Contents
Preface
A junction of Solanaceae and Cucurbitaceae researches: SOL&ICuGI2011
Hiroshi Ezura . . . . . . . 207[PDF]
Reviews
Molecular mechanisms controlling plant organ abscission
Toshitsugu Nakano, Yasuhiro Ito . . . . . . . 209[PDF]
Plants shed organs by abscission when they are senescent, mature or dispensable. Abscission typically occurs in a predetermined tissue, the abscission zone (AZ). In this review, we discuss the functions of genes involved in AZ differentiation and abscission activation, the developmental regulation of AZ tissues, and the signaling pathways of abscission induction. Also, we discuss the emerging concept that the regulation of abscission involves regulators that function in cell fate determination of shoot apical meristem.
Smoking out the masters: transcriptional regulators for nicotine biosynthesis in tobacco
Tsubasa Shoji, Takashi Hashimoto . . . . . . . 217[PDF]
Nicotine is a predominant alkaloid in tobacco. Nicotine production is increased in response to insect attacks and jasmonate signaling plays a regulatory role in the response. A set of nicotine metabolic and transport genes are directly regulated by ERF and bHLH transcription factors, which are connected upstream with jasmonate signaling components.
Micro-Tom mutants for functional analysis of target genes and discovery of new alleles in tomato
Daniel Just, Virginie Garcia, Lucie Fernandez, Ce’cile Bres, Jean-Philippe Mauxion, Johann Petit, Joana Jorly, Julien Assali, Ce’line Bournonville, Carine Ferrand, Pierre Baldet, Martine Lemaire-Chamley, Kentaro Mori, Yoshihiro Okabe, Tohru Ariizumi, Erika Asamizu, Hiroshi Ezura, Christophe Rothan . . . . . . . 225[PDF]
The wealth of genomic information now available on the fleshy fruit and Solanaceae model tomato has considerably increased the interest of generating artificially-induced genetic diversity in this crop species. This review describes the creation and use of EMS (ethyl methanesulfonate) tomato mutants in the miniature cultivar Micro-Tom and shows how it can be used for identifying new fruit size mutants. It further discuss how the large genetic diversity available can be exploited for the identification of allelic variants through TILLING (Targeting Induced Local Lesions IN Genomes) and proposes new deep sequencing-based strategies for the discovery of mutations underlying phenotypic variations observed in mutant collections.
Induction of RNA-directed DNA methylation and heritable transcriptional gene silencing as a tool to engineer novel traits in plants
Megumi Kasai, Akira Kanazawa . . . . . . . 233[PDF]
RNA-mediated transcriptional gene silencing allows production of plants that have altered traits but do not carry a transgene. Thus, modification of the epigenetic state of a plant is now a feasible tool to engineer novel traits. Here we review epigenetic changes induced in a particular gene through RNA-directed DNA methylation and those induced randomly on the genome in terms of their use for plant biotechnology.
Advances in tomato research in the post-genome era
Naama Menda, Susan R. Strickler, Lukas A. Mueller . . . . . . . 243[PDF]
The tomato (Solanum lycopersicum) draft genome, along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012, almost a decade after the International Tomato Genome project was initiated. Tomato is an important domesticated crop species, as well as a model organism for many aspects of plant biology such as fleshy fruit development, ripening, disease resistance, plant architecture, and compound leaf development. For these reasons, there has been a substantial effort for producing a high quality reference genome that will serve as an anchor for tomato species, and for closely related Solanaceae plants. The utility of this genome has already been demonstrated by a relatively large number of studies that have been published since the release of the sequence, covering a wide range of topics including gene expression, genetic diversity, phylogeny, comparative genomics, and epigenetics. With the availability of the potato genome, it is now possible to perform detailed comparative genomic analysis of gene families in the Solanaceae, facilitated by conservation and synteny between their genomes. A large number of ongoing efforts will result in the sequencing of hundreds of wild and domesticated tomato accessions from various populations, uncovering the breeding history of tomatoes and introducing new genomic technologies to accelerate breeding processes. In this review, we provide an overview of the origins of tomato and its position in the wider Solanaceae, and demonstrate the impact of the tomato genome sequence on Solanaceae research on the basis of recent literature that has made use of this new resource.
Structural analyses of the tomato genome
Shusei Sato, Kenta Shirasawa, Satoshi Tabata . . . . . . . 257[PDF]
Tomato is regarded as a model plant for the Solanaceae family and for other fruiting plant species. Thus, the considerable efforts have been made toward developing genomic resources for more than 10 years. One of the milestone achievements of these efforts was the completion of the whole genome sequencing project. Here we summarized the recent studies on the genome structure of tomato, focusing on high-density genetic linkage maps and sequence information.
A genomics perspective on cucurbit-oomycete interactions
Alyssa Burkhardt, Brad Day . . . . . . . 265[PDF]
Pseudoperonospora cubensis and Phytophthora capsici are plant pathogenic oomycetes that are severe threats to cucurbit cultivation because of the their global distribution, their broad host range among the Cucurbitaceae family, and their ability to overcome susceptibilities to host, environment, and chemical management. To idenfity possible mechanisms associated with virulence and resistance, we sequenced the transcriptomes of Ps. cubensis and Cucumis sativus (cucumber, and this data is being analyzed to determine the function of Ps. cubensis effectors and the role of alternative splicing in the regulation of pathogen gene expression. Future work is needed to give biological meaning to genomics data and to determine mechanisms of pathogenicity in oomycetes and resistance in cucurbits. Herein, we will present an overview of the current and future objectives of genome-based research in this area, describing the molecular mechanisms of pathogen virulence and host response to infection.
Phenotypic diversity in wild and cultivated melons (Cucumis melo)
Michel Pitrat. . . . . . . 273[PDF]
Cultivated melons (Cucumis melo) present a very large phenotypic polymorphism compared with the low phenotypic polymorphism of wild melons. Domestication has not been intensively studied and the genetic control of domestication traits is still poorly understood. Present day types of melons are the results of the subsequent diversification and human selection processes. Genetic control of a majority of the diversification traits is under recessive genetic control, even if some phenotypic traits are under dominant control, for instance most of the disease resistances. According to the phenotypic diversity, three groups corresponding maybe to three independent domestication events can be identified: one leading to the sub-species agrestis in India and Eastern Asia, another one leading to the subspecies melo in Africa and Western Asia and a third one in Africa for the tibish group also belonging to the sub-species agrestis. The absolute and relative time of these domestications events is unknown. The chito group found in Central America could represent feral melons i.e. melons returning to the wild state from domesticated forms.
Original Papers
Isolation and characterisation of the ADP-glucose pyrophosphorylase small subunit gene (AgpS1) promoter in tomato (Solanum lycopersicum L.)
Yukihisa Goto, Satoko Nonaka, Yong-Gen Yin, Teruyuki Koiwa, Erika Asamizu, Hiroshi Ezura, Chiaki Matsukura. . . . . . . 279[PDF]
In this research, 2,885 bp of the predicted promoter sequence for the AgpS1 gene encoding AGPase small subunit was isolated from tomato. The spatial expression pattern and tissue/organ specificity of AgpS1 were analysed utilizing promoter-GUS transgenic tomato plants. GUS staining analysis revealed AgpS1 expresses in both sink and source tissues/organs including seedling, stem, flower, fruit stalk, fruit and root. The expression tended to be confined to vascular tissues in seedling, stem, fruit stalk and ripening fruit.
Improving the transformation eciency of Cucurbita species: factors and strategy for practical application
Yoshihiko Nanasato, Ayako Okuzaki, Yutaka Tabei. . . . . . . 287[PDF]
Improvement of transformation efficiency of Cucurbita moschata (cv. Heiankogiku) was reported. The highest efficiency was obtained using wounded 1-day-old or 2-day-old explants. Histochemical GUS assay revealed that wounding allowed Agrobacterium access to the deeper layer of explants. Moreover we applied vacuum infiltration to wounded explants for the purpose of enhancing Agrobacterium access to the deeper layers, which resulted in improvement of transformation efficiency by 3-fold (9.2±2.9%). We have succeeded in transforming other Cucurbita species, C. maxima (cv. Ebisu) and C. pepo (cv. Black Tosca) using our transformation protocol.
Comparative analysis of common genes involved in early fruit development in tomato and grape
Kentaro Mori, Martine Lemaire-Chamley, Erika Asamizu, Tsuyoshi Mizoguchi, Hiroshi Ezura, Christophe Rothan. . . . . . . 295[PDF]
This study attempted to identify genes involved in the regulation of early fruit development by focusing on genes displaying similar patterns of expression in tomato and grape. By mining public sequences and microarray database, several transcription factors having known and unknown biological role were found as the candidate genes.
Short Communication
The structural and molecular analysis of endoreduplicated nuclei in tomato (Solanum lycopersicum) fruit provides evidence for a ploidy-dependent increase in transcriptional activity
Julien Pirrello, Matthieu Bourdon, Catherine Cheniclet, Olivier Coriton, Mickae”l Bourge, Spencer Brown, Jean-Pierre Renaudin, Nathalie Frangne, Christian Chevalier. . . . . . . 301[PDF]
The growth of a plant organ depends upon cell division and cell expansion. Among the various mechanisms that may influence cell size, endoreduplication, i.e. the amplification of genomic DNA without mitosis, appears to be of great importance. Although widespread in plants, the functional role of endoreduplication is not fully understood, although it is commonly associated to ploidy-dependent cell expansion. During the development of tomato fruit, cells from the (fleshy) pericarp tissue are characterized by a wide range of ploidy levels (from 2C to 256C). Recent investigations using tomato fruit development as a model provided new data in favor of the karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication does act as a morphogenetic factor supporting cell growth during tomato fruit development, and contributes to increase transcriptional activity.
Note
Investigating the role of vitamin C in tomato through TILLING identication of ascorbate-decient tomato mutants
Pierre Baldet, Ce’cile Bres, Yoshihiro Okabe, Jean-Philippe Mauxion, Daniel Just, Ce’line Bournonville, Carine Ferrand, Kentaro Mori, Hiroshi Ezura, Christophe Rothan. . . . . . . 309[PDF]
Tomato EMS (ethyl methanesulfonate) mutant collections provide a large source of genetic variability for identifying allelic series of mutations in target genes. We describe here the use of TILLING (Targeting Induced Local Lesions IN Genomes) for the discovery of allelic variants in three tomato ascorbate biosynthetic genes encoding the GDP-D-mannose pyrophosphorylase (GMP), the GDP-D-mannose epimerase (GME) and the GDP-L-galactose phosphorylase (GGP) respectively. Several tomato mutant lines with strongly reduced ascorbate content undergo severe bleaching upon exposure to high light intensity.