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Kuromori T, Fujita M, Urano K, Tanabata T, Sugimoto E, Shinozaki K. Overexpression of AtABCG25 enhances the abscisic acid signal in guard cells and improves plant water use efficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 251:75-81. [PMID: 27593465 DOI: 10.1016/j.plantsci.2016.02.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 05/06/2023]
Abstract
In addition to improving drought tolerance, improvement of water use efficiency is a major challenge in plant physiology. Due to their trade-off relationships, it is generally considered that achieving stress tolerance is incompatible with maintaining stable growth. Abscisic acid (ABA) is a key phytohormone that regulates the balance between intrinsic growth and environmental responses. Previously, we identified AtABCG25 as a cell-membrane ABA transporter that export ABA from the inside to the outside of cells. AtABCG25-overexpressing plants showed a lower transpiration phenotype without any growth retardation. Here, we dissected this useful trait using precise phenotyping approaches. AtABCG25 overexpression stimulated a local ABA response in guard cells. Furthermore, AtABCG25 overexpression enhanced drought tolerance, probably resulting from maintenance of water contents over the common threshold for survival after drought stress treatment. Finally, we observed enhanced water use efficiency by overexpression of AtABCG25, in addition to drought tolerance. These results were consistent with the function of AtABCG25 as an ABA efflux transporter. This unique trait may be generally useful for improving the water use efficiency and drought tolerance of plants.
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Affiliation(s)
- Takashi Kuromori
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Fujita
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Kaoru Urano
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Takanari Tanabata
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan
| | - Eriko Sugimoto
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki 305-0074, Japan.
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102
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Clauw P, Coppens F, Korte A, Herman D, Slabbinck B, Dhondt S, Van Daele T, De Milde L, Vermeersch M, Maleux K, Maere S, Gonzalez N, Inzé D. Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture. THE PLANT CELL 2016; 28:2417-2434. [PMID: 27729396 PMCID: PMC5134983 DOI: 10.1105/tpc.16.00483] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/02/2016] [Accepted: 10/10/2016] [Indexed: 05/04/2023]
Abstract
Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under nonlethal drought conditions is lacking. Recent advances in genomics, phenomics, and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The genetic architecture of the growth responses upon mild drought was investigated by subjecting the different leaf growth phenotypes to genome-wide association mapping and by characterizing the transcriptome of young developing leaves. Although no major effect locus was found to be associated with growth in mild drought, the transcriptome analysis delivered further insight into the natural variation of transcriptional responses to mild drought in a specific tissue. Coexpression analysis indicated the presence of gene clusters that co-vary over different genetic backgrounds, among others a cluster of genes with important regulatory functions in the growth response to osmotic stress. It was found that the occurrence of a mild drought stress response in leaves can be inferred with high accuracy across accessions based on the expression profile of 283 genes. A genome-wide association study on the expression data revealed that trans regulation seems to be more important than cis regulation in the transcriptional response to environmental perturbations.
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Affiliation(s)
- Pieter Clauw
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Arthur Korte
- Gregor Mendel Institute of Molecular Plant Biology, 1030 Vienna, Austria
| | - Dorota Herman
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Bram Slabbinck
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stijn Dhondt
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Twiggy Van Daele
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Mattias Vermeersch
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Katrien Maleux
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Address correspondence to
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103
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Gray SB, Brady SM. Plant developmental responses to climate change. Dev Biol 2016; 419:64-77. [PMID: 27521050 DOI: 10.1016/j.ydbio.2016.07.023] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/30/2016] [Accepted: 07/31/2016] [Indexed: 02/02/2023]
Abstract
Climate change is multi-faceted, and includes changing concentrations of greenhouse gases in the atmosphere, rising temperatures, changes in precipitation patterns, and increasing frequency of extreme weather events. Here, we focus on the effects of rising atmospheric CO2 concentrations, rising temperature, and drought stress and their interaction on plant developmental processes in leaves, roots, and in reproductive structures. While in some cases these responses are conserved across species, such as decreased root elongation, perturbation of root growth angle and reduced seed yield in response to drought, or an increase in root biomass in shallow soil in response to elevated CO2, most responses are variable within and between species and are dependent on developmental stage. These variable responses include species-specific thresholds that arrest development of reproductive structures, reduce root growth rate and the rate of leaf initiation and expansion in response to elevated temperature. Leaf developmental responses to elevated CO2 vary by cell type and by species. Variability also exists between C3 and C4 species in response to elevated CO2, especially in terms of growth and seed yield stimulation. At the molecular level, significantly less is understood regarding conservation and variability in molecular mechanisms underlying these traits. Abscisic acid-mediated changes in cell wall expansion likely underlie reductions in growth rate in response to drought, and changes in known regulators of flowering time likely underlie altered reproductive transitions in response to elevated temperature and CO2. Genes that underlie most other organ or tissue-level responses have largely only been identified in a single species in response to a single stress and their level of conservation is unknown. We conclude that there is a need for further research regarding the molecular mechanisms of plant developmental responses to climate change factors in general, and that this lack of data is particularly prevalent in the case of interactive effects of multiple climate change factors. As future growing conditions will likely expose plants to multiple climate change factors simultaneously, with a sum negative influence on global agriculture, further research in this area is critical.
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Affiliation(s)
- Sharon B Gray
- Department of Plant Biology, University of California, Davis, 2243 Life Sciences Addition, One Shields Avenue, Davis, CA 95616, USA.
| | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, 2243 Life Sciences Addition, One Shields Avenue, Davis, CA 95616, USA; Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, USA.
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104
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Sun T, Renner SS, Xu Y, Qin Y, Wu J, Sun G. Two hAT transposon genes were transferred from Brassicaceae to broomrapes and are actively expressed in some recipients. Sci Rep 2016; 6:30192. [PMID: 27452947 PMCID: PMC4958966 DOI: 10.1038/srep30192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/30/2016] [Indexed: 11/23/2022] Open
Abstract
A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce, and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information, and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure, and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.
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Affiliation(s)
- Ting Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Susanne S. Renner
- Systematic Botany and Mycology, University of Munich (LMU), Munich 80638, Germany
| | - Yuxing Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Qin
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, Kaifeng 475004, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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105
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Armbruster U, Leonelli L, Correa Galvis V, Strand D, Quinn EH, Jonikas MC, Niyogi KK. Regulation and Levels of the Thylakoid K+/H+ Antiporter KEA3 Shape the Dynamic Response of Photosynthesis in Fluctuating Light. PLANT & CELL PHYSIOLOGY 2016; 57:1557-1567. [PMID: 27335350 PMCID: PMC4937787 DOI: 10.1093/pcp/pcw085] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/24/2016] [Indexed: 05/22/2023]
Abstract
Crop canopies create environments of highly fluctuating light intensities. In such environments, photoprotective mechanisms and their relaxation kinetics have been hypothesized to limit photosynthetic efficiency and therefore crop yield potential. Here, we show that overexpression of the Arabidopsis thylakoid K+/H+ antiporter KEA3 accelerates the relaxation of photoprotective energy-dependent quenching after transitions from high to low light in Arabidopsis and tobacco. This, in turn, enhances PSII quantum efficiency in both organisms, supporting that in wild-type plants, residual light energy quenching following a high to low light transition represents a limitation to photosynthetic efficiency in fluctuating light. This finding underscores the potential of accelerating quenching relaxation as a building block for improving photosynthetic efficiency in the field. Additionally, by overexpressing natural KEA3 variants with modification to the C-terminus, we show that KEA3 activity is regulated by a mechanism involving its lumen-localized C-terminus, which lowers KEA3 activity in high light. This regulatory mechanism fine-tunes the balance between photoprotective energy dissipation in high light and maximum quantum yield in low light, likely to be critical for efficient photosynthesis in fluctuating light conditions.
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Affiliation(s)
- Ute Armbruster
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Lauriebeth Leonelli
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Viviana Correa Galvis
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Deserah Strand
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam, Germany
| | - Erica H Quinn
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Martin C Jonikas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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106
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Viaene T, Langendries S, Beirinckx S, Maes M, Goormachtig S. Streptomycesas a plant's best friend? FEMS Microbiol Ecol 2016; 92:fiw119. [DOI: 10.1093/femsec/fiw119] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 11/14/2022] Open
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107
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Coolen S, Proietti S, Hickman R, Davila Olivas NH, Huang PP, Van Verk MC, Van Pelt JA, Wittenberg AHJ, De Vos M, Prins M, Van Loon JJA, Aarts MGM, Dicke M, Pieterse CMJ, Van Wees SCM. Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:249-67. [PMID: 26991768 DOI: 10.1111/tpj.13167] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 05/19/2023]
Abstract
In nature, plants have to cope with a wide range of stress conditions that often occur simultaneously or in sequence. To investigate how plants cope with multi-stress conditions, we analyzed the dynamics of whole-transcriptome profiles of Arabidopsis thaliana exposed to six sequential double stresses inflicted by combinations of: (i) infection by the necrotrophic fungus Botrytis cinerea, (ii) herbivory by chewing larvae of Pieris rapae, and (iii) drought stress. Each of these stresses induced specific expression profiles over time, in which one-third of all differentially expressed genes was shared by at least two single stresses. Of these, 394 genes were differentially expressed during all three stress conditions, albeit often in opposite directions. When two stresses were applied in sequence, plants displayed transcriptome profiles that were very similar to the second stress, irrespective of the nature of the first stress. Nevertheless, significant first-stress signatures could be identified in the sequential stress profiles. Bioinformatic analysis of the dynamics of co-expressed gene clusters highlighted specific clusters and biological processes of which the timing of activation or repression was altered by a prior stress. The first-stress signatures in second stress transcriptional profiles were remarkably often related to responses to phytohormones, strengthening the notion that hormones are global modulators of interactions between different types of stress. Because prior stresses can affect the level of tolerance against a subsequent stress (e.g. prior herbivory strongly affected resistance to B. cinerea), the first-stress signatures can provide important leads for the identification of molecular players that are decisive in the interactions between stress response pathways.
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Affiliation(s)
- Silvia Coolen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Silvia Proietti
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Richard Hickman
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Nelson H Davila Olivas
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Ping-Ping Huang
- Laboratory of Genetics, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Marcel C Van Verk
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
- Bioinformatics, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | | | - Martin De Vos
- Keygene N.V., PO Box 216, 6700 AE, Wageningen, The Netherlands
| | - Marcel Prins
- Keygene N.V., PO Box 216, 6700 AE, Wageningen, The Netherlands
| | - Joop J A Van Loon
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University, PO Box 16, 6700 AA, Wageningen, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Utrecht University, PO Box 800.56, 3508 TB, Utrecht, The Netherlands
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108
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Tapia G, Méndez J, Inostroza L. Different combinations of morpho-physiological traits are responsible for tolerance to drought in wild tomatoes Solanum chilense and Solanum peruvianum. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:406-16. [PMID: 26499789 DOI: 10.1111/plb.12409] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/21/2015] [Indexed: 05/23/2023]
Abstract
Herbaceous species can modify leaf structure during the growing season in response to drought stress and water loss. Evolution can select combinations of traits in plants for efficient water use in restricted environments. We investigated plant traits that mediate adaptation and acclimation to water stress in two herbaceous drought-tolerant species. Anatomical, morphological and physiological traits related to stems and leaves were examined under optimal watering (OW) and a long period of restricted watering (RW) in 11 accessions from three Solanaceae species (Solanum chilense, S. peruvianum and S. lycopersicum). The relationships between these traits were tested using linear regression and PCA. There were significant differences in anatomical traits between the species under both OW and RW, where leaf area correlated with stem diameter. Proline and total carbohydrates accumulated highly in S. chilense and S. peruvianum, respectively, and these osmolytes were strongly correlated with increased osmotic potential. Stomatal density varied between species but not between acclimation treatments, while stomatal rate was significantly higher in wild tomatoes. There was a strong positive relationship between stem growth rate and a group of traits together expressed as total stomatal number. Total stomata is described by integration of leaf area, stomatal density, height and internode length. It is proposed that constitutive adaptations and modifications through acclimation that mediate RW play an important role in tolerance to drought stress in herbaceous plants. The capacity for growth under drought stress was not associated with any single combination of traits in wild tomatoes, since the two species differed in relative levels of expression of various phenotypic traits.
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Affiliation(s)
- G Tapia
- Unidad de Recursos Genéticos Vegetales, Instituto de Investigaciones Agropecuarias, INIA-Quilamapu, Chillán, Chile
| | - J Méndez
- Unidad de Recursos Genéticos Vegetales, Instituto de Investigaciones Agropecuarias, INIA-Quilamapu, Chillán, Chile
| | - L Inostroza
- Unidad de Recursos Genéticos Vegetales, Instituto de Investigaciones Agropecuarias, INIA-Quilamapu, Chillán, Chile
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109
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Wang Y, Lu W, Deng D. Bioinformatic landscapes for plant transcription factor system research. PLANTA 2016; 243:297-304. [PMID: 26719053 DOI: 10.1007/s00425-015-2453-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/16/2015] [Indexed: 06/05/2023]
Abstract
Diverse bioinformatic resources have been developed for plant transcription factor (TF) research. This review presents the bioinformatic resources and methodologies for the elucidation of plant TF-mediated biological events. Such information is helpful to dissect the transcriptional regulatory systems in the three reference plants Arabidopsis , rice, and maize and translation to other plants. Transcription factors (TFs) orchestrate diverse biological programs by the modulation of spatiotemporal patterns of gene expression via binding cis-regulatory elements. Advanced sequencing platforms accompanied by emerging bioinformatic tools revolutionize the scope and extent of TF research. The system-level integration of bioinformatic resources is beneficial to the decoding of TF-involved networks. Herein, we first briefly introduce general and specialized databases for TF research in three reference plants Arabidopsis, rice, and maize. Then, as proof of concept, we identified and characterized heat shock transcription factor (HSF) members through the TF databases. Finally, we present how the integration of bioinformatic resources at -omics layers can aid the dissection of TF-mediated pathways. We also suggest ways forward to improve the bioinformatic resources of plant TFs. Leveraging these bioinformatic resources and methodologies opens new avenues for the elucidation of transcriptional regulatory systems in the three model systems and translation to other plants.
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Affiliation(s)
- Yijun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Wenjie Lu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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110
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Iovieno P, Punzo P, Guida G, Mistretta C, Van Oosten MJ, Nurcato R, Bostan H, Colantuono C, Costa A, Bagnaresi P, Chiusano ML, Albrizio R, Giorio P, Batelli G, Grillo S. Transcriptomic Changes Drive Physiological Responses to Progressive Drought Stress and Rehydration in Tomato. FRONTIERS IN PLANT SCIENCE 2016; 7:371. [PMID: 27066027 PMCID: PMC4814702 DOI: 10.3389/fpls.2016.00371] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/10/2016] [Indexed: 05/07/2023]
Abstract
Tomato is a major crop in the Mediterranean basin, where the cultivation in the open field is often vulnerable to drought. In order to adapt and survive to naturally occurring cycles of drought stress and recovery, plants employ a coordinated array of physiological, biochemical, and molecular responses. Transcriptomic studies on tomato responses to drought and subsequent recovery are few in number. As the search for novel traits to improve the genetic tolerance to drought increases, a better understanding of these responses is required. To address this need we designed a study in which we induced two cycles of prolonged drought stress and a single recovery by rewatering in tomato. In order to dissect the complexity of plant responses to drought, we analyzed the physiological responses (stomatal conductance, CO2 assimilation, and chlorophyll fluorescence), abscisic acid (ABA), and proline contents. In addition to the physiological and metabolite assays, we generated transcriptomes for multiple points during the stress and recovery cycles. Cluster analysis of differentially expressed genes (DEGs) between the conditions has revealed potential novel components in stress response. The observed reduction in leaf gas exchanges and efficiency of the photosystem PSII was concomitant with a general down-regulation of genes belonging to the photosynthesis, light harvesting, and photosystem I and II category induced by drought stress. Gene ontology (GO) categories such as cell proliferation and cell cycle were also significantly enriched in the down-regulated fraction of genes upon drought stress, which may contribute to explain the observed growth reduction. Several histone variants were also repressed during drought stress, indicating that chromatin associated processes are also affected by drought. As expected, ABA accumulated after prolonged water deficit, driving the observed enrichment of stress related GOs in the up-regulated gene fractions, which included transcripts putatively involved in stomatal movements. This transcriptomic study has yielded promising candidate genes that merit further functional studies to confirm their involvement in drought tolerance and recovery. Together, our results contribute to a better understanding of the coordinated responses taking place under drought stress and recovery in adult plants of tomato.
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Affiliation(s)
- Paolo Iovieno
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Paola Punzo
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Gianpiero Guida
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Carmela Mistretta
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | | | - Roberta Nurcato
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Hamed Bostan
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Chiara Colantuono
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Antonello Costa
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Paolo Bagnaresi
- CREA - Council for Agricultural Research and Economics, Genomics Research Centre Fiorenzuola d'Arda, Italy
| | - Maria L Chiusano
- Department of Agriculture, University of Naples "Federico II," Portici, Italy
| | - Rossella Albrizio
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Pasquale Giorio
- National Research Council of Italy, Institute for Agricultural and Forestry Systems in the Mediterranean (CNR-ISAFoM) Ercolano, Italy
| | - Giorgia Batelli
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
| | - Stefania Grillo
- National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici (CNR-IBBR) Portici, Italy
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Bac-Molenaar JA, Granier C, Keurentjes JJB, Vreugdenhil D. Genome-wide association mapping of time-dependent growth responses to moderate drought stress in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:88-102. [PMID: 26138664 DOI: 10.1111/pce.12595] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 05/25/2023]
Abstract
Large areas of arable land are often confronted with irregular rainfall resulting in limited water availability for part(s) of the growing seasons, which demands research for drought tolerance of plants. Natural variation was observed for biomass accumulation upon controlled moderate drought stress in 324 natural accessions of Arabidopsis. Improved performance under drought stress was correlated with early flowering and lack of vernalization requirement, indicating overlap in the regulatory networks of flowering time and drought response or correlated responses of these traits to natural selection. In addition, plant size was negatively correlated with relative water content (RWC) independent of the absolute water content (WC), indicating a prominent role for soluble compounds. Growth in control and drought conditions was determined over time and was modelled by an exponential function. Genome-wide association (GWA) mapping of temporal plant size data and of model parameters resulted in the detection of six time-dependent quantitative trait loci (QTLs) strongly associated with drought. Most QTLs would not have been identified if plant size was determined at a single time point. Analysis of earlier reported gene expression changes upon drought enabled us to identify for each QTL the most likely candidates.
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Affiliation(s)
| | - Christine Granier
- Laboratoire d'Ecop0068ysiologie des Plantes sous Stress Environnementaux, UMR 759, Institut National de la Recherche Agronomique/Ecole Nationale Supérieure d'Agronomie, Place Viala, F-34060, Montpellier, Cedex 1, France
| | | | - Dick Vreugdenhil
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Nagler M, Nukarinen E, Weckwerth W, Nägele T. Integrative molecular profiling indicates a central role of transitory starch breakdown in establishing a stable C/N homeostasis during cold acclimation in two natural accessions of Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:284. [PMID: 26628055 PMCID: PMC4667452 DOI: 10.1186/s12870-015-0668-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/23/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND The variation of growth and cold tolerance of two natural Arabidopsis accessions, Cvi (cold sensitive) and Rschew (cold tolerant), was analysed on a proteomic, phosphoproteomic and metabolomic level to derive characteristic information about genotypically distinct strategies of metabolic reprogramming and growth maintenance during cold acclimation. RESULTS Growth regulation before and after a cold acclimation period was monitored by recording fresh weight of leaf rosettes. Significant differences in the shoot fresh weight of Cvi and Rschew were detected both before and after acclimation to low temperature. During cold acclimation, starch levels were found to accumulate to a significantly higher level in Cvi compared to Rschew. Concomitantly, statistical analysis revealed a cold-induced decrease of beta-amylase 3 (BAM3; AT4G17090) in Cvi but not in Rschew. Further, only in Rschew we observed an increase of the protein level of the debranching enzyme isoamylase 3 (ISA3; AT4G09020). Additionally, the cold response of both accessions was observed to severely affect ribosomal complexes, but only Rschew showed a pronounced accumulation of carbon and nitrogen compounds. The abundance of the Cold Regulated (COR) protein COR78 (AT5G52310) as well as its phosphorylation was observed to be positively correlated with the acclimation state of both accessions. In addition, transcription factors being involved in growth and developmental regulation were found to characteristically separate the cold sensitive from the cold tolerant accession. Predicted protein-protein interaction networks (PPIN) of significantly changed proteins during cold acclimation allowed for a differentiation between both accessions. The PPIN revealed the central role of carbon/nitrogen allocation and ribosomal complex formation to establish a new cold-induced metabolic homeostasis as also observed on the level of the metabolome and proteome. CONCLUSION Our results provide evidence for a comprehensive multi-functional molecular interaction network orchestrating growth regulation and cold acclimation in two natural accessions of Arabidopsis thaliana. The differential abundance of beta-amylase 3 and isoamylase 3 indicates a central role of transitory starch degradation in the coordination of growth regulation and the development of stress tolerance. Finally, our study indicates naturally occurring differential patterns of C/N balance and protein synthesis during cold acclimation.
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Affiliation(s)
- Matthias Nagler
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Ella Nukarinen
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
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113
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Bazakos C, Manioudaki ME, Sarropoulou E, Spano T, Kalaitzis P. 454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity. PLoS One 2015; 10:e0143000. [PMID: 26576008 PMCID: PMC4648586 DOI: 10.1371/journal.pone.0143000] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.
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Affiliation(s)
- Christos Bazakos
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria E. Manioudaki
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Thodhoraq Spano
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- * E-mail:
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114
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Dell'Acqua M, Gatti DM, Pea G, Cattonaro F, Coppens F, Magris G, Hlaing AL, Aung HH, Nelissen H, Baute J, Frascaroli E, Churchill GA, Inzé D, Morgante M, Pè ME. Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays. Genome Biol 2015; 16:167. [PMID: 26357913 PMCID: PMC4566846 DOI: 10.1186/s13059-015-0716-z] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/03/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Maize (Zea mays) is a globally produced crop with broad genetic and phenotypic variation. New tools that improve our understanding of the genetic basis of quantitative traits are needed to guide predictive crop breeding. We have produced the first balanced multi-parental population in maize, a tool that provides high diversity and dense recombination events to allow routine quantitative trait loci (QTL) mapping in maize. RESULTS We produced 1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines. The characterization of 529 MAGIC maize lines shows that the population is a balanced, evenly differentiated mosaic of the eight founders, with mapping power and resolution strengthened by high minor allele frequencies and a fast decay of linkage disequilibrium. We show how MAGIC maize may find strong candidate genes by incorporating genome sequencing and transcriptomics data. We discuss three QTL for grain yield and three for flowering time, reporting candidate genes. Power simulations show that subsets of MAGIC maize might achieve high-power and high-definition QTL mapping. CONCLUSIONS We demonstrate MAGIC maize's value in identifying the genetic bases of complex traits of agronomic relevance. The design of MAGIC maize allows the accumulation of sequencing and transcriptomics layers to guide the identification of candidate genes for a number of maize traits at different developmental stages. The characterization of the full MAGIC maize population will lead to higher power and definition in QTL mapping, and lay the basis for improved understanding of maize phenotypes, heterosis included. MAGIC maize is available to researchers.
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Affiliation(s)
- Matteo Dell'Acqua
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
| | | | - Giorgio Pea
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
- Current address: Thermo Fisher Scientific, Via G.B Tiepolo 18, 20900, Monza, MB, Italy.
| | | | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
| | - Gabriele Magris
- Institute of Applied Genomics, Udine, Italy.
- Department of Agricultural and Environmental Sciences, University of Udine, Udine, Italy.
| | - Aye L Hlaing
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
- Current address: Department of Agricultural Research, Nay Pyi Taw, Myanmar.
| | - Htay H Aung
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
- Current address: Plant Biotechnology Center, Yangon, Myanmar.
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Department of Plant Systems Biology, VIB, Gent, Belgium.
| | - Joke Baute
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Department of Plant Systems Biology, VIB, Gent, Belgium.
| | | | | | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium.
- Department of Plant Systems Biology, VIB, Gent, Belgium.
| | - Michele Morgante
- Institute of Applied Genomics, Udine, Italy.
- Department of Agricultural and Environmental Sciences, University of Udine, Udine, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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Yoshida T, Mogami J, Yamaguchi-Shinozaki K. Omics Approaches Toward Defining the Comprehensive Abscisic Acid Signaling Network in Plants. PLANT & CELL PHYSIOLOGY 2015; 56:1043-52. [PMID: 25917608 DOI: 10.1093/pcp/pcv060] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/13/2015] [Indexed: 05/19/2023]
Abstract
ABA is a plant hormone that plays crucial roles in controlling cellular and physiological responses to osmotic stress and in developmental processes. Endogenous ABA levels are increased in response to a decrease in water availability in cells, and ABA sensing and signaling are thought to be mediated according to the current model established in Arabidopsis thaliana, which involves pyrabactin resistance 1 (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR), protein phosphatase 2C (PP2C) and sucrose non-fermenting-1 (SNF1)-related protein kinase 2 (SnRK2). These core components of ABA signaling have a pivotal role in stress-responsive gene expression and stomatal regulation. However, because a limited number of their upstream and downstream factors have been characterized, it is still difficult to define the comprehensive network of ABA signaling in plants. This review focuses on current progress in the study of PYR/PYL/RCARs, PP2Cs and SnRK2s, with particular emphasis on omics approaches, such as interactome and phosphoproteome studies. Moreover, the role of ABA in plant growth and development is discussed based on recent metabolomic profiling studies.
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Affiliation(s)
- Takuya Yoshida
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Junro Mogami
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657 Japan
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