Plant Biotechnology
Online ISSN : 1347-6114
Print ISSN : 1342-4580
ISSN-L : 1342-4580
Volume 24 , Issue 1
Showing 1-19 articles out of 19 articles from the selected issue
Editorial Overview
Genome sequencing
  • Erika Asamizu
    2007 Volume 24 Issue 1 Pages 5-9
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    As a member of the Solanaceae Genomics Network International Tomato Sequencing Project, we launched on sequencing of the chromosome 8. Our task is to sequence the euchromatin region of the chromosome, the estimated size of which is 17 megabases. BAC-by-BAC strategy is adopted for sequencing. We initially received BAC clone candidates anchored to overgo probes developed from 33 markers mapped on chromosome 8. For confirmation of the BAC candidates, we analyzed the sequence of PCR product amplified from the BAC DNA with primers designed on the marker sequence. Twenty-five BAC clones were verified and subjected to shotgun sequencing. As of Nov. 2006, we finished 40 clones to Phase 3 (total non-redundant length 4,429,168 bases) of 25 are seed and 15 are extended clones. In order to find additional seed points, we performed PCR screening of markers against 3D DNA-pool of LE-HBa, SL-MboI and SL-EcoRI BAC libraries, and succeeded in obtaining 9 new seeds. We report the current status of our project and future perspectives toward the final goal, which include development of new microsatellite markers from tomato EST sequences and Selected BAC Mixture shotgun sequencing for the gap filling.
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  • Sanghyeob Lee, Sung Hwan Jo, Doil Choi
    2007 Volume 24 Issue 1 Pages 11-16
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Unique developmental aspects, divergent phenotypes and habitats of Solanaceae make the family an ideal model to investigate the basis of diversification and adaptation. In view of this uniqueness, a global tomato genome sequencing project designated “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” has been launched. The goal of this initiative is to sequence the 220 Mb euchromatin that is expected to contain the majority of coding sequences, rather than 950 Mb full-length tomato genome. Given the high degree of similarity of tomato and pepper genomes, it will be particularly interesting to apply tomato genome information to pepper using a comparative genomics approach. In this review, we discuss the current progress in sequencing of tomato in Korea, genomics resources of pepper and beneficiary of the tomato sequence.
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Collection of ESTs and building databases for the tomato genomics
  • Kentaro Yano, Koh Aoki, Daisuke Shibata
    2007 Volume 24 Issue 1 Pages 17-25
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Tomato (Solanum lycopersicum) is a model plant of the Solanaceae family. Various biological aspects of tomato have been investigated with molecular biological approaches, and a significant amount of DNA and protein sequencing data on tomato has been accumulated. Recently, the number of tomato genome sequences in the International Nucleotide Sequence Databases has been rapidly increasing due to the progress of the international tomato genome sequencing project. Here, we summarize the current status of tomato genetic and genomic databases currently available in the public domain. The wealth of tomato genetic and genomic information facilitates elucidation of gene functions and metabolic pathways that will lead to the understanding of genetic diversity in the Solanaceae family.
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  • C. Delalande, F. Regad, M. Zouine, P. Frasse, A. Latche, J.C. Pech, M. ...
    2007 Volume 24 Issue 1 Pages 27-31
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    The Solanaceae family comprises many species of prime agronomical importance among which tomato and potato are the most important food source crops. In despite of their tremendous morphological diversity, the Solanaceae are closely related at the genetic level and display remarkable similarity in gene content and order. The Solanaceae Genome Project emerged in recent years as an international initiative aiming at generating genomic resources on the Solanaceae species and at coordinating national research efforts across the world. European countries made a substantial contribution to the activity of the Solanaceae International Consortium either through their respective national programs or with the advent of the EU-SOL integrated project. The present paper gives an overview on the specific contribution of the French Solanaceae Programs and on how they fit as an integral part of the European and international initiatives.
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Construction of extensive databases of phenotypic information for mutagenized tomato populations
  • Shin Watanabe, Tsuyoshi Mizoguchi, Koh Aoki, Yasutaka Kubo, Hitoshi Mo ...
    2007 Volume 24 Issue 1 Pages 33-38
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Sequencing a whole genome, cataloguing full-length cDNAs and ESTs, and construction of a comprehensive mutant population are essential steps in genome projects of individual model species. Tomato is one of the most important model crops to be undertaken for study over the next few decades, and the Solanaceae Genomics Project (SOL) has begun genome projects as international collaborations. The Solanum lycopersicum cultivar Micro-Tom shares several advantages with Arabidopsis, including its small size, short life cycle (approximately 90 days), and growth normally under artificial light. Here we demonstrate an initial attempt to generate a comprehensive mutant population in Micro-Tom. A total of 3,839 M2 families derived from ethylmethanesulfonate (EMS) mutagenesis were visually phenotyped, and putative mutants were classified into 15 primary and 48 secondary categories based on the SOL database, “The Genes That Make Tomatoes”.
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  • Chiaki Matsukura, Isao Yamaguchi, Mami Inamura, Yusuke Ban, Yoshie Kob ...
    2007 Volume 24 Issue 1 Pages 39-44
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    One direct way to identify a gene and its function is a forward genetic approach based on mutation analyses. To accumulate genetic resources for breeding and functional genomics in the tomato, we generated 6,347 lines of an M2 population with 300 Gy of gamma-ray irradiation in the inbred miniature dwarf variety ‘Micro-Tom.’ In total, 6,301 M2 lines were screened based on morphological alteration and brix-aberration, and 237 lines were selected as mutant candidates at the first screening. Subsequent screening of the self-fertilized M3 and M4 progeny yielded 24 lines of morphological mutants and 11 lines of aberrant brix mutants. Segregation data suggested that most of the mutant lines had single recessive mutations, with the exception of two lines. The chlorophyll mutation ratio in germinated M2 seedlings was 0.37% and the actual mutant frequency was 0.5%. The selected mutant lines exhibited a wide range of mutations, including whole plant properties with a severe phenotype, which allowed for more efficient screening of knockout mutants. Three characterized mutants, pale leaf, pink, and short root are also described.
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Metabolomics
  • Fernando Carrari, Ramón Asis, Alisdair R. Fernie
    2007 Volume 24 Issue 1 Pages 45-55
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Tomato (Solanum lycopersicum) became a model crop species to study development and maturation of fleshy fruits. The network of information and resources recently established by the International Solanaceae Genome Project (SOL www.sgn.cornell.edu) will not only provide valuable sequence information but also new tools applicable to large scale profiles at different levels of cell organization. This will surely render to the discovery of new potential targets for manipulation of fruit compositional traits. To date, a large amount of knowledge has been gathered on ethylene biosynthesis and response and cell wall metabolism during tomato fruit development and ripening. Less attention, however, has been given to the central metabolism that underpins these responses. Here we review recent reports focussed on the identification of key points on the metabolic regulation underlying tomato fruit development. Additionally, an overview of the combined application of metabolic and transcriptional profiling, aimed at identifying candidate genes for modifying metabolite contents, is discussed in the context of the usefulness for tomato breeding programs.
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  • Alka Srivastava, Sang Ho Chung, Tahira Fatima, Tatsiana Datsenka, Avta ...
    2007 Volume 24 Issue 1 Pages 57-70
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Transgenic tomato (Solanum lycopersicum) genotypes that were engineered to contain high endogenous polyamines levels in fruit due to a ripening targeted expression of yeast SAM decarboxylase were used as a model system to determine the effects of enhanced spermidine (Spd) and spermine (Spm) on gene expression. Subtractive cloning of total RNA of transgenic from wild type ripening fruits resulted in isolation of several genes that were up-regulated and represented a wide range of functional classifications. To establish the global pattern of gene expression in transgenic and wild-type fruit, a custom array containing 1066 unique fruit cDNA was constructed and used to quantify levels of a large number of transcripts in transgenic and wild-type fruits during the ripening. About one-quarter of genes on the array were differentially regulated in transgenic compared to wild type fruits. The differentially up-regulated genes were twice as abundant as down-regulated genes in the high polyamine fruits. The differentially expressed genes represented functional categories including transcription, translation, signal transduction, chaperone family, stress related, amino acid biosynthesis, ethylene biosynthesis and action, polyamine biosynthesis, isoprenoid pathway, and flavonoid biosynthesis. About 44% of the differentially regulated cDNAs included genes encoding products not yet classified for the functional attributes. Based on the results presented here on the limited transcriptome in conjunction with metabolite profiles showing significant enhancement of anabolic pathways in transgenic fruits, we propose that Spd/Spm act as anabolic growth regulator.
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Signal transduction and development
  • Alon Samach, Hamutal Lotan
    2007 Volume 24 Issue 1 Pages 71-82
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Tomato (Solanum lycopersicum L.) is a very important commercial crop and also a useful model to study the transition to flowering in a sympodial perennial plant. Here we try and summarize past and recent progress in understanding the environmental cues that affect the initial transition to flowering in this species and the genes that are involved in this transition and additional transitions occurring on the sympodial shoot. Environmental cues discussed are daylength, light intensity and growth temperature. In the last eight years much progress has been made in identifying the genes and in analyzing genetic interactions of the different mutations. Most of the genes isolated so far seem to play similar roles in Arabidopsis flowering. For example, mutations in the tomato SINGLE FLOWER TRUSS gene cause late flowering and this gene was recently shown to encode a protein similar to that encoded by the Arabidopsis FT gene. FT-like proteins seem to act as major flower promoters in diverse species. We also discuss issues in tomato flowering that we believe still require further research.
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  • Tsuyoshi Mizoguchi, Kanae Niinuma, Riichiro Yoshida
    2007 Volume 24 Issue 1 Pages 83-86
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Photoperiodic flowering responses are classified into three major types: long day (LD), short day (SD), and day neutral (DN). Arabidopsis is one of the best-characterized LD plants and flowers much earlier under LD than SD conditions. In contrast, SD conditions promote flowering of SD plants such as rice and Pharbitis nil. Recently, molecular genetics of Arabidopsis (LD) and rice (SD) have identified genes that play key roles in the photoperiodic flowering of these plants. A common role of the GIGANTEA (GI)-CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway in Arabidopsis and rice, and a specific role of EARLY HEADING DATE 1 (EHD1) in rice, but not in Arabidopsis, have been demonstrated. The DN response is the most poorly characterized among the three types of photoperiodic flowering responses. In this short review, we discuss how the DN flowering response is achieved in tomato based on recent progress in the analysis of Arabidopsis mutations in the photoperiodic flowering pathway and circadian rhythms.
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  • Kanae Niinuma, Mayu Nakagawa, Martin Calvino, Tsuyoshi Mizoguchi
    2007 Volume 24 Issue 1 Pages 87-97
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Endogenous oscillator called circadian clock controls many physiological aspects. Since the identification of LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) genes as the 1st candidates for clock components in plants, many clock-associated genes have been identified in Arabidopsis and other plant species. The 1st negative feedback model composed of LHY, CCA1 and TIMING OF CAB EXPRESSION 1 (TOC1) has recently been modified based on possible functions of new players. Photoperiodic flowering is controlled by clock and our knowledge on molecular mechanisms underlying the clock-controlled process has much advanced in this decade. Recently, we have started to understand how the clock regulates organ movements and elongations in a model plant, Arabidopsis. In this short review, i) a history of construction of models on circadian rhythms in Arabidopsis, ii) modified models on circadian system in Arabidopsis, iii) recent progress on understanding molecular mechanisms underlying organ movements controlled by a circadian clock and iv) advantages of using tomato as a model system for chronobiology are summarized and discussed.
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  • Masashi Asahina, Yukika Yamauchi, Atsushi Hanada, Yuji Kamiya, Hiroshi ...
    2007 Volume 24 Issue 1 Pages 99-106
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    We have previously shown that gibberellin (GA) is required for tissue-reunion in the cortex of cut hypocotyls in cucumber (Cucumis sativus) and tomato (Solanum lycopersicum) seedlings, and that intact cotyledons are also necessary for this process. These results suggested that cotyledons might play an important role in controlling GA levels in the hypocotyl in these plant species. In this study, we found that a local application of a GA biosynthesis inhibitor uniconazole to cotyledons was effective to inhibit hypocotyl elongation, and that simultaneous application of GA canceled this inhibition. To study the role of cotyledons in GA content in the hypocotyl directly, cotyledons were removed from 7-days-old seedlings and endogenous GA levels in the hypocotyl were determined. Our results demonstrated that the cotyledon-removed seedlings contained lower levels of bioactive GAs and their precursors in the hypocotyls than did intact seedlings. Quantitative RT-PCR analysis indicated that transcript levels of LeGA20ox1 and LeGA3ox2 genes were elevated in the hypocotyl after the removal of cotyledons, suggesting that the reduced bioactive GA levels caused upregulation of these genes via the feedback regulation mechanism. Taken together, our results suggest that cotyledons are necessary for maintaining normal GA levels in young cucumber and tomato hypocotyls.
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  • Toshikazu Omura, Shin Watanabe, Yoko Iijima, Koh Aoki, Daisuke Shibata ...
    2007 Volume 24 Issue 1 Pages 107-115
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Mevalonic acid (MVA) pathway, in parallel with methylerythritol phosphate (MEP) pathway, produces precursor metabolites for isoprenoids, and affect fruit development in plants. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is supposed to be a key enzyme in the MVA pathway. To understand the role of HMGR in fruit development, we previously generated transgenic tomato (Solanum lycopersicum) expressing a melon HMGR gene (CmHMGR) and observed increased fruit size in these plants. To further examine this effect, we performed molecular and genetic characterization of the transgenic tomato line in the T4 generation. The line showed stable expression of CmHMGR mRNA and protein, an effect that could lead to the increase in fruit weight observed, which exceeded 20%. Interestingly, the CmHMGR mRNA was highly expressed during tomato fruit development, whereas expression of the endogenous HMGRs (SlHMGR1, SlHMGR2, and SlHMGR3) was lower than in the wild type, suggesting the presence of a regulatory mechanism at the transcriptional level, as in mammalian systems. A preliminary analysis using cDNA macroarray filters was performed, and genes showing more than 2.5-fold differences in expression between transgenic and wild-type plants were identified. Most of the genes involved in isoprenoid biosynthesis did not show significantly different transcription levels, but 121 annotated genes and 152 genes of unknown function were found to be differentially expressed. These results demonstrate that the transgenic tomato line expressing the HMGR gene is genetically stable and could be used as a comprehensive material to elucidate the roles of HMGRs in tomato fruit development.
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  • Ji-Hong Liu, Hiroyasu Kitashiba, Jing Wang, Yusuke Ban, Takaya Moriguc ...
    2007 Volume 24 Issue 1 Pages 117-126
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    The present review highlights some recent advances regarding the function of polyamines in the environmental stress tolerance of plants. When exposed to adverse environmental stresses, such as salt, drought, low temperature, and ozone, the complex dynamic kinetics of polyamine biosynthesis was observed. Polyamines titers altered in different manners dependent upon several factors, such as plant species, tolerance or sensitivity to stress, and duration of stress. The exogenous addition of polyamines to stress-treated cells or tissues could lead to injury alleviation and growth promotion in most cases, although the effects varied between polyamines and among plant species. Key genes responsible for polyamine biosynthesis have been cloned from a variety of plant species, whose expressions following stress have been investigated on a molecular basis. Overexpression of the genes caused the modification of polyamine biosynthesis in the transformants coupled with enhancement of stress tolerance. All of these results seem to indicate that polyamines are an important component in a plant's response to stress and that they play a significant role in counteracting stress.
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  • Katsuhiro Shiratake, Enrico Martinoia
    2007 Volume 24 Issue 1 Pages 127-133
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    The vacuole is by far the largest organelle in fruits and can occupy more than 90 percent of the cell volume. Therefore, if we eat fruits and their products, we mainly eat the compounds stored within the vacuole. The main compounds are sugars, organic acids and secondary metabolites, such as phenolics and terpenoids, that are important for fruit quality. High concentrations of sugars, organic acids and inorganic ions in fruits generate a high osmotic pressure leading to a strong negative water potential that attracts water, allowing the fruit to grow. Accumulation of solutes within the vacuole requires many transporters in the vacuolar membrane, which is also called tonoplast. This review summarizes studies of transporters in fruit vacuoles, including proton pumps, aquaporins, sugar transporters, organic acid transporters and ABC transporters.
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  • Tsutomu Arie, Hideki Takahashi, Motoichiro Kodama, Tohru Teraoka
    2007 Volume 24 Issue 1 Pages 135-147
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Tomato has been a good model plant to analyze plant-pathogen interactions and its prospects for the future are promising. An international consortium named International Solanaceae Genomics Project (SOL) is proceeding with whole genome sequencing of tomato. In order to be relevant in the post-genomic era, accumulation of information on tomato-pathogen interactions is important. In this review, the following topics are addressed from the perspective of plant pathology: cultivars of tomato, wild species of tomato, disease-resistance in modern breeding of tomato, fungal, bacterial, and viral pathogens of tomato, known interactions between tomato and pathogens, fungicides and biocontrol agents applicable to tomato, and systemic resistance induced by microbes and by plant activators. Tomato is one of the most popular vegetables worldwide, however, its cultivation has been limited by an abundant attack by pathogens. In order to establish effective control methods to control them, analysis of tomato-pathogen interactions is also important.
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  • Yasufumi Hikichi, Takeshi Yoshimochi, Shintaro Tsujimoto, Rena Shinoha ...
    2007 Volume 24 Issue 1 Pages 149-154
    Published: 2007
    Released: December 10, 2007
    JOURNALS FREE ACCESS
    Bacterial wilt caused by Ralstonia solanacearum is one of the most devastating plant diseases worldwide. R. solanacearum first invades intercellular spaces of roots where it multiplies before invading xylem vessels and producing exopolysaccharide (EPS), leading to wilt of the infected plant. In this review, we focus on regulation of R. solanacearum pathogenicity, which requires proliferation in intercellular spaces. R. solanacearum possesses hrp encoding the type III secretion system (T3SS), and its pathogenicity depends on interactions between the host plant and type III effectors. HrpB positively regulates expression of not only hrp but also genes encoding exoproteins secreted through the type II secretion system (T2SS). A consortium of T2SS-secreted exocellular proteins containing plant cell wall-degrading enzymes contributes to not only invasion of xylem vessels, leading to systemic infection, but also quantitative control of virulence. Moreover, T2SS functionally interacts with T3SS. PhcA activated by quorum sensing in response to the bacterial cell density induces expression of xpsR, leading to biosynthesis of EPS. Moreover, active PhcA also suppresses expression of prhIR, resulting in suppression of hrp expression. These results suggest that R. solanacearum pathogenicity is globally regulated by mutual regulation by pathogenicity factors through multiplication of the bacteria in intercellular spaces.
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