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We explored array-based single feature polymorphism (SFP) discovery as a high-throughput approach for marker development in cultivated tomato.","publication_date":"2009,,","publication_name":"BMC Genomics","grobid_abstract_attachment_id":"48072835"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [52091391]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loswp.appleClientId = 'edu.academia.applesignon';</script><script defer="" 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PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/10069472/SNP_genotyping_reveals_genetic_diversity_between_cultivated_landraces_and_contemporary_varieties_of_tomato"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="24565431" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/24565431/High_Density_SNP_Genotyping_of_Tomato_Solanum_lycopersicum_L_Reveals_Patterns_of_Genetic_Variation_Due_to_Breeding">High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33059927" href="https://ncsu.academia.edu/DilipPanthee">Dilip Panthee</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLoS ONE, 2012</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) 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data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/78775453/Genomic_variation_in_tomato_from_wild_ancestors_to_contemporary_breeding_accessions">Genomic variation in tomato, from wild ancestors to contemporary breeding accessions</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="154363326" href="https://independent.academia.edu/Mar%C3%ADaJos%C3%A9D%C3%ADez">María José Díez</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2015</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Genomic variation in tomato, from wild ancestors to contemporary breeding accessions","attachmentId":85794512,"attachmentType":"pdf","work_url":"https://www.academia.edu/78775453/Genomic_variation_in_tomato_from_wild_ancestors_to_contemporary_breeding_accessions","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/78775453/Genomic_variation_in_tomato_from_wild_ancestors_to_contemporary_breeding_accessions"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="34801560" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/34801560/Genetic_variation_in_tomato_populations_from_four_breeding_programs_revealed_by_single_nucleotide_polymorphism_and_simple_sequence_repeat_markers">Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="6690290" href="https://usn-no.academia.edu/JiaChen">Jia Chen</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Scientia Horticulturae, 2009</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Genetic variation in tomato populations from four breeding programs revealed by single nucleotide polymorphism and simple sequence repeat markers","attachmentId":54660845,"attachmentType":"pdf","work_url":"https://www.academia.edu/34801560/Genetic_variation_in_tomato_populations_from_four_breeding_programs_revealed_by_single_nucleotide_polymorphism_and_simple_sequence_repeat_markers","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/34801560/Genetic_variation_in_tomato_populations_from_four_breeding_programs_revealed_by_single_nucleotide_polymorphism_and_simple_sequence_repeat_markers"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="84598307" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/84598307/Tomato_breeding_in_the_genomics_era_insights_from_a_SNP_array">Tomato breeding in the genomics era: insights from a SNP array</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="32186047" href="https://wageningen-ur.academia.edu/RichardVisser">Richard Visser</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2013</p><p class="ds-related-work--abstract ds2-5-body-sm">Background The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. Results From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers. Genotyping different tomato samples allowed the evaluation of the level of heterozygosity and introgressions among commercial varieties. Cherry tomatoes were especially different from round/beefs in chromosomes 4, 5 and 12. We were able to identify a set of 750 unique markers distinguishing S. lycopersicum ‘Moneymaker’ from all its distantly related wild relatives. Clustering and neighbour joining analysis among varieties and species showed expected gr...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Tomato breeding in the genomics era: insights from a SNP array","attachmentId":89564656,"attachmentType":"pdf","work_url":"https://www.academia.edu/84598307/Tomato_breeding_in_the_genomics_era_insights_from_a_SNP_array","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/84598307/Tomato_breeding_in_the_genomics_era_insights_from_a_SNP_array"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="63002689" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/63002689/Development_of_a_Large_SNP_Genotyping_Array_and_Generation_of_High_Density_Genetic_Maps_in_Tomato">Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="43847176" href="https://independent.academia.edu/MartinGanal">Martin Ganal</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLoS ONE, 2012</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Development 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class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/57635356/Mapping_and_linkage_disequilibrium_analysis_with_a_genome_wide_collection_of_SNPs_that_detect_polymorphism_in_cultivated_tomato">Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="34974913" href="https://independent.academia.edu/Tarekjoobeur">Tarek joobeur</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Experimental Botany, 2011</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato","attachmentId":72440432,"attachmentType":"pdf","work_url":"https://www.academia.edu/57635356/Mapping_and_linkage_disequilibrium_analysis_with_a_genome_wide_collection_of_SNPs_that_detect_polymorphism_in_cultivated_tomato","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/57635356/Mapping_and_linkage_disequilibrium_analysis_with_a_genome_wide_collection_of_SNPs_that_detect_polymorphism_in_cultivated_tomato"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="118684278" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/118684278/Exploring_genetic_diversity_of_tomato_Solanum_lycopersicum_L_germplasm_of_genebank_collection_employing_SSR_and_SCAR_markers">Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="34564642" href="https://independent.academia.edu/AthanasiosTsaftaris">Athanasios Tsaftaris</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genetic Resources and Crop Evolution, 2019</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Exploring genetic diversity of tomato (Solanum lycopersicum L.) germplasm of genebank collection employing SSR and SCAR markers","attachmentId":114252232,"attachmentType":"pdf","work_url":"https://www.academia.edu/118684278/Exploring_genetic_diversity_of_tomato_Solanum_lycopersicum_L_germplasm_of_genebank_collection_employing_SSR_and_SCAR_markers","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/118684278/Exploring_genetic_diversity_of_tomato_Solanum_lycopersicum_L_germplasm_of_genebank_collection_employing_SSR_and_SCAR_markers"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="84624035" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/84624035/Reanalysis_of_Genome_Sequences_of_tomato_accessions_and_its_wild_relatives_Development_of_tomato_genomic_variation_TGV_database_integrating_SNPs_and_INDELs_polymorphisms">Reanalysis of Genome Sequences of tomato accessions and its wild relatives: Development of tomato genomic variation (TGV) database integrating SNPs and INDELs polymorphisms</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="78437281" href="https://independent.academia.edu/PankajSingh385">Pankaj S Dholaniya</a></div><p class="ds-related-work--metadata ds2-5-body-xs">2020</p><p class="ds-related-work--abstract ds2-5-body-sm">MotivationFacilitated by technological advances and expeditious decrease in the sequencing costs, whole-genome sequencing (WGS) is increasingly implemented to uncover variations in cultivars/accessions of many crop plants. In tomato (Solanum lycopersicum), the availability of the genome sequence, followed by the resequencing of tomato cultivars and its wild relatives, has provided a prodigious resource for the improvement of traits. A high-quality genome resequencing of 84 tomato accessions and wild relatives generated a dataset that can be used as a resource to identify agronomically important alleles across the genome. Converting this dataset into a searchable database, including information about the influence of SNPs on protein function, provides valuable information about the genetic variations. The database will assist in searching for functional variants of a gene for introgression into tomato cultivars.ResultsA recent release of better-quality tomato genome reference assembl...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Reanalysis of Genome Sequences of tomato accessions and its wild relatives: Development of tomato genomic variation (TGV) database integrating SNPs and INDELs polymorphisms","attachmentId":89580946,"attachmentType":"pdf","work_url":"https://www.academia.edu/84624035/Reanalysis_of_Genome_Sequences_of_tomato_accessions_and_its_wild_relatives_Development_of_tomato_genomic_variation_TGV_database_integrating_SNPs_and_INDELs_polymorphisms","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/84624035/Reanalysis_of_Genome_Sequences_of_tomato_accessions_and_its_wild_relatives_Development_of_tomato_genomic_variation_TGV_database_integrating_SNPs_and_INDELs_polymorphisms"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="33841325" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/33841325/In_Silico_identification_of_SNP_diversity_in_cultivated_and_wild_tomato_species_insight_from_molecular_simulations">In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="2375241" href="https://nationalbotanicalresearch.academia.edu/YogeshwarVikramDhar">Yogeshwar Vikram Dhar</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program. The Solanaceae are the highly valuable plant taxon in terms of vegetable crops as well as agricultural utility. Various members of Solanaceae have been used as a model plants such as tomato (Solanum lycopersicum) and pepper, mainly to study the fruit development 1. The genus Solanum is composed of approximately 1500 tomato species, originated in Central and North America, and spread all over the world. Despite the availability of numerous wild tomato species, only Solanum habrochaites has been exploited extensively for domestication purposes. This species typically grows on the western slopes of central Ecuador to central Peru, making it extremely tailored to the particular soil type and climatic conditions 2. Moreover, this species has many unusual properties including maintenance of green color and hardness during fruit ripening 3. Various changes have been observed in its physiological processes such as respiration, photosynthesis and Reactive Oxygen Species (ROS) productivity , which leads to its survival to cold stress conditions 4. Earlier transcriptome studies 5 of both the species have reported many changes in plants transferred from warm to cold conditions. Most of the phenotypic variation that exists among both species are listed in Table 1. All these properties indicated the presence of the desirable set of genes that could be used for the domestication of cultivated tomato (Solanum lycopersicum) species 3. Fleshy fruits undergo a ripening process that includes a series of changes in the fruit color, texture, aroma, flavour and thus making the fruit edible 6. Therefore, rapid phenotypic divergence associated with domestication is coupled to particular genomic loci that can be explored at the genetic level. In order to grasp the advance network of cli-macteric fruit ripening, numerous studies have been carried out that recommended tomato as a model plant due to its moderately short life cycle 7 and availability of developmental mutant 8. It is notable that there is a necessity to upgrade point-by-point information of genes directing fruit ripening, defense response against plant pathogen and other cellular processes. Single Nucleotide Polymorphisms (SNPs) have gained the center stage in the era of molecular genetics, because of its high abundance, considerable information content and improvement in sequencing technology 9 .</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations","attachmentId":53823213,"attachmentType":"pdf","work_url":"https://www.academia.edu/33841325/In_Silico_identification_of_SNP_diversity_in_cultivated_and_wild_tomato_species_insight_from_molecular_simulations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/33841325/In_Silico_identification_of_SNP_diversity_in_cultivated_and_wild_tomato_species_insight_from_molecular_simulations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":48072835,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":48072835,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_48072835" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. 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