Global Dissemination of a Single Mutation Conferring White Pericarp in Rice
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{"title"=>"Global dissemination of a single mutation conferring white pericarp in rice", "type"=>"journal", "authors"=>[{"first_name"=>"Megan T.", "last_name"=>"Sweeney", "scopus_author_id"=>"14025009100"}, {"first_name"=>"Michael J.", "last_name"=>"Thomson", "scopus_author_id"=>"7203013260"}, {"first_name"=>"Gu Cho", "last_name"=>"Yong", "scopus_author_id"=>"56275988500"}, {"first_name"=>"Jin Park", "last_name"=>"Yong", "scopus_author_id"=>"20736050500"}, {"first_name"=>"Scott H.", "last_name"=>"Williamson", "scopus_author_id"=>"7203080385"}, {"first_name"=>"Carlos D.", "last_name"=>"Bustamante", "scopus_author_id"=>"35228607000"}, {"first_name"=>"Susan R.", "last_name"=>"McCouch", "scopus_author_id"=>"35468212900"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-34548457747", "sgr"=>"34548457747", "issn"=>"15537390", "isbn"=>"1553-7404 (Electronic)", "pmid"=>"17696613", "doi"=>"10.1371/journal.pgen.0030133", "pui"=>"47358080"}, "id"=>"5047566c-0a98-33cc-82a7-b4f113e3ba9b", "abstract"=>"Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.", "link"=>"http://www.mendeley.com/research/global-dissemination-single-mutation-conferring-white-pericarp-rice", "reader_count"=>101, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>34, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>34, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>7, "Student > Bachelor"=>4, "Lecturer"=>2, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>87, "Arts and Humanities"=>1, "Social Sciences"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>87}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "United States"=>3, "Philippines"=>2, "Brazil"=>3, "United Kingdom"=>1, "Italy"=>1, "Spain"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/466030", "https://ndownloader.figshare.com/files/466046", "https://ndownloader.figshare.com/files/466060", "https://ndownloader.figshare.com/files/466080"], "description"=>"<div><p>Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice <em>(Oryza sativa)</em> resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the <em>Rc</em> gene that is found in 97.9% of white rice varieties today. A second mutation, also within <em>Rc,</em> is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the <em>japonica</em> subspecies and crossed both geographic and sterility barriers to move into the <em>indica</em> subspecies. A little less than one Mb of <em>japonica</em> DNA hitchhiked with the <em>rc</em> allele into most <em>indica</em> varieties, suggesting that other linked domestication alleles may have been transferred from <em>japonica</em> to <em>indica</em> along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.</p></div>", "links"=>[], "tags"=>["dissemination", "mutation", "conferring", "pericarp"], "article_id"=>151858, "categories"=>["Genetics", "Cell Biology", "Evolutionary Biology"], "users"=>["Megan T Sweeney", "Michael J Thomson", "Yong Gu Cho", "Yong Jin Park", "Scott H Williamson", "Carlos D Bustamante", "Susan R McCouch"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0030133.st001", "https://dx.doi.org/10.1371/journal.pgen.0030133.st002", "https://dx.doi.org/10.1371/journal.pgen.0030133.st003", "https://dx.doi.org/10.1371/journal.pgen.0030133.st004"], "stats"=>{"downloads"=>15, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Global_Dissemination_of_a_Single_Mutation_Conferring_White_Pericarp_in_Rice/151858", "title"=>"Global Dissemination of a Single Mutation Conferring White Pericarp in Rice", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-08-10 00:30:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/946952"], "description"=>"<p>Arrows indicate the location of markers on the physical map of Chromosome 7, numbers are in Mb. <i>F</i><sub>ST</sub> values for red <i>indica</i> versus <i>japonica</i> are plotted across the chromosome using diamonds, white <i>indica</i> versus <i>japonica</i> are plotted using squares. The expanded region shows a detailed view of the 1-Mb window around the <i>Rc</i> gene. All varieties genotyped are white <i>indicas</i> containing the 14-bp deletion. DNA segments containing alleles of <i>japonica</i> ancestry (in the <i>indica</i> background) are shown in white, segments containing alleles of <i>indica</i> ancestry are shown in black, and segments containing a breakpoint between alleles of <i>japonica</i> and <i>indica</i> ancestry are shown in grey. Locations of the <i>Rc</i> and <i>Hsh</i> genes indicated by brackets.</p>", "links"=>[], "tags"=>["introgressions"], "article_id"=>617298, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Megan T Sweeney", "Michael J Thomson", "Yong Gu Cho", "Yong Jin Park", "Scott H Williamson", "Carlos D Bustamante", "Susan R McCouch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030133.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Japonica_Introgressions_in_White_Indica_/617298", "title"=>"<i>Japonica</i> Introgressions in White <i>Indica</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-10 02:01:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/946711"], "description"=>"<p>For details about the geographical distribution of accessions used in this study, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030133#pgen-0030133-st001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["subpopulations"], "article_id"=>617058, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Megan T Sweeney", "Michael J Thomson", "Yong Gu Cho", "Yong Jin Park", "Scott H Williamson", "Carlos D Bustamante", "Susan R McCouch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030133.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Current_Distribution_of_the_Five_Major_Subpopulations_of_Rice_in_Asia_/617058", "title"=>"Current Distribution of the Five Major Subpopulations of Rice in Asia", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-10 01:57:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/946872"], "description"=>"<p>Sequence alignment adjusted manually in MacClade 4.05. A heuristic parsimony search was conducted on the data matrix, excluding gapped characters, with TBR branch swapping. This identified a single tree at 53 steps, with a consistency index of 0.98 (0.97 without autapomorphies) and a retention index of 0.99. Bootstrap support was estimated using 100 replications of the same search strategy. Pericarp color and subpopulation of each variety sequenced is labeled.</p>", "links"=>[], "tags"=>["genome-wide", "phylogenetic"], "article_id"=>617230, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Megan T Sweeney", "Michael J Thomson", "Yong Gu Cho", "Yong Jin Park", "Scott H Williamson", "Carlos D Bustamante", "Susan R McCouch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030133.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_Rc_Gene_and_Rice_Genome_Wide_Phylogenetic_Trees_/617230", "title"=>"Comparison of <i>Rc</i> Gene and Rice Genome-Wide Phylogenetic Trees", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-10 02:00:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/946790"], "description"=>"<p>The gene model for <i>Rc,</i> containing seven exons and comprising a region of approximately 8 kb, is shown horizontally along the top; arrows on the gene model and promoter region of <i>Rc</i> indicate positions of markers: RID-number markers amplify rice insertion/deletion polymorhisms, RM-number markers amplify rice microsatellite polymorphisms, and the RS-number marker detects a rice SNP. Physical positions along the rice Chromosome 7 pseudomolecule are indicated by the ruler below the gene model. In the tables below, allele sizes for RID marker loci are given in bp and allele sizes for RM markers show the number of repeats at each microsatellite locus. The number of varieties in each subpopulation that carry each haplotype is provided in boxed squares in the table to the right. Haplotypes found in varieties with red pericarp are shaded red.</p>", "links"=>[], "tags"=>["Evolutionary biology", "genetics and genomics", "plant biology"], "article_id"=>617138, "categories"=>["Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Megan T Sweeney", "Michael J Thomson", "Yong Gu Cho", "Yong Jin Park", "Scott H Williamson", "Carlos D Bustamante", "Susan R McCouch"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030133.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_Data_across_the_Rc_Gene_/617138", "title"=>"Haplotype Data across the <i>Rc</i> Gene", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-08-10 01:58:58"}

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  • {"unique-ip"=>"21", "full-text"=>"9", "pdf"=>"19", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"13", "full-text"=>"6", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"15", "full-text"=>"7", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"15", "full-text"=>"13", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

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