Associated Research Group

19 groups have been newly added since April, 2016.
We promote this New Area of Scientific Study with these new teams and core research groups.


Arimura group
Memory and transition system for defense responses via plant-plant communications
Ashikari group
Molecular analysis of plasticity of
Awn formation in rice
Buzas group
The DNA elements of vernalization insensitive 3 gene for quantitative and priming epigenetic memory of cold
Fujii group
Self-pollen recognition system in the pollination of the Brassicaceae species
Kanaoka group
Molecular analysis of phenotypic plasticity in relation to water environment in allotetraploid species
Kawasaki group
MAPK-mediated regulation of plant immunological memory
Kiba group
Molecular mechanisms and physiological roles of long-distance cytokinin transport
Kimura group
Studies on phenotypic plasticity on leaf shape of Rorippa aquatica
Matsushita group
Memory and transition system for defense responses via plant-plant communications
Miura group
Elucidation of transcriptional regulation by sumoylation of histone
Nagano group
Development of quantification methods for plant memory under fluctuating environments.
Notaguchi group
Study on systemic RNAs that respond to specific environments
Saijo group
Polycomb group protein-mediated control for immune activation and priming in plants
Seki group
Analysis of antisense ncRNA-mediated plant environmental stress adaptation
Suzaki group
Systemic and local regulatory mechanisms of symbiotic organ formation in response to nitrogen
Takahashi group
Analysis of a small peptide-mediated long-distance signaling under water-deficit conditions
Takezawa group
Studies of integrated signaling pathways for ABA, low temperature and osmotic responses in bryophytes
Uchida group
Elucidation of phloem-derived signal in stem elongation
Yamaguchi group
Molecular genetic analysis of JUMONJI-mediated heat acclimation in Arabidopsis for improvement of heat memory

Arimura Group:
Memory and transition system for defense responses via plant-plant communications

  • Research plan representative Gen-ichiro Arimura
    Associate Professor, Department of Biological Science & Technology, Faculty of Industrial Science & Technology, Tokyo University of Science
    Collaborative researcher Kaori Shiojiri
    Associate Professor, Faculty of Agriculture, Ryukoku University
    Gen-ichiro Arimura
    Gen-ichiro Arimura
    Plants are able to eavesdrop on volatile organic chemicals emitted from their neighboring plants in response to herbivore attack. Such plant behaviors are defined as plant-plant communications. To reveal the mechanisms underlying defense responses promoted via plant-plant communications, we focus on aroma-rich mint species serving as volatile emitters. We conduct our analyses to understand the maintenance system for defense responses in receiver plants exposed with mint aroma as well as epigenetic regulation for enhanced defense across generations. The basic knowledge from this study would accordingly be of great use for the development of a novel pest control system.

Ashikari Group:
Molecular analysis of plasticity of Awn formation in rice

  • Research plan representative Motoyuki Ashikari
    Professor, Bioscience and Biotechnology Center, Nagoya University
    Collaborative researcher Hitoshi Mori
    Professor, Graduate School of Agriculture, Nagoya University
    Collaborative researcher Tetsuya Higashiyama
    Professor, Institute of Transformative Bio-Molecules, Nagoya University
    Motoyuki Ashikari
    Motoyuki Ashikari
    Awns are slender, bristle-like extensions of grass spikelets enhancing the seed dispersal and protect against predation in the wild. To facilitate seed processing and harvesting, the awnless phenotype has been selected during domestication in both Asian and African rice. Cultivated rice generally does not have awn, however it sometimes produces awn due to some environmental condition. In this project, we determine the environmental factor to control awn production and we also identify the gene regulating awn. And we elucidate the molecular mechanism of awn production by environmental condition. We also try to show the domestication process of awnless phenotype during wild rice to cultivated rice.

Buzas Group:
The DNA elements of vernalization insensitive 3 gene for quantitative and priming epigenetic memory of cold

  • Research plan representative Diana Buzas
    Associate Professor, University of Tsukuba
    Collaborative researcher Hiroshi Kudoh
    Professor, Kyoto University
    Diana Buzas
    Diana Buzas
    Some gene expression programs may persist even after their originating signals fade away; such stability is often attributed to epigenetic mechanisms. A number of key integrator genes responsive to cold follow such pattern to promote flowering in favorable spring conditions after the prolonged cold in winter (vernalization). How signal perception and epigenetic memory converge at these genes is not understood. In case of the Vernalization INsensitive 3 (VIN3) gene, a long period of cold is mirrored by increasing gene expression and high VIN3 expression is reached faster during a second exposure to cold. This study will dissect cis acting elements mediating distinct types of epigenetic memory and their responsiveness to temperature.

Fujii Group:
Self-pollen recognition system in the pollination of the Brassicaceae species

  • Research plan representative Sota Fujii
    Assistant Professor, Graduate School of Agricultural and Life Sciences, The University of Tokyo
    Collaborative researcher Seiji Takayama
    Professor, Nara Institute of Science and Technology
    Sota Fujii
    Sota Fujii
    More than half of the plants discriminates self/non-self pollen via the mechanism known as the 'self-incompatibility' ; to avoid self-breeding, and to promote out-crossing. This system maintains the genetic diversity in the population, and species selection maintains this system. In this project, we aim to study the mechanism to process the molecular information passed from the self-pollen to the pistils, using the Brassicaceae self-incompatibility system as the model. We especially focus on the calcium dynamics to elucidate how pistil cells memorize the attached self-pollen, and to know how non-self pollen is selectively accepted for seed fertilization.

Kanaoka Group:
Molecular analysis of phenotypic plasticity in relation to water environment in allotetraploid species

  • Research plan representative Masahiro Kanaoka
    Associate Professor, Graduate School of Science, Nagoya University
    Collaborative researcher Kentaro Shimizu
    Associate Professor, Department of Evolutionary Biology and Environmental Studies, University of Zurich
    Collaborative researcher Kiwako Araki
    Assistant Professor, Department of Biotechnology, Ritsumeikan University
    Masahiro Kanaoka
    Masahiro Kanaoka
    Allotetraploid species possess two sets of genomes from different parental species. It is thought that high plasticity of gene expression in allotetraploid species allows them to show unique and variable phenotypes, however, the relationship between phenotypic plasticity and gene expression pattern is not well understood. In Brassicaceae family, Cardamine flexuosa, a known allotetraploid whose parental species are C. amara and C. hirsuta, inhabits in wide range of environments encompassing wet and dry habitats. To understand the relationship between adaptation to the environment and gene expression pattern in these species, we will investigate phenotypic plasticity and gene expression profiles of these species grown in different water-related environments, both in field sites and laboratory conditions.

Kawasaki Group:
MAPK-mediated regulation of plant immunological memory

  • Research plan representative Tsutomu Kawasaki
    Professor, Graduate School of Agriculture Kindai University
    Collaborative researcher Koji Yamaguchi
    Assistant Professor, Graduate School of Agriculture Kindai University
    Tsutomu Kawasaki
    Tsutomu Kawasaki
    Recognition of pathogens with plant receptors rapidly induces a series of immune responses through activation of MAP kinase cascades. Plants can retain and recall the immunological memory, which enable cells to respond more rapidly and effectively to the pathogens that have been previously encountered. Although the memory is predicted to be associated with epigenetic regulation, the molecular mechanisms remain to be identified. Since the MAPK cascade plays important role in immune response, it is possible that the MAPK cascade may regulate the immunological memory through epigenetic control. In this study, we aim to elucidate the molecular mechanism of MAPK-mediated immunological memory in plants.

Kiba Group:
Molecular mechanisms and physiological roles of long-distance cytokinin transport

  • Research plan representative Takatoshi Kiba
    Research Scientist, RIKEN Center for Sustainable Resource Science
    Collaborative researcher Asami Osugi
    Postdoctoral Fellow, Graduate School of Bioagricultural Sciences, Nagoya Univ.
    Collaborative researcher Hitoshi Sakakibara
    Group Director, Graduate School of Bioagricultural Sciences, Nagoya Univ./ RIKEN Center for Sustainable Resource Science
    Takatoshi Kiba
    Takatoshi Kiba
    Plants maximize fitness by coordinating growth and development of organs such as the shoot and the root in response to environmental changes. Cytokinins have been implicated in the coordination acting as a long-distance signal translocated via vasculature. We aim at understanding mechanisms and physiological roles of the translocation. The project is organized into two tasks: (i) identification of the molecular basis underlying xylem loading of cytokinins and (ii) elucidation of the physiological role of root-to-shoot translocated cytokinins.

Kimura Group:
Studies on phenotypic plasticity on leaf shape of Rorippa aquatica

  • Research plan representative Seisuke Kimura
    Associate Professor, Department of Bioresource and Environmental Sciences, Kyoto Sangyo Universityy
    Collaborative researcher Kengo Morohashi
    Associate Professor, Department of Applied Biological Science, Tokyo University of Science
    Collaborative researcher Tomoaki Sakamoto
    Research Associate, Department of Bioresource and Environmental Sciences, Kyoto Sangyo University
    Collaborative researcher Yasunori Ichihasi
    Postdoctoral Fellow, RIKEN Center for Sustainable Resource Science
    Collaborative researcher Hokuto Nakayama
    Postdoctoral Fellow, Department of Plant Sciences, University of California, Davis
    Seisuke Kimura
    Seisuke Kimura
    Phenotypic plasticity is the ability of an organism to change its development and physiology depending on environmental conditions. Some plants demonstrate alterations in leaf form in response to changes in the environment, which is called heterophylly. Rorippa aquatica is a perennial herbaceous semiaquatic plant whose habitat is riparian area in North America. This plant shows heteropylly and develops pinnately dissected leaves under submerged conditions, while it forms simple leaves with serrated margins under terrestrial conditions. We also observed that leaf form is affected by ambient temperature and light intensity. We will investigate the mechanism of the heterophylly of R. aquatica, especially by focusing on the role of epigenetic regulation of gene expression and light sensing mechanism of plant.

Matsushita Group:
Light-regulated modulation of protein subcellular localization

  • Research plan representative Tomonao Matsushita
    Associate Professor, Faculty of Agriculture, Kyushu University
    Tomonao Matsushita
    Tomonao Matsushita
    It is widely believed that phytochrome regulates the transcription of light-responsive genes by modulating the activity of several transcription factors. However, we recently found that phytochrome controls not only transcription, but also other aspects of gene expression, to mediate light responses in Arabidopsis. The goal of this study is to reveal this novel mechanism of light-regulated gene exparession at a molecular level. Moreover, we try to investigate the possibility that, through this mechanism, plants may memorize protein subcellular localization patterns dependeing on the environmental light information.

Miura Group:
Elucidation of transcriptional regulation by sumoylation of histone

  • Research plan representative Kenji Miura
    Associate Professor, Faculty of Life and Environmental Sciences, University of Tsukuba
    Collaborative researcher Yasuomi Tada
    Professor, Graduate School of Science, Nagoya University
    Kenji Miura
    Kenji Miura
    Sumoylation, a post-translational modification, is involved in regulation of environmental stress responses and accumulation of salicylic acid. However, a comprehensive understanding how sumoylation regulates responses to environmental stresses and salicylic acid. In this study, the following points will be elucidated.
    1. To clarify the regulatory mechanism of methylated histone H3K4 by SUMO E3 ligase SIZ1.
    2. To clarify the mechanism how sumoylation of histone controls transcription in response to environmental stresses, such as cold stress, and accumulation of salicylic acid.

Nagano Group:
Development of quantification methods for plant memory under fluctuating environments.

  • Research plan representative Atsushi J. Nagano
    Associate Professor, Faculty of Agriculture, Ryukoku University
    Atsushi J. Nagano
    Atsushi J. Nagano
    How long do plants keep past information for their environmental responses under complex and fluctuating field environments? In other words, how long plants keep and use their memory of environmental signals? To investigate the plant memory of environments, quantitative methods to measure the memory are needed regardless of field or laboratory study. In this study, we develop methods quantify length and amplitude of the plant memory with using time series of environmental data, e.g. temperature, and time series of plant responses, e.g. transcriptome.

Notaguchi Group:
Study on systemic RNAs that respond to specific environments

  • Research plan representative Michitaka Notaguchi
    Postdoctoral Fellow, Graduate School of Science, Nagoya University
    Michitaka Notaguchi
    Michitaka Notaguchi
    This research aims to identify phloem-mobile RNAs that respond to specific environments, such as the level of available macronutrients, N, P and K under the soil conditions. Micrografting and RNA-Seq techniques will be applied for genome-wide identification of the mobile RNAs. Moreover, to investigate the dynamics of mobile RNAs at the whole plant level, a system to visualize RNA molecules in living plant tissues will be constructed and applied to the mobile RNAs.

Saijo Group:
Polycomb group protein-mediated control for immune activation and priming in plants

  • Research plan representative Yusuke Saijo
    Associate Professor, Graduate School of Biological Sciences Nara Institute of Science and Technology
    Collaborative researcher Yuri Tajima
    Designated Assistant Professor, Graduate School of Biological Sciences Nara Institute of Science and Technology
    Yusuke Saijo
    Yusuke Saijo
    In plants, pathogen recognition leads to immune activation through extensive transcriptional reprogramming in both challenged and distal unchallenged sites. This is followed by the establishment of defense priming, in which defense-related genes are poised for a greater and/or faster activation in response to second stimulation. Our findings indicate a positive role for both transcription-permissive and transcription-repressive histone modifications on defense-related genes and that for the polycomb group protein complex (PRC2) in defense priming in Arabidopsis. We pursue the mechanisms by which PRC2 promotes defense priming, with a focus on its role and mode of action in defense-related transcriptional reprogramming. We expect that these studies will deepen our understanding of how PRC2 modulates immune response and memory in plants.

Seki Group:
Analysis of antisense ncRNA-mediated plant environmental stress adaptation

  • Research plan representative Motoaki Seki
    Team Leader, RIKEN CSRS, Plant Genomic Network Research Team
    Collaborative researcher Akihiro Matsui
    Postdoctoral Fellow, RIKEN CSRS, Plant Genomic Network Research Team
    Motoaki Seki
    Motoaki Seki
    Recently, we demonstrated that abiotic stress-responsive antisense non-coding RNAs (ncRNAs) are synthesized from sense transcripts of protein-coding genes without the involvement of siRNA biosynthesis by RNA-dependent RNA polymerases (RDRs) and function in drought stress adaptation. In this study, we will identify novel genes involved in the biogenesis of the stress-responsive antisense ncRNAs, and elucidate the molecular mechanisms of the antisense ncRNAs-mediated plant environmental stress adaptation and memory.

Suzaki Group:
Systemic and local regulatory mechanisms of symbiotic organ formation in response to nitrogen

  • Research plan representative Takuya Suzaki
    Associate Professor, University of Tsukuba
    Collaborative researcher Masayoshi Kawaguchi
    Professor, National Institute for Basic Biology
    Takuya Suzaki
    Takuya Suzaki
    Root nodule symbiosis is a mutualistic interaction observed between mainly leguminous plants and nitrogen-fixing soil rhizobia, in which plants can obtain fixed atmospheric nitrogen, and provide rhizobia with photosynthate as a carbon source. In response to nitrogen amount in the soil, plants control the formation of root nodules: nodulation is significantly inhibited under nitrogen-abundant environment, whereas nitrogen-deficient condition promotes nodulation. In this research, we aim to elucidate the molecular mechanisms of the nitrogen-mediated control of nodulation, in which systemic and local regulatory mechanism are involved depending on each developmental stage of nodulation.

Takahashi Group:
Analysis of a small peptide-mediated long-distance signaling under water-deficit conditions

  • Research plan representative Fuminori Takahashi
    Postdoctoral Fellow, RIKEN Center for Sustainable Resource Science, Biomass Research Platform Team
    Collaborative researcher Kazuo Shinozaki
    Team Leader, RIKEN Center for Sustainable Resource Science, Biomass Research Platform Team
    Fuminori Takahashi
    Fuminori Takahashi
    Water-deficit response is an important and rapid mechanism of sensing and propagation of information about water status. It is thought that water-deficit signal is transmitted rapidly from roots to shoots and promotes abscisic acid (ABA), one of the plant hormones, accumulation in leaves. However, no long-distance signaling molecules that mediate root-to-shoot communication and trigger ABA accumulation in leaves have been identified.
    In this study, we focus on the small peptide mediating root-to-shoot signaling, and figure out both the transduction mechanism which the peptide regulates long-distance signaling and the perception mechanism which the receptors recognize peptide signaling under water-deficit conditions.

Takezawa Group:
Studies of integrated signaling pathways for ABA, low temperature and osmotic responses in bryophytes

  • Research plan representative Daisuke Takezawa
    Associate Professor, Graduate School of Science and Engineering, Saitama University
    Daisuke Takezawa
    Daisuke Takezawa
    Environmental signals such as desiccation, hyperosmosis and low temperature affect levels of the stress hormone abscisic acid (ABA), which plays a key role in protection of cells from stress-induced lethal damage. How different environmental signals as well as the ABA signal are integrated to control genes necessary for the cellular tolerance has not been understood. To elucidate mechanisms underlying autonomous responses of plant cells to various environmental stress signals, our study will focus on identification a signaling factor integrating stress signals by analysis of mutants of bryophytes. We will analyze interactions between the identified factors and known signaling factors to determine a series of processes necessary for integrative control of the signals.

Uchida Group:
Elucidation of phloem-derived signal in stem elongation

  • Research plan representative Naoyuki Uchida
    Designated Associate Professor, Institute of Transformative Bio-Molecules, Nagoya University,
    Naoyuki Uchida
    Naoyuki Uchida
    Two peptide hormones, EPFL4 and EPFL6, are secreted from the endodermis of inflorescence stems and perceived by their receptor, ERECTA (ER), at phloem companion cells. It is hypothesized that the activation of ER triggers production of unknown secondary signal in the phloem to promote stem elongation. In this project, I aim to elucidate the nature of this phloem-derived signal and also investigate how this signal affects behaviors of its target cells/tissues in the stem elongation.

Yamaguchi Group:
Molecular genetic analysis of JUMONJI-mediated heat acclimation in Arabidopsis for improvement of heat memory

  • Research plan representative Nobutoshi Yamaguchi
    Assistant Professor, Nara Institute of Science and Technology
    Nobutoshi Yamaguchi
    Nobutoshi Yamaguchi
    As sessile organisms, plants need to adapt to surrounding environmental changes for survival. Heat experience is memorized in plants to become responsive to future thermal stimuli. Histone modification is known to mediate the changes in gene expression over long timescale. Although acclimation to relatively high temperature enables plants to tolerate subsequent lethal conditions, little is known about a molecular basis of this regulation. We have found that histone demethylases, JUMONJI30 (JMJ30) and JMJ32, play an important role in heat acclimation in Arabidopsis. Based on a molecular genetic approach, we will establish a way for 'improvement of heat memory' in plants.