsson", "Bertrand Bed'hom", "Michele Tixier-Boichard", "Lina Strömstedt", "Dominic Wright", "Annemieke Jungerius", "Addie Vereijken", "Ettore Randi", "Per Jensen", "Leif Andersson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000010.t001", "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequencies_at_SNPs_around_BCDO2_on_chicken_chromosome_24_among_birds_with_the_yellow_or_white_skin_phenotype_/607410", "title"=>"Allele frequencies at SNPs around <i>BCDO2</i> on chicken chromosome 24 among birds with the yellow or white skin phenotype.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-02-29 02:03:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/936908"], "description"=>"<p>In total, eleven birds were re-sequenced (the identity number of each bird is given in parenthesis); UCD1 represents the reference genome sequence. Wild and domestic samples possessing white and yellow skin clearly separate into two divergent clades. Node support values were generated from 1000 bootstrap replicates. The relative position of the Grey junglefowl (Delhi) is a result of the fact that this sample was heterozygous for two alleles, one of which most closely matched GryJF_04-7 and another which more closely matched TY_216372. Heterozygous positions were coded using degenerate bases and thus the algorithm used to draw the neighbor-joining tree placed this sample into a relatively basal position. <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000010#pgen.1000010.s007\" target=\"_blank\">Figure S7</a> shows the differing nucleotide positions across this region.</p>", "links"=>[], "tags"=>["neighbor-joining", "depicting", "relationships", "sequences", "derived", "kb"], "article_id"=>607339, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jonas Eriksson", "Greger Larson", "Ulrika Gunnarsson", "Bertrand Bed'hom", "Michele Tixier-Boichard", "Lina Strömstedt", "Dominic Wright", "Annemieke Jungerius", "Addie Vereijken", "Ettore Randi", "Per Jensen", "Leif Andersson"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000010.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_neighbor_joining_tree_depicting_the_relationships_between_sequences_derived_from_23_8_kb_of_the_BCDO2_locus_/607339", "title"=>"A neighbor-joining tree depicting the relationships between sequences derived from 23.8 kb of the <i>BCDO2</i> locus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-02-29 02:02:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/461378", "https://ndownloader.figshare.com/files/461425", "https://ndownloader.figshare.com/files/461450", "https://ndownloader.figshare.com/files/461470", "https://ndownloader.figshare.com/files/461489", "https://ndownloader.figshare.com/files/461510", "https://ndownloader.figshare.com/files/461528", "https://ndownloader.figshare.com/files/461547", "https://ndownloader.figshare.com/files/461606", "https://ndownloader.figshare.com/files/461657"], "description"=>"<div><p>Yellow skin is an abundant phenotype among domestic chickens and is caused by a recessive allele (<em>W*Y</em>) that allows deposition of yellow carotenoids in the skin. Here we show that yellow skin is caused by one or more cis-acting and tissue-specific regulatory mutation(s) that inhibit expression of <em>BCDO2</em> (beta-carotene dioxygenase 2) in skin. Our data imply that carotenoids are taken up from the circulation in both genotypes but are degraded by BCDO2 in skin from animals carrying the <em>white skin</em> allele (<em>W*W</em>). Surprisingly, our results demonstrate that <em>yellow skin</em> does not originate from the red junglefowl (<em>Gallus gallus</em>), the presumed sole wild ancestor of the domestic chicken, but most likely from the closely related grey junglefowl (<em>Gallus sonneratii</em>). This is the first conclusive evidence for a hybrid origin of the domestic chicken, and it has important implications for our views of the domestication process.</p></div>", "links"=>[], "tags"=>["reveals", "hybrid"], "article_id"=>150923, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jonas Eriksson", "Greger Larson", "Ulrika Gunnarsson", "Bertrand Bed'hom", "Michele Tixier-Boichard", "Lina Strömstedt", "Dominic Wright", "Annemieke Jungerius", "Addie Vereijken", "Ettore Randi", "Per Jensen", "Leif Andersson"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000010.s001", "https://dx.doi.org/10.1371/journal.pgen.1000010.s002", "https://dx.doi.org/10.1371/journal.pgen.1000010.s003", "https://dx.doi.org/10.1371/journal.pgen.1000010.s004", "https://dx.doi.org/10.1371/journal.pgen.1000010.s005", "https://dx.doi.org/10.1371/journal.pgen.1000010.s006", "https://dx.doi.org/10.1371/journal.pgen.1000010.s007", "https://dx.doi.org/10.1371/journal.pgen.1000010.s008", "https://dx.doi.org/10.1371/journal.pgen.1000010.s009", "https://dx.doi.org/10.1371/journal.pgen.1000010.s010"], "stats"=>{"downloads"=>53, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_the_Yellow_Skin_Gene_Reveals_a_Hybrid_Origin_of_the_Domestic_Chicken/150923", "title"=>"Identification of the <em>Yellow Skin</em> Gene Reveals a Hybrid Origin of the Domestic Chicken", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-02-29 00:15:23"}

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Relative Metric

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