Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
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{"title"=>"Development of a large snp genotyping array and generation of high-density genetic maps in tomato", "type"=>"journal", "authors"=>[{"first_name"=>"Sung Chur", "last_name"=>"Sim", "scopus_author_id"=>"7101953773"}, {"first_name"=>"Gregor", "last_name"=>"Durstewitz", "scopus_author_id"=>"6603177575"}, {"first_name"=>"Jörg", "last_name"=>"Plieske", "scopus_author_id"=>"6506187388"}, {"first_name"=>"Ralf", "last_name"=>"Wieseke", "scopus_author_id"=>"42762533600"}, {"first_name"=>"Martin W.", "last_name"=>"Ganal", "scopus_author_id"=>"7003799206"}, {"first_name"=>"Allen", "last_name"=>"van Deynze", "scopus_author_id"=>"6603401656"}, {"first_name"=>"John P.", "last_name"=>"Hamilton", "scopus_author_id"=>"8955405700"}, {"first_name"=>"C. Robin", "last_name"=>"Buell", "scopus_author_id"=>"7003436847"}, {"first_name"=>"Mathilde", "last_name"=>"Causse", "scopus_author_id"=>"6701844949"}, {"first_name"=>"Saranga", "last_name"=>"Wijeratne", "scopus_author_id"=>"54884632700"}, {"first_name"=>"David M.", "last_name"=>"Francis", "scopus_author_id"=>"35274951200"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22802968", "doi"=>"10.1371/journal.pone.0040563", "sgr"=>"84863672047", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84863672047", "issn"=>"19326203", "pui"=>"365221598"}, "id"=>"004fc7e7-736b-3922-bf54-d6ef5946f07a", "abstract"=>"The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F(2) populations: EXPEN 2000 (Solanum lycopersicum LA0925 x S. pennellii LA0716, 79 individuals), EXPEN 2012 (S. lycopersicum Moneymaker x S. pennellii LA0716, 160 individuals), and EXPIM 2012 (S. lycopersicum Moneymaker x S. pimpinellifolium LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.", "link"=>"http://www.mendeley.com/research/development-large-snp-genotyping-array-generation-highdensity-genetic-maps-tomato", "reader_count"=>145, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Researcher"=>44, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>9, "Student > Master"=>28, "Other"=>5, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>10, "Researcher"=>44, "Student > Doctoral Student"=>2, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/319204", "https://ndownloader.figshare.com/files/319292", "https://ndownloader.figshare.com/files/319327", "https://ndownloader.figshare.com/files/319351", "https://ndownloader.figshare.com/files/319390", "https://ndownloader.figshare.com/files/319425", "https://ndownloader.figshare.com/files/319440", "https://ndownloader.figshare.com/files/319466"], "description"=>"<div><p>The concurrent development of high-throughput genotyping platforms and next generation sequencing (NGS) has increased the number and density of genetic markers, the efficiency of constructing detailed linkage maps, and our ability to overlay recombination and physical maps of the genome. We developed an array for tomato with 8,784 Single Nucleotide Polymorphisms (SNPs) mainly discovered based on NGS-derived transcriptome sequences. Of the SNPs, 7,720 (88%) passed manufacturing quality control and could be scored in tomato germplasm. The array was used to generate high-density linkage maps for three interspecific F<sub>2</sub> populations: EXPEN 2000 (<em>Solanum lycopersicum</em> LA0925 x <em>S. pennellii</em> LA0716, 79 individuals), EXPEN 2012 (<em>S. lycopersicum</em> Moneymaker x <em>S. pennellii</em> LA0716, 160 individuals), and EXPIM 2012 (<em>S. lycopersicum</em> Moneymaker x <em>S. pimpinellifolium</em> LA0121, 183 individuals). The EXPEN 2000-SNP and EXPEN 2012 maps consisted of 3,503 and 3,687 markers representing 1,076 and 1,229 unique map positions (genetic bins), respectively. The EXPEN 2000-SNP map had an average marker bin interval of 1.6 cM, while the EXPEN 2012 map had an average bin interval of 0.9 cM. The EXPIM 2012 map was constructed with 4,491 markers (1,358 bins) and an average bin interval of 0.8 cM. All three linkage maps revealed an uneven distribution of markers across the genome. The dense EXPEN 2012 and EXPIM 2012 maps showed high levels of colinearity across all 12 chromosomes, and also revealed evidence of small inversions between LA0716 and LA0121. Physical positions of 7,666 SNPs were identified relative to the tomato genome sequence. The genetic and physical positions were mostly consistent. Exceptions were observed for chromosomes 3, 10 and 12. Comparing genetic positions relative to physical positions revealed that genomic regions with high recombination rates were consistent with the known distribution of euchromatin across the 12 chromosomes, while very low recombination rates were observed in the heterochromatic regions.</p> </div>", "links"=>[], "tags"=>["snp", "genotyping", "high-density", "maps"], "article_id"=>123017, "categories"=>["Biological Sciences", "Genetics", "Cell Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0040563.s001", "https://dx.doi.org/10.1371/journal.pone.0040563.s002", "https://dx.doi.org/10.1371/journal.pone.0040563.s003", "https://dx.doi.org/10.1371/journal.pone.0040563.s004", "https://dx.doi.org/10.1371/journal.pone.0040563.s005", "https://dx.doi.org/10.1371/journal.pone.0040563.s006", "https://dx.doi.org/10.1371/journal.pone.0040563.s007", "https://dx.doi.org/10.1371/journal.pone.0040563.s008"], "stats"=>{"downloads"=>15, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Development_of_a_Large_SNP_Genotyping_Array_and_Generation_of_High_Density_Genetic_Maps_in_Tomato/123017", "title"=>"Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-10 00:50:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/611889"], "description"=>"<p>Flanking sequences of SNPs were used for the automatic batch BLAST against the Tomato WGS chromosome database (v SL2.40; <a href=\"http://solgenomics.net/organism/Solanum_lycopersicum/genome\" target=\"_blank\">http://solgenomics.net/organism/Solanum_lycopersicum/genome</a>). The actual SNP positions relative to the Tomato genome sequence were identified using a custom Python script.</p>", "links"=>[], "tags"=>["snp"], "article_id"=>282376, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Physical_coverage_of_7_666_SNP_markers_/282376", "title"=>"Physical coverage of 7,666 SNP markers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-10 00:39:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/611694"], "description"=>"<p>The genetic positions of SNP markers are indicated by red circles for the EXPEN 2012 population and blue triangles for the EXPIM 2012 population.</p>", "links"=>[], "tags"=>["positions"], "article_id"=>282179, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_genetic_and_physical_positions_within_each_chromosome_/282179", "title"=>"Relationship between genetic and physical positions within each chromosome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-10 00:36:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/611824"], "description"=>"1<p>Unique map positions covered by SNP markers.</p>2<p>Average marker interval (cM) = coverage/number of unique bins.</p>3<p>Map length recalculated based on subsets of markers that were separated by at least 5 cM interval.</p>", "links"=>[], "tags"=>["snp", "markers", "cm", "chromosome", "linkage"], "article_id"=>282306, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.t001", "stats"=>{"downloads"=>1, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_SNP_markers_and_coverage_in_cM_of_each_chromosome_in_three_linkage_maps_/282306", "title"=>"Number of SNP markers and coverage in cM of each chromosome in three linkage maps.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-10 00:38:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/611434"], "description"=>"<p>The 2,841 SNP markers common to both maps were ranked based on their map positions within chromosomes for each map and the rank orders were used for regression analysis.</p>", "links"=>[], "tags"=>["expen", "2012", "expim", "linkage"], "article_id"=>281913, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.g001", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regression_of_marker_order_between_the_EXPEN_2012_and_EXPIM_2012_linkage_maps_/281913", "title"=>"Regression of marker order between the EXPEN 2012 and EXPIM 2012 linkage maps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-10 00:31:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/611855"], "description"=>"1<p>Colinearity within each chromosome was assessed using common markers. The markers were ranked based on their map positions and the rank order was used for regression analysis, and expressed as R<sup>2</sup>.</p>", "links"=>[], "tags"=>["markers", "linkage"], "article_id"=>282341, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.t002", "stats"=>{"downloads"=>1, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Colinearity_between_common_markers_for_the_three_linkage_maps_/282341", "title"=>"Colinearity between common markers for the three linkage maps.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-10 00:39:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/611585"], "description"=>"<p>\n <a href=\"http://solgenomics.net/organism/Solanum_lycopersicum/genome\" target=\"_blank\">http://solgenomics.net/organism/Solanum_lycopersicum/genome</a><b>) of the tomato reference genome sequence.</b></p>", "links"=>[], "tags"=>["expen", "2012", "expim", "maps"], "article_id"=>282066, "categories"=>["Biological Sciences", "Genetics", "Plant Biology"], "users"=>["Sung-Chur Sim", "Gregor Durstewitz", "Jörg Plieske", "Ralf Wieseke", "Martin W. Ganal", "Allen Van Deynze", "John P. Hamilton", "C. Robin Buell", "Mathilde Causse", "Saranga Wijeratne", "David M. Francis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0040563.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_the_EXPEN_2012_and_EXPIM_2012_genetic_maps_relative_to_the_draft_assembly_v_SL2_40_/282066", "title"=>"Comparative analysis of the EXPEN 2012 and EXPIM 2012 genetic maps relative to the draft assembly (v SL2.40;", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-10 00:34:26"}

PMC Usage Stats | Further Information

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Relative Metric

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