Web Databases for Omics Data in Tomato

Suzuki, Ayako; Suwabe, Keita; Yano, Kentarô

doi:10.2503/jjshs1.78.23

Cited by 5 publications

(3 citation statements)

References 64 publications

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“…Even broader approaches, involving headspace-GCMS, LC-DAD, GC-TOF MS, NMR, ICP-MS and LCMS datasets, have also been initiated for melon (Moing et al, 2011). The current status of 'omics databases for tomato has been recently reviewed (Suzuki et al, 2009). In order to improve our knowledge of the regulation of tomato metabolite biosynthesis, integration of metabolomics data with other omics data is indispensable.…”

Section: Data Integration Between Metabolomics Platforms and Between mentioning

confidence: 99%

Metabolomics of a Model Fruit: Tomato

Vos

Hall

Moing

2011

Annual Plant Reviews Volume 43

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Tomato has quickly become a favoured species for metabolomics research. Tomato fills a niche that cannot be occupied by Arabidopsis, particularly regarding studies on fleshy fruit. Variations in genotype and phenotype have been broadly exploited using metabolomics approaches in order to gain a better understanding of fundamental aspects of plant physiology, fruit growth and fruit development. The commercial importance of tomato as one of the world's most important and widely grown and consumed vegetables is a significant driving force behind this fruit research. Therefore, many metabolomics studies have specifically been focused on traits of importance to the food and agro-industries. Fruit quality, nutritional value as well as the influence on these traits of fruit storage, transport and processing into pasteurized and cooked products have also been subjects for extensive metabolomics analyses. These studies have already considerably expanded our knowledge, and continue to do so, concerning many aspects of the tomato fruit phenotype, both visible and chemical. Furthermore, increased knowledge of the genetics of tomato, the recently available draft of the tomato genome sequence as well as the emerging technologies for next generation sequencing, large-scale phenotyping and systems biology approaches have generated many novel research concepts that are also placing metabolomics analyses of tomatoes right at the forefront of fruit research.

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Section: Data Integration Between Metabolomics Platforms and Between mentioning

confidence: 99%

Metabolomics of a Model Fruit: Tomato

Vos

Hall

Moing

2011

Annual Plant Reviews Volume 43

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“…Tomato is one of the major model crops for genetic analysis and it has been widely studied (Suzuki et al, 2009). It is also an important commercial crop for both fresh market and processing industries as well as a popular home garden vegetable for the seed packet trade.…”

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confidence: 99%

Phenotyping of Tomato for SolCAP and Onward into the Void

Scott¹

2010

horts

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Standardized phenotyping is being used in tomato (Solanum lycopersicum) and potato (S. tuberosum) as part of the USDA-funded Solanaceae coordinated agricultural project (SolCAP). In tomato, a panel of 480 lines, 144 fresh market, 144 processing, 44 vintage lines, 48 landraces, and 101 related Solanum species accessions, are being grown over two seasons at multiple locations. These tomato genotypes will also be screened for over 7600 single nucleotide polymorphism markers that are being developed. Characters being phenotyped are hypocotyl color, plant habit, inflorescence (simple or compound), flower fasciation, flowering time, time to maturity, size of blossom scar, and pedicel type (jointless or jointed). Transverse and equatorial cross-sections of fruit are also being scanned to obtain measures of fruit shape and color by tomato analyzer computer software. Other fruit characters being measured are pH, titratable acidity, and soluble solids. Some useful information may come from this phenotyping and genotyping effort. However, in this author's opinion, the value of measuring some of the traits is very limited in the face of much more important breeding traits that are difficult to fit into a standardized phenotyping format. For instance, proper assessment of several fruit disorders is not being attempted, but such data might yield some invaluable marker information. Part of this is the result of funding limitations for the phenotyping effort. However, a major benefit of the SolCAP analysis will be the development of markers that will differentiate the lines being studied, because there is a present lack of polymorphisms in tomato germplasm where wild species introgressions are minimal or distant in time. This will allow breeders to proactively select for recurrent parent backgrounds in backcrossing projects and may aid in the identification of associations of markers with important characteristics. As one looks to the future of standardized phenotyping, there are some important traits that will be difficult to phenotype such as tomato flavor, which is quite subjective and for which there are no good objective measures.

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“…Phylogenic analysis of tomato and its inclusion in the Genus Solanum (Asamizu and Ezura, 2009), 2) Mutant resources for tomato and the status of newly developed tools for using the mutant resource (Saito et al, 2009), 3) Application of metabolomics to improve tomato fruit productivity and quality (Iijima and Aoki, 2009), and 4) Web databases for omics data in tomato (Suzuki et al, 2009). I hope the information in this special issue will be useful not only for researchers who are currently working on tomato, but also for young investigators who are planning to jump in the research area of the tomato.…”

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confidence: 99%

Tomato is a Next-generation Model Plant for Research and Development

Ezura

2009

J. Japan. Soc. Hort. Sci.

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As a preface for the tomato special issue, a significance of tomato for research and development was described. Tomato is a model species of Solanaceae, and its genome is currently being sequenced. In order to fully utilize the genome information, scientists have to develop resources and tools for tomato functional genomics. In this special issue, such resources and tools, mainly developed by Japanese scientists were reviewed. In addition, scientific name of tomato was discussed because, for tomato being a model plant, scientists should use a common word for tomato.

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Web Databases for Omics Data in Tomato

Cited by 5 publications

References 64 publications

Metabolomics of a Model Fruit: Tomato

Metabolomics of a Model Fruit: Tomato

Phenotyping of Tomato for SolCAP and Onward into the Void

Tomato is a Next-generation Model Plant for Research and Development

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