An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (Arachis hypogaea L.)
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{"title"=>"An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (arachis hypogaea l.)", "type"=>"journal", "authors"=>[{"first_name"=>"Bhimana", "last_name"=>"Gautami", "scopus_author_id"=>"23472328400"}, {"first_name"=>"Daniel", "last_name"=>"Foncéka", "scopus_author_id"=>"34167705500"}, {"first_name"=>"Manish K.", "last_name"=>"Pandey", "scopus_author_id"=>"35113734100"}, {"first_name"=>"Márcio C.", "last_name"=>"Moretzsohn", "scopus_author_id"=>"6508187974"}, {"first_name"=>"Venkataswamy", "last_name"=>"Sujay", "scopus_author_id"=>"24825779500"}, {"first_name"=>"Hongde", "last_name"=>"Qin", "scopus_author_id"=>"24438022500"}, {"first_name"=>"Yanbin", "last_name"=>"Hong", "scopus_author_id"=>"26639504100"}, {"first_name"=>"Issa", "last_name"=>"Faye", "scopus_author_id"=>"34167682100"}, {"first_name"=>"Xiaoping", "last_name"=>"Chen", "scopus_author_id"=>"55739139900"}, {"first_name"=>"Amindala", "last_name"=>"BhanuPrakash", "scopus_author_id"=>"35519541800"}, {"first_name"=>"Trushar M.", "last_name"=>"Shah", "scopus_author_id"=>"24282044800"}, {"first_name"=>"Makanahally V.C.", "last_name"=>"Gowda", "scopus_author_id"=>"57196582771"}, {"first_name"=>"Shyam N.", "last_name"=>"Nigam", "scopus_author_id"=>"55236844400"}, {"first_name"=>"Xuanqiang", "last_name"=>"Liang", "scopus_author_id"=>"55621865700"}, {"first_name"=>"Dave A.", "last_name"=>"Hoisington", "scopus_author_id"=>"55077054300"}, {"first_name"=>"Baozhu", "last_name"=>"Guo", "scopus_author_id"=>"55312346100"}, {"first_name"=>"David J.", "last_name"=>"Bertioli", "scopus_author_id"=>"16210131000"}, {"first_name"=>"Jean Francois", "last_name"=>"Rami", "scopus_author_id"=>"7003907916"}, {"first_name"=>"Rajeev K.", "last_name"=>"Varshney", "scopus_author_id"=>"7006648166"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0041213", "sgr"=>"84864007904", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22815973", "issn"=>"19326203", "scopus"=>"2-s2.0-84864007904", "pui"=>"365274758"}, "id"=>"e9180f75-7956-32bb-8323-3f34bfd0a2da", "abstract"=>"Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.", "link"=>"http://www.mendeley.com/research/international-reference-consensus-genetic-map-897-marker-loci-based-11-mapping-populations-tetraploi", "reader_count"=>50, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Librarian"=>1, "Researcher"=>14, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Librarian"=>1, "Researcher"=>14, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>17, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>1, "Agricultural and Biological Sciences"=>42, "Social Sciences"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>42}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Brazil"=>1, "Mexico"=>1, "India"=>3}, "group_count"=>1}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/608506"], "description"=>"<p>Source of marker data used for constructing the reference consensus genetic map.</p>", "links"=>[], "tags"=>["constructing"], "article_id"=>278976, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.t001", "stats"=>{"downloads"=>8, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Source_of_marker_data_used_for_constructing_the_reference_consensus_genetic_map_/278976", "title"=>"Source of marker data used for constructing the reference consensus genetic map.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-18 02:29:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/608452"], "description"=>"<p>Features of the component and reference consensus genetic maps.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "biotechnology", "Computational biology"], "article_id"=>278914, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.t002", "stats"=>{"downloads"=>5, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Features_of_the_component_and_reference_consensus_genetic_maps_/278914", "title"=>"Features of the component and reference consensus genetic maps.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-18 02:28:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/607974"], "description"=>"<p>Markers are shown on <i>right</i> side of the LG while map distances are shown on the <i>left</i> side. Each LG has been divided into 203 BINs of 20 cM each. The homoeologous loci between the corresponding LGs in the reference consensus map are indicated in red colour.</p>", "links"=>[], "tags"=>["microsatellite", "comprising", "897", "loci", "11"], "article_id"=>278436, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.g001", "stats"=>{"downloads"=>0, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_microsatellite_consensus_genetic_map_comprising_897_marker_loci_based_on_11_mapping_populations_/278436", "title"=>"A microsatellite consensus genetic map comprising 897 marker loci based on 11 mapping populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-18 02:20:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/317627", "https://ndownloader.figshare.com/files/317676", "https://ndownloader.figshare.com/files/317729", "https://ndownloader.figshare.com/files/317746", "https://ndownloader.figshare.com/files/317765", "https://ndownloader.figshare.com/files/317785", "https://ndownloader.figshare.com/files/317802", "https://ndownloader.figshare.com/files/317893"], "description"=>"<div><p>Only a few genetic maps based on recombinant inbred line (RIL) and backcross (BC) populations have been developed for tetraploid groundnut. The marker density, however, is not very satisfactory especially in the context of large genome size (2800 Mb/1C) and 20 linkage groups (LGs). Therefore, using marker segregation data for 10 RILs and one BC population from the international groundnut community, with the help of common markers across different populations, a reference consensus genetic map has been developed. This map is comprised of 897 marker loci including 895 simple sequence repeat (SSR) and 2 cleaved amplified polymorphic sequence (CAPS) loci distributed on 20 LGs (a01–a10 and b01–b10) spanning a map distance of 3, 863.6 cM with an average map density of 4.4 cM. The highest numbers of markers (70) were integrated on a01 and the least number of markers (21) on b09. The marker density, however, was lowest (6.4 cM) on a08 and highest (2.5 cM) on a01. The reference consensus map has been divided into 20 cM long 203 BINs. These BINs carry 1 (a10_02, a10_08 and a10_09) to 20 (a10_04) loci with an average of 4 marker loci per BIN. Although the polymorphism information content (PIC) value was available for 526 markers in 190 BINs, 36 and 111 BINs have at least one marker with >0.70 and >0.50 PIC values, respectively. This information will be useful for selecting highly informative and uniformly distributed markers for developing new genetic maps, background selection and diversity analysis. Most importantly, this reference consensus map will serve as a reliable reference for aligning new genetic and physical maps, performing QTL analysis in a multi-populations design, evaluating the genetic background effect on QTL expression, and serving other genetic and molecular breeding activities in groundnut.</p> </div>", "links"=>[], "tags"=>["897", "loci", "based", "11", "populations", "tetraploid", "groundnut"], "article_id"=>122693, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Cell Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041213.s001", "https://dx.doi.org/10.1371/journal.pone.0041213.s002", "https://dx.doi.org/10.1371/journal.pone.0041213.s003", "https://dx.doi.org/10.1371/journal.pone.0041213.s004", "https://dx.doi.org/10.1371/journal.pone.0041213.s005", "https://dx.doi.org/10.1371/journal.pone.0041213.s006", "https://dx.doi.org/10.1371/journal.pone.0041213.s007", "https://dx.doi.org/10.1371/journal.pone.0041213.s008"], "stats"=>{"downloads"=>8, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/An_International_Reference_Consensus_Genetic_Map_with_897_Marker_Loci_Based_on_11_Mapping_Populations_for_Tetraploid_Groundnut_Arachis_hypogaea_L_/122693", "title"=>"An International Reference Consensus Genetic Map with 897 Marker Loci Based on 11 Mapping Populations for Tetraploid Groundnut (<em>Arachis hypogaea</em> L.)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-18 00:44:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/608128"], "description"=>"<p>Only common markers i.e. landmarks are included to visually asses the co-linearity of marker orders and marker positions. LGs are aligned together using comparative mapping program CMap version 1.01. Figure can also be accessed from <a href=\"http://cmap.icrisat.ac.in/cmap/sm/gn/gautami/\" target=\"_blank\">http://cmap.icrisat.ac.in/cmap/sm/gn/gautami/</a>.</p>", "links"=>[], "tags"=>["correspondence", "a03"], "article_id"=>278599, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.g002", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_marker_based_correspondence_for_a03_among_reference_consensus_and_individual_genetic_maps_/278599", "title"=>"A marker based correspondence for a03 among reference consensus and individual genetic maps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-18 02:23:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/608391"], "description"=>"<p>Summary of number of loci common between genetic maps for different mapping populations.</p>", "links"=>[], "tags"=>["loci", "maps"], "article_id"=>278862, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.t003", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_number_of_loci_common_between_genetic_maps_for_different_mapping_populations_/278862", "title"=>"Summary of number of loci common between genetic maps for different mapping populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-18 02:27:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/608560"], "description"=>"<p>Features of the reference consensus genetic map.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "biotechnology", "Computational biology"], "article_id"=>279031, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.t004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Features_of_the_reference_consensus_genetic_map_/279031", "title"=>"Features of the reference consensus genetic map.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-18 02:30:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/608281"], "description"=>"<p>The LGs of the reference consensus map are represented as a01 to a10 and b01 to b10. The LGs of AA map are named as Group 1 to Group 11 and for BB map as B1 to B10 respectively (published by Moretzsohn et al 2005, 2009). The AA map was represented by a red bar and the BB map with green colour. The common markers between corresponding LGs in the reference consensus map and AA map are indicated in red colour and pink colour with BB map.</p>", "links"=>[], "tags"=>["lgs", "diploid", "aa", "bb"], "article_id"=>278748, "categories"=>["Biotechnology", "Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Bhimana Gautami", "Daniel Fonceka", "Manish K. Pandey", "Márcio C. Moretzsohn", "Venkataswamy Sujay", "Hongde Qin", "Yanbin Hong", "Issa Faye", "Xiaoping Chen", "Amindala BhanuPrakash", "Trushar M. Shah", "Makanahally V. C. Gowda", "Shyam N. Nigam", "Xuanqiang Liang", "Dave A. Hoisington", "Baozhu Guo", "David J. Bertioli", "Jean-François Rami", "Rajeev K. Varshney"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041213.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_the_LGs_of_the_reference_consensus_map_and_the_diploid_AA_and_BB_maps_/278748", "title"=>"Comparison between the LGs of the reference consensus map and the diploid AA and BB maps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-18 02:25:48"}

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Relative Metric

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