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window.loswp.showSignupCaptcha = false window.loswp.willEdgeCache = false; window.loswp.work = {"work":{"id":10069472,"created_at":"2015-01-08T04:22:24.525-08:00","from_world_paper_id":null,"updated_at":"2024-11-27T20:29:45.717-08:00","_data":{"ai_title_tag":"Genetic Diversity in Tomato Landraces vs. Modern Varieties","grobid_abstract":"Background: The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes. Results: With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties. Conclusions: Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.","grobid_abstract_attachment_id":"36196299"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato","broadcastable":true,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [24521323]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "control"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon'; window.userInChina = "false";</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":36196299,"attachmentType":"pdf"}"><img alt="First page of “SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/36196299/mini_magick20190309-16882-5qipgp.png?1552181512" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="24521323" href="https://entecra.academia.edu/martinacaramante"><img alt="Profile image of martina caramante" class="ds-work-card--author-avatar" src="//a.academia-assets.com/images/s65_no_pic.png" />martina caramante</a></div><div class="ds-work-card--detail"><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">14 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 10069472; const worksViewsPath = "/v0/works/views?subdomain_param=api&work_ids%5B%5D=10069472"; const getWorkViews = async (workId) => { const response = await fetch(worksViewsPath); if (!response.ok) { throw new Error('Failed to load work views'); } const data = await response.json(); return data.views[workId]; }; // Get the view count for the work - we send this immediately rather than waiting for // the DOM to load, so it can be available as soon as possible (but without holding up // the backend or other resource requests, because it's a bit expensive and not critical). const viewCount = await getWorkViews(workId); const updateViewCount = (viewCount) => { try { const viewCountNumber = parseInt(viewCount, 10); if (viewCountNumber === 0) { // Remove the whole views element if there are zero views. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); return; } const commaizedViewCount = viewCountNumber.toLocaleString(); const viewCountBody = document.getElementById('work-metadata-view-count'); if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">Background: The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes. Results: With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties. Conclusions: Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":36196299,"attachmentType":"pdf","workUrl":"https://www.academia.edu/10069472/SNP_genotyping_reveals_genetic_diversity_between_cultivated_landraces_and_contemporary_varieties_of_tomato"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":36196299,"attachmentType":"pdf","workUrl":"https://www.academia.edu/10069472/SNP_genotyping_reveals_genetic_diversity_between_cultivated_landraces_and_contemporary_varieties_of_tomato"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div><div class="ds-signup-banner-trigger-container"><div class="ds-signup-banner-trigger ds-signup-banner-trigger-control"></div></div><div class="ds-signup-banner ds-signup-banner-control"><div id="ds-signup-banner-close-button"><button class="ds2-5-button ds2-5-button--secondary ds2-5-button--inverse"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">close</span></button></div><div class="ds-signup-banner-ctas"><img src="//a.academia-assets.com/images/academia-logo-capital-white.svg" /><h4 class="ds2-5-heading-serif-sm">Sign up for access to the world's latest research</h4><button class="ds2-5-button ds2-5-button--inverse ds2-5-button--full-width js-swp-download-button" data-signup-modal="{"location":"signup-banner"}">Sign up for free<span class="material-symbols-outlined" style="font-size: 20px" translate="no">arrow_forward</span></button></div><div class="ds-signup-banner-divider"></div><div class="ds-signup-banner-reasons"><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Get notified about relevant papers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Save papers to use in your research</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Join the discussion with peers</span></div><div class="ds-signup-banner-reasons-item"><span class="material-symbols-outlined" style="font-size: 24px" translate="no">check</span><span>Track your impact</span></div></div></div><script>(() => { // Set up signup banner show/hide behavior: // 1. 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Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. Results: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. Conclusions: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.</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="1" data-entity-id="10069475" 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/10069475/Genetic_diversity_in_Italian_tomato_landraces_Implications_for_the_development_of_a_core_collection">Genetic diversity in Italian tomato landraces: Implications for the development of a core collection</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="24521323" href="https://entecra.academia.edu/martinacaramante">martina caramante</a></div><p class="ds-related-work--abstract ds2-5-body-sm">The tomato (Solanum lycopersium L.) was domesticated in Latin America. Italy and Spain are considered secondary centers of diversification, where tomato cultivation has been characterized by a wealth of landraces. These are an essential element of the tomato diversity that has not been explored exhaustively. To increase the efficiency of the characterization and the utilization of cultivated tomato germplasm, we examined patterns of polymorphism and characterized the population structure of 75 landraces (mainly collected in Southern Italy) using a custom-made Illumina SNP-panel. The 152 SNPs were able to clearly distinguish the landraces from a set of 25 contemporary varieties. A good proportion of the genetic diversity was represented by alleles with low frequency. Within-landrace variability was detected in around 30% of the samples. The landraces had a genetic structure that is mainly related to the fruit type. In order to provide information useful at preserving the genetic diversity of open-pollinated tomato accessions, we extracted core collections (CC) using three different strategies and six sampling intensities. CCs were evaluated considering distance-based criteria, diversity indices and class/category coverage. Our analysis indicated that a sampling intensity between 15% and 25% is optimal to guarantee an extensive allelic coverage with a reduced redundancy. Our findings provide a useful framework not only for the characterization and efficient conservation of tomato landraces, but also for their possible use in genetics and breeding.</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 diversity in Italian tomato landraces: Implications for the development of a core collection","attachmentId":36196308,"attachmentType":"pdf","work_url":"https://www.academia.edu/10069475/Genetic_diversity_in_Italian_tomato_landraces_Implications_for_the_development_of_a_core_collection","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/10069475/Genetic_diversity_in_Italian_tomato_landraces_Implications_for_the_development_of_a_core_collection"><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="2" 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><p class="ds-related-work--abstract ds2-5-body-sm">Genetic variability in modern crops is limited due to domestication and breeding. To investigate genetic variation in different populations, 216 tomato (Solanum lycopersicum L.) cultivars, hybrids, and elite breeding lines from four breeding programs were genotyped using single nucleotide polymorphism and simple sequence repeat markers. Of 47 markers analyzed, 72.3% were polymorphic in the whole collection of 216 genotypes and 51.06-59.57% showed polymorphisms in individual populations. However, genetic variation was narrow in all four populations. Nei's genetic distance varied from 0.0422 to 0.1135 between populations and from 0.0085 to 0.3187 between lines in individual populations. Cluster and principal coordinate analysis indicated that the four populations could be grouped into three clades. Lines from Shenyang Agricultural University and China Agricultural University population formed the first clade, lines from Beijing Vegetable Research Center were in the second clade, and lines from Nunhems were in the third clade. This was further supported by population structure analysis using STRUCTURE2.2, and suggested that a lack of germplasm exchange might exist among breeding programs. It might be the reason that the progress of developing new varieties with significant improvement of horticultural traits in China is slow in recent years. ß</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="3" 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><p class="ds-related-work--abstract ds2-5-body-sm">The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA) and pairwise estimates of F st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage), particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD) was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and subpopulations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization. Citation: Sim S-C, Van Deynze A, Stoffel K, Douches DS, Zarka D, et al. (2012) High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding. PLoS ONE 7(9): e45520.</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.) Reveals Patterns of Genetic Variation Due to Breeding","attachmentId":44895197,"attachmentType":"pdf","work_url":"https://www.academia.edu/24565431/High_Density_SNP_Genotyping_of_Tomato_Solanum_lycopersicum_L_Reveals_Patterns_of_Genetic_Variation_Due_to_Breeding","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/24565431/High_Density_SNP_Genotyping_of_Tomato_Solanum_lycopersicum_L_Reveals_Patterns_of_Genetic_Variation_Due_to_Breeding"><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="126702267" 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/126702267/_6_Highly_Polymorphic_Genesin_Cultivated_Tomato">(6) Highly Polymorphic Genesin 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="312774613" href="https://independent.academia.edu/angelabaldo2">angela baldo</a></div><p class="ds-related-work--metadata ds2-5-body-xs">HortScience, 2005</p><p class="ds-related-work--abstract ds2-5-body-sm">Cultivated tomato varieties are genetically extremely similar. We identified 764 Unigenes with potential single nucleotide polymorphisms (SNPs) among more than 15 cultivars from public expressed tomato data. By sequencing regions from 53 of these Unigenes in two to three cultivars, we discovered an unexpected wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes). This included a high proportion of predicted nonsynonymous nucleotide (17 of 33 SNPs in exons) and nonconservative amino acid (6 of 16 nonsynonymous SNPs) changes. We hypothesize that five of these regions are associated with introgressions from wild relatives. Identifying polymorphic, expressed genes in the tomato genome will be useful for both tomato improvement and germplasm conservation.</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":"(6) Highly Polymorphic Genesin Cultivated Tomato","attachmentId":120540292,"attachmentType":"pdf","work_url":"https://www.academia.edu/126702267/_6_Highly_Polymorphic_Genesin_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/126702267/_6_Highly_Polymorphic_Genesin_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="6" data-entity-id="25890102" 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/25890102/Exploring_a_Tomato_Landraces_Collection_for_Fruit_Related_Traits_by_the_Aid_of_a_High_Throughput_Genomic_Platform">Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform</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="32423695" href="https://independent.academia.edu/AmaliaBarone">Amalia Barone</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PloS one, 2015</p><p class="ds-related-work--abstract ds2-5-body-sm">During its evolution and domestication Solanum lycopersicum has undergone various genetic &#39;bottlenecks&#39; and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit ...</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 a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform","attachmentId":46255530,"attachmentType":"pdf","work_url":"https://www.academia.edu/25890102/Exploring_a_Tomato_Landraces_Collection_for_Fruit_Related_Traits_by_the_Aid_of_a_High_Throughput_Genomic_Platform","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/25890102/Exploring_a_Tomato_Landraces_Collection_for_Fruit_Related_Traits_by_the_Aid_of_a_High_Throughput_Genomic_Platform"><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="78775678" 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/78775678/The_Study_of_Molecular_Diversity_in_Natural_Populations_of_Wild_and_Weedy_Tomatoes_and_Its_Implications_in_Tomato_Breeding">The Study of Molecular Diversity in Natural Populations of Wild and Weedy Tomatoes and Its Implications in Tomato 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="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">XV Meeting of the EUCARPIA Tomato Working Group, 2008</p><p class="ds-related-work--abstract ds2-5-body-sm">Wild and weedy tomatoes are genetic resources of great value for tomato (Lycopersicon esculentum) breeding. The study of genetic variation among these materials, the distribution of genetic diversity in their region of origin and the genetic structure of the natural populations provides relevant information for the conservation of these genetic resources and for tomato breeding. Here we present the results of three experiments carried out on these subjects in the subgenus Eulycopersicon, which comprises the wild L. pimpinellifolium and L. cheesmanii and the weedy L. esculentum var. cerasiforme. Morphological and molecular (AFLP and SSRs) studies performed with these materials show that, although typical forms of L. esculentum var. cerasiforme and L. pimpinellifolium can be distinguished by both types of data, many intermediate forms exist, suggesting that these forms are the extremes in a continuous range of variation. The study of genetic variation of L. pimpinellifolium populations from an extended area of northern Peru revealed a low genetic differentiation among populations, although hot spots of diversity existed in some areas. The Galápagos endemism L. cheesmanii is genetically and morphologically different from the other Eulycopersicon taxa, although no genetic differentiation (using AFLPs) could be found among the different forms of this species. Despite its restricted area of distribution and limited morphological variability, it has a considerable genetic variation when compared to L. pimpinellifolium accessions from the mainland. All this information is of great interest for the in situ and ex situ conservation of genetic resources of tomato and has important implications for tomato breeding.</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":"The Study of Molecular Diversity in Natural Populations of Wild and Weedy Tomatoes and Its Implications in Tomato Breeding","attachmentId":85701689,"attachmentType":"pdf","work_url":"https://www.academia.edu/78775678/The_Study_of_Molecular_Diversity_in_Natural_Populations_of_Wild_and_Weedy_Tomatoes_and_Its_Implications_in_Tomato_Breeding","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/78775678/The_Study_of_Molecular_Diversity_in_Natural_Populations_of_Wild_and_Weedy_Tomatoes_and_Its_Implications_in_Tomato_Breeding"><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="27792857" 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/27792857/Oligonucleotide_array_discovery_of_polymorphisms_in_cultivated_tomato_Solanum_lycopersicum_L_reveals_patterns_of_SNP_variation_associated_with_breeding">Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with 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="52091391" href="https://independent.academia.edu/CharlesChilcott">Charles Chilcott</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BMC Genomics, 2009</p><p class="ds-related-work--abstract ds2-5-body-sm">Background: Cultivated tomato (Solanum lycopersicum L.) has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP) discovery as a high-throughput approach for marker development in cultivated tomato.</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":"Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding","attachmentId":48072835,"attachmentType":"pdf","work_url":"https://www.academia.edu/27792857/Oligonucleotide_array_discovery_of_polymorphisms_in_cultivated_tomato_Solanum_lycopersicum_L_reveals_patterns_of_SNP_variation_associated_with_breeding","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/27792857/Oligonucleotide_array_discovery_of_polymorphisms_in_cultivated_tomato_Solanum_lycopersicum_L_reveals_patterns_of_SNP_variation_associated_with_breeding"><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="98964701" 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/98964701/Elucidating_Morpho_Molecular_Diversity_and_Population_Structure_of_Elite_Tomato_Solanum_lycopersicum_L_Germplasm">Elucidating Morpho-Molecular Diversity and Population Structure of Elite Tomato (Solanum lycopersicum L.) Germplasm</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="4417499" href="https://skuastkashmir.academia.edu/ReetikaMahajan">Reetika Mahajan</a></div><p class="ds-related-work--abstract ds2-5-body-sm">Background Tomato (Solanum lycopersicum L.) crop is well known for its versatility worldwide and recognized as model species used extensively for various genetic studies. This study was carried out to evaluate some indigenous and exotic tomato genotypes for divergence studies using a combined multidisciplinary approach. Regardless of its significant contributions to nutritional and economic status globally, lack of diversity among the cultivated species has been witnessed extensively due to the intensive selection of genotypes with respect to specific traits and severe genetic bottlenecks. Methods and Results As a part of the countermeasure to restore the genetic diversity in tomato, the incorporation of wild varieties, landraces, and traditional varieties in the crop-breeding scheme is highly acknowledged. On these grounds, inter and intra-genetic diversity was assessed among 51 tomato genotypes morphologically, biochemically, and by using DNA-based marker SSR markers. A total of 1...</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":"Elucidating Morpho-Molecular Diversity and Population Structure of Elite Tomato (Solanum lycopersicum L.) Germplasm","attachmentId":100175643,"attachmentType":"pdf","work_url":"https://www.academia.edu/98964701/Elucidating_Morpho_Molecular_Diversity_and_Population_Structure_of_Elite_Tomato_Solanum_lycopersicum_L_Germplasm","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/98964701/Elucidating_Morpho_Molecular_Diversity_and_Population_Structure_of_Elite_Tomato_Solanum_lycopersicum_L_Germplasm"><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":36196299,"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":36196299,"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_36196299" 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. You can download the paper by clicking the button above.</p></div></div></div></div><div class="ds-sidebar--container js-work-sidebar"><div class="ds-related-content--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-related-work-sidebar-card" data-collection-position="0" data-entity-id="4922219" data-sort-order="default"><a class="ds-related-work--title js-related-work-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/4922219/Genetic_diversity_and_distinctiveness_in_tomato_Solanum_lycopersicum_L_landraces_The_Italian_case_study_of_A_pera_Abruzzese">Genetic diversity and distinctiveness in tomato ( Solanum lycopersicum L.) landraces: The Italian case study of ‘A pera Abruzzese</a><div class="ds-related-work--metadata"><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="6451684" href="https://independent.academia.edu/SaraSestili">Sara Sestili</a><span>, </span><a class="js-related-work-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="46426717" href="https://independent.academia.edu/EnricoPiccinini">Enrico Piccinini</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Scientia Horticulturae, 2010</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 diversity and distinctiveness in tomato ( Solanum lycopersicum L.) landraces: The Italian case study of ‘A pera Abruzzese","attachmentId":37182119,"attachmentType":"pdf","work_url":"https://www.academia.edu/4922219/Genetic_diversity_and_distinctiveness_in_tomato_Solanum_lycopersicum_L_landraces_The_Italian_case_study_of_A_pera_Abruzzese","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free 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