A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation
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{"title"=>"A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation", "type"=>"journal", "authors"=>[{"first_name"=>"Lorenzo", "last_name"=>"Barchi", "scopus_author_id"=>"8385780700"}, {"first_name"=>"Sergio", "last_name"=>"Lanteri", "scopus_author_id"=>"7004305653"}, {"first_name"=>"Ezio", "last_name"=>"Portis", "scopus_author_id"=>"6602657344"}, {"first_name"=>"Giampiero", "last_name"=>"Valè", "scopus_author_id"=>"56415126900"}, {"first_name"=>"Andrea", "last_name"=>"Volante", "scopus_author_id"=>"57193961166"}, {"first_name"=>"Laura", "last_name"=>"Pulcini", "scopus_author_id"=>"23989548900"}, {"first_name"=>"Tommaso", "last_name"=>"Ciriaci", "scopus_author_id"=>"6503940775"}, {"first_name"=>"Nazareno", "last_name"=>"Acciarri", "scopus_author_id"=>"7004221140"}, {"first_name"=>"Valeria", "last_name"=>"Barbierato", "scopus_author_id"=>"55338267600"}, {"first_name"=>"Laura", "last_name"=>"Toppino", "scopus_author_id"=>"24178008400"}, {"first_name"=>"Giuseppe Leonardo", "last_name"=>"Rotino", "scopus_author_id"=>"6602221950"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84865082446", "pui"=>"365452333", "pmid"=>"22912903", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0043740", "sgr"=>"84865082446"}, "id"=>"7839ee15-5e09-3a7e-ad15-24d7a362048c", "abstract"=>"Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2) mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.", "link"=>"http://www.mendeley.com/research/rad-tag-derived-marker-based-eggplant-linkage-map-location-qtls-determining-anthocyanin-pigmentation", "reader_count"=>95, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>29, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>5, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Researcher"=>29, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>5, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>5, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>80, "Chemistry"=>3, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>80}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Greece"=>1, "Colombia"=>2, "Netherlands"=>1, "United States"=>1, "Gambia"=>1, "United Kingdom"=>1, "Germany"=>1, "Spain"=>2}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/591080"], "description"=>"<p>Parameters associated with the framework eggplant genetic map.</p>", "links"=>[], "tags"=>["eggplant"], "article_id"=>261568, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t001", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameters_associated_with_the_framework_eggplant_genetic_map_/261568", "title"=>"Parameters associated with the framework eggplant genetic map.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:26:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/590961"], "description"=>"<p>For each trait the genome-wide LOD thresholds (GW) at p = 0.05 (as determined from 1,000 permutations) is indicated. The closest mapping marker to each QTL and which parent contributed positively to the trait are indicated, along with the LOD value of the QTL, the confidence interval (CI), the percentage of variation explained (PVE) and the additive (A)/dominance (D) contribution.</p>", "links"=>[], "tags"=>["genetics and genomics", "plant biology", "biotechnology"], "article_id"=>261443, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_QTLs_detected_in_the_mapping_population_/261443", "title"=>"QTLs detected in the mapping population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:24:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/309369", "https://ndownloader.figshare.com/files/309408", "https://ndownloader.figshare.com/files/309466"], "description"=>"<div><p>Both inter- and intra-specific maps have been developed in eggplant (<em>Solanum melongena</em> L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines ‘305E40’ and ‘67/3’. A set of 347 <em>de novo</em> SNPs, together with 84 anchoring markers, were applied to the F<sub>2</sub> mapping population bred from the cross ‘305E40’ x ‘67/3’ to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.</p> </div>", "links"=>[], "tags"=>["rad", "derived", "based", "eggplant", "linkage", "qtls", "determining", "anthocyanin", "pigmentation"], "article_id"=>121030, "categories"=>["Biotechnology", "Genetics", "Cell Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0043740.s001", "https://dx.doi.org/10.1371/journal.pone.0043740.s002", "https://dx.doi.org/10.1371/journal.pone.0043740.s003"], "stats"=>{"downloads"=>27, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_RAD_Tag_Derived_Marker_Based_Eggplant_Linkage_Map_and_the_Location_of_QTLs_Determining_Anthocyanin_Pigmentation/121030", "title"=>"A RAD Tag Derived Marker Based Eggplant Linkage Map and the Location of QTLs Determining Anthocyanin Pigmentation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-17 00:17:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/590873"], "description"=>"<p>BLAST results for marker sequences linked to an eggplant QTL.</p>", "links"=>[], "tags"=>["sequences", "linked", "eggplant"], "article_id"=>261355, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_BLAST_results_for_marker_sequences_linked_to_an_eggplant_QTL_/261355", "title"=>"BLAST results for marker sequences linked to an eggplant QTL.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:22:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/590997"], "description"=>"<p>The table lists the15 loci which mapped to non-homogous locations in eggplant and tomato.</p>", "links"=>[], "tags"=>["synteny", "eggplant"], "article_id"=>261487, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loss_of_synteny_between_eggplant_and_tomato_/261487", "title"=>"Loss of synteny between eggplant and tomato.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:24:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/590763"], "description"=>"<p>The physical location of the tomato genes encoding chalcone synthase (<i>CHS</i>), UDP-glucose anthocyanidin 3-0 glucosyltansferase (<i>3GT</i>), UDP-glucose anthocyanidin 5-0 glucosyltansferase (<i>5GT</i>) and the transcription factors <i>an2</i> and <i>ant1</i> is <u>underlined</u>. QTLs involved in anthocyanin pigmentation in eggplant are also shown. Distances on the eggplant chromosomes are given in cM, and on the tomato chromosome segments in Mbp.</p>", "links"=>[], "tags"=>["eggplant", "chromosomes", "e5", "e10", "segments", "t10"], "article_id"=>261239, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.g002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synteny_between_eggplant_chromosomes_E5_and_E10_and_tomato_chromosomes_segments_T5_T10_and_T12_/261239", "title"=>"Synteny between eggplant chromosomes E5 and E10 and tomato chromosomes segments T5, T10 and T12.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-17 00:20:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/591043"], "description"=>"<p>Skewness and kurtosis (with their standard errors (SE)) are also listed.</p>", "links"=>[], "tags"=>["deviations", "coefficients", "heritability"], "article_id"=>261528, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Trait_means_standard_deviations_SD_coefficients_of_variation_cv_and_broad_sense_heritability_for_the_traits_/261528", "title"=>"Trait means, standard deviations (SD), coefficients of variation (cv) and broad sense heritability for the traits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:25:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/590917"], "description"=>"<p>The values in diagonal represent correlations of the same trait between the two environments. All correlations were significant (p<0.05).</p>", "links"=>[], "tags"=>["spearman", "correlations", "assessed"], "article_id"=>261401, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inter_trait_Spearman_correlations_assessed_in_the_mapping_population_/261401", "title"=>"Inter-trait Spearman correlations assessed in the mapping population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-17 00:23:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/590639"], "description"=>"<p>A) chromosomes E01 to E06; B) chromosomes E07 to E12. Marker names are shown to the <i>right</i> of each chromosome, with map distances (in cM) shown on the <i>left</i>. Map positions of the QTL identified on each chromosome (or LG) are also given on the <i>right</i>. The length of the vertical bars represents the confidence interval of the QTL (LODmax-1 interval). QTL shown in <i>blue</i> were detected only at ML, and those in <i>red</i> only at MT.</p>", "links"=>[], "tags"=>["eggplant", "graphical", "qtls"], "article_id"=>261117, "categories"=>["Biotechnology", "Genetics", "Plant Biology"], "users"=>["Lorenzo Barchi", "Sergio Lanteri", "Ezio Portis", "Giampiero Valè", "Andrea Volante", "Laura Pulcini", "Tommaso Ciriaci", "Nazareno Acciarri", "Valeria Barbierato", "Laura Toppino", "Giuseppe Leonardo Rotino"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043740.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linkage_map_of_eggplant_and_graphical_representation_of_the_QTLs_detected_/261117", "title"=>"Linkage map of eggplant and graphical representation of the QTLs detected.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-17 00:18:37"}

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Relative Metric

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