Department of Plant Production Sciences


FAX: +81-52-789-4064
Prof. TANIGUCHI, Mitsutaka D. Agr. taniguti@
Asst. Prof. OI, Takao D. Agr. oitaka@

Chloroplasts (red) and actin filaments (green) in mesophyll (M) and bundle sheath (BS) cells of finger millet, a C4 plant, as visualized by immuno-fluorescence confocal laser microscopy.

Plant resources are defined as various kinds of utilizable plants in addition to crop species. The research objective of this laboratory is to explore the structure, function and environmental responses of higher plants with the aid of experimental anatomy, electron microscopy and molecular biology for the basis of exploitation of plant resources. In recent years special efforts have been made for the differentiation mechanism of photosynthetic cells and epidermal cells in C4 plants.

The current research projects are;

  1. Mechanisms of chloroplast movement in response to environmental stresses
  2. Differential sensitivity of C4 photosynthetic cells to salinity stress
  3. Salt excretion mechanism from salt glands
  4. Mechanisms of metabolite transport across chloroplast envelope membranes

Recent publications:

  1. Oi T, Miyake H, Taniguchi M. (2014) Salt excretion through the cuticle without disintegration of fine structures in the salt glands of Rhodes grass (Chloris gayana Kunth). Flora 209: 185-190.
  2. Oi T, Hirunagi K, Taniguchi M, Miyake H (2013) Salt excretion from the salt glands in Rhodes grass (Chloris gayana Kunth) as evidenced by low-vacuum scanning electron microscopy. Flora 208: 52-57.
  3. Omoto E, Nagao H, Taniguchi M, Miyake H. (2013) Localization of reactive oxygen species and change of antioxidant capacities in mesophyll and bundle sheath chloroplasts of maize under salinity. Physiologia Plantarum 149: 1-12.
  4. Taniguchi M, Miyake H (2012) Redox-shuttling between chloroplast and cytosol: integration of intra-chloroplast and extra-chloroplast metabolism. Current Opinion in Plant Biology 15: 252-260.
  5. Maai E, Shimada S, Yamada M, Sugiyama T, Miyake H, Taniguchi M (2011) The avoidance and aggregative movement of mesophyll chloroplasts in C4 monocots in response to blue light and abscisic acid. Journal of Experimental Botany 62: 3213-3221.


FAX: +81-52-789-4017
Prof. NAKAZONO, Mikio D. Agr. nakazono@
Asst. Prof. TAKAHASHI, Hirokazu D. Agr. hiro_t@

The primary research objective of this laboratory is to study the principles of genetics and breeding of crop plants. For this purpose, we are trying to understand molecular and genetic mechanisms of shoot and root development in rice using mutants or natural variations as genetic resources. We also try to understand molecular mechanism of adaptation of crops to environmental stresses such as flooding and drought, with the aim of producing crops tolerant to these stresses.

Our recent research projects seek to understand

  1. The mechanisms of formation of aerenchyma and radial oxygen loss barrier, which contribute to flooding tolerance, in plant roots.
  2. The molecular and genetic mechanisms of shoot development and embryogenesis in rice.
  3. The molecular evolution of small RNAs in the rice genome.
  4. The molecular and genetic mechanisms of root development and root system development in rice and soybean
  5. QTL analysis of iron toxicity tolerance in rice.

Recent publications:

  1. Suzuki, M., Sato, Y., Wu, S., Kang, B. and McCartly, D.R. (2015) Conserved functions of the MATE transporter BIG EMBRYO 1 in regulation of lateral organ size and initiation rate. Plant Cell, 27: 2288-2300.
  2. Yamauchi, T., Shiono, K., Nagano, M., Fukazawa, A., Ando, M., Takamure, I., Mori, H., Nishizawa, N.K., Kawai-Yamada, M., Tsutsumi, N., Kato, K. and Nakazono, M. (2015) Ethylene biosynthesis is promoted by very-long-chain fatty acids during lysigenous aerenchyma formation in rice roots. Plant Physiology, 169: 180-193.
  3. Takahashi, H., Yamauchi, T., Rajhi, I., Nishizawa, N.K. and Nakazono, M. (2015) Transcript profiles in cortical cells of maize primary root during ethylene-induced lysigenous aerenchyma formation under aerobic conditions. Annals of Botany, 115: 879-894.
  4. Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R., Shitan, N., Nishizawa, N.K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014) RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). Plant Journal, 80: 40-51.
  5. Kulichikhin, K., Yamauchi, T., Watanabe, K. and Nakazono, M.: Biochemical and molecular characterization of rice (Oryza sativa L.) roots forming a barrier to radial oxygen loss. (2014) Plant, Cell & Environment, 37: 2406-2420.
  6. Yamauchi, T., Watanabe, K., Fukazawa, A., Mori, H., Abe, F., Kawaguchi, K., Oyanagi, A. and Nakazono, M. (2014) Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions. Journal of Experimental Botany, 65: 261-273.
  7. Ishiwata, A., Ozawa, M., Nagasaki, H., Kato, M., Noda, Y., Yamaguchi, T., Nosaka, M., Shimizu-Sato, S., Nagasaki, A., Maekawa, M., Hirano, H. and Sato, Y. (2013) Two WUSCHEL- related homeobox genes, narrow leaf2 and narrow leaf3, control leaf width in rice. Plant and Cell Physiology 54: 779-792.
  8. Nosaka, M., Ono, A., Ishiwata, A., Shimizu-Sato, S., Ishimoto, K., Noda, Y. and Sato, Y. (2013) Expression of the rice microRNA miR820 is associated with epigenetic modifications at its own locus. Genes & Genetic Systems, 88: 105-112.
  9. Nosaka, M., Itoh, J., Nagato, Y., Ono, A., Ishiwata, A. and Sato, Y. (2012) Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genetics, 8: e1002953.
  10. Tabuchi, H., Zhang, Y., Hattori, S., Omae, M., Shimizu-Sato, S., Oikawa, T., Qian, Q., Nishimura, M., Kitano, H., Xie, H., Fang, X., Yoshida, H., Kyozuka, J., Chen, F. and Sato, Y. (2011) LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems. Plant Cell, 23: 3276-3287.


  FAX: +81-52-789-5558
Prof. KONDO, Motohiko D. Agr. chokai@
Assoc. Prof. YANO, Katsuya D. Agr. kyano@
Asst. Prof. SUGIURA, Daisuke D. Sci. dsugiura@

Our research interest covers physiology and ecology of crop plants at various scales from the molecular to the field level. Our goal is to improve crop yields establishing sustainable agriculture.

Our major research focus are;

  1. Sink-source relationship
  2. Crop response to environment, such as elevated atmospheric CO2
  3. Crop-microorganisms symbiosis
  4. Nutrient acquisition mechanisms by root system

Recent publications:

  1. Kondo M., Maeda H., Goto A., Nakano H., Kiho N., Makino T., Sato M., Fujimura S., Eguchi T., Hachinohe M., Hamamatsu S., Ihara H., Takai T., Arai-Sanoh Y. and Kimura T. (2015) Exchangeable Cs/K ratio in soil is an index to estimate accumulation of radioactive and stable Cs in rice plant. Soil Sci. Plant Nutr. 61: 133-143.
  2. Kondo M., Makino T., Eguchi T., Goto A., Nakano H., Takai T., Arai-Sanoh Y. and Kimura T. (2015) Comparative analysis on relationship between Cs and K in soil and plant parts toward control of Cs accumulation in rice. Soil Sci. Plant Nutr. 61: 144-151.
  3. Ohsumi A., Takai T., Ida M., Yamamoto T., Arai-Sanoh Y., Yano M., Ando T. and Kondo M. (2011) Evaluation of yield performance in rice near-isogenic lines with increased spikelet number. Field Crop. Res. 120: 68-75.
  4. Laza M.R., Kondo M., Ideta O., Barlaan E. and Imbe T. (2010) Quantitative trait loci for stomatal density and size in lowland rice. Euphytica 172: 149–158.
  5. Sekiya, N., Araki, H. and Yano, K. (2011) Applying hydraulic lift in an agroecosystem: forage plants with shoots removed supply water to neighboring vegetable crops. Plant Soil 341, 39-50.
  6. Sekiya, N. and Yano, K. (2010) Seed P-enrichment as an effective P supply to wheat. Plant Soil 327, 347-354.
  7. Sekiya, N. and Yano, K. (2008) Stomatal density of cowpea correlates carbon isotope discrimination in different phosphorus, water and Co2 environments. New Phytol. 179, 799-807.


Fax: +81-52-789-4022
Prof. YAMAUCHI, Akira D. Agr. ayama@
Lecturer MITSUYA, Shiro D. Agr. mitsuya@
Des. Asst. Prof. NAKATA, Mana D. Agr. mnakata@

Plant root is equipped with various structures that regulate water and solute movement from soil to root and within a root.

Our main research interests currently lie in the plant-root relationship with special emphasis on the development and function of plant root. Resource cycling in biosphere is inherently regulated by the roots that constitutes an interface between plants and soils. Understanding biological, chemical and physical processes of the relationship is essential for the fundamentals for crop production and soil environmental management.

Specifically, the following research subjects are now being studied;

Abiotic tolerance of crop plants like drought, O2 deficiency, soil moisture fluctuation, nutrient deficiency.
Developmental and physiological responses of roots to environmental stresses. Genetic basis for root system development and function using chromosome segment substitution line and mutant.
Anatomical, developmental and physiological bases for water flow from soil to roots and within a root.
Industrial waste utilization for sustainable crop production and soil management.
International research collaborations are in progress with several institutions like International Rice Research Institute, PhilRootcrop, Leyte State University in the Philippines.

Recent Publications:

  1. Ogawa, A. and A. Yamauchi 2006. Root Osmotic Adjustment under Osmotic Stress Conditions in Maize Seedlings. 1. Transient response of growth and water relations in roots to osmotic stress. Plant Production Science 9 (1): 27-38.
  2. Wang, H. and A. Yamauchi. 2006. Growth and Function of Roots under Abiotic Stress in Soil. In Plant-Environment Interactions (3rd) (ed. Huang, B.). CRC Press, New York. pp. 271-320.
  3. Siopongco, J. D. L. C., K. Sekiya, A. Yamauchi, J. Egdane, A. M. Ismail and L. J. Wade. 2008. Stomatal Responses in Rainfed Lowland Rice to Partial Soil Drying; Evidence for Root Signals. Plant Production Science. 11: 28-41.
  4. Suralta, R. R. and Yamauchi, A. 2008. Root growth, aerenchyma development, and oxygen transport in rice genotypes subjected to drought and waterlogging. Environmental and Experimental Botany 64:75–82.
  5. Suralta, R. R., Inukai Y. and Yamauchi, A. 2008. Utilizing chromosome segment substitution lines (CSSLs) for evaluation of root responses under transient moisture stresses in rice. Plant Production Science 11: 457-465.
  6. Wang, H., Siopongco, J. D. L. C, Wade, L. J. and Yamauchi, A. 2009. Fractal Analysis on Root Systems of Rice Plants in Response to Drought Stress. Environmental and Experimental Botany. 65: 338-344.


  FAX: +81-52-789-4025
Prof. MATSUMOTO, Shogo D. Sci. shogo@
Assoc. Prof. SHIRATAKE, Katsuhiro D. Agr. shira@
Lecturer OTAGAKI, Shungo D. Agr. sotagaki@
Asst. Prof. NOTAGUCHI, Michitaka D. Sci.  

Molecllar Approach to The Mechanism of Sugar Accumulation in Rasaceae Fruit

Growth and development of horticultural crops are studied for their practical application, covering pomology, vegetable crop science, floricultural science and postharvest physiology. We identify genes, which relate to important traits of horticultural crops as followings and clarify their physiological functions by biochemical and molecular biological techniques. We produce genetically modified plants of the genes.

  1. Self-incompatibility of Rosaceae family
  2. Molecular mechanisms in the reproductive/nutritional growth of Rosaceae family
  3. Coloration mechanism and effective breeding of Rosaceae family using DNA marker
  4. Long distance sugar transport and sugar metabolism in Rosaceae fruit trees, such as apple, peach and pear. (Enzyme for sorbitol metabolism, Sorbitol transporter)
  5. Functional study of transporters (aquaporin, sugar transporter, ABC transporter) in horticultural crops
  6. Molecular breeding of floricultural crops
  7. Omics study of fruits (genomics, transcriptomics, proteomics, metabolomics, ionomics)
  8. Genome editing of genes related to important traits of horticultural crops

Key Words: Omics study, Genome editing, Epigenetics, Molecular breeding, DNA marker

Recent Publications:

  1. Azuma M., Morimoto R., Hirose M., Morita Y., Hoshino A., Iida S., Oshima Y., Mitsuda N., Ohme-Takagi M. and Shiratake K. (2015) A petal-specific InMYB1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops. Plant Biotechnol. J. Accepted (10.1111/pbi.12389)
  2. Otagaki S., Ogawa Y., Oyant L. H., Foucher F., Kawamura K., Horibe T. and Matsumoto S. (2015) Genotype of FLOWERING LOCUS T homologue contributes to the flowering time differences in wild and cultivated roses. Plant Biology 17: 808-815.
  3. Suzuki M., Nakabayashi R., Ogata Y., Sakurai N., Tokimatsu T., Goto S., Suzuki M., Jasinski M., Martinoia E., Otagaki S., Matsumoto S., Saito K. and Shiratake K. (2015) Multi omics in grape berry skin revealed specific induction of stilbene synthetic pathway by UV-C irradiation. Plant Physiol. 168: 47-59.
  4. Nakajima R., Otagaki S., Shiratake K. and Matsumoto S. (2015) Energy-saving seedling production system for super-forcing cultivation of June-bearing commercial strawberry. HortScience 50: 685-687.
  5. Hamada Y., Sato H., Otagaki S., Okada K., Abe K. and Matsumoto S. (2015) Breeding depression of red flesh apple progenies containing both functional MdMYB10 and MYB110a_JP genes. Plant Breeding 134: 239-246.
  6. Reuscher S., Akiyama M., Yasuda T., Aoki K., Shibata D. and Shiratake K. (2014) The sugar transporter inventory of tomato: Genome-wide identification and expression analysis. Plant Cell Physiol. 55: 1123-1141.
  7. Nakajima R., Otagaki S., Yamada K., Shiratake K. and Matsumoto S. (2014) Molecular cloning and expression analysis of FaFT, FaTFL and FaAP1 genes in cultivated strawberry: their correlation to flower bud formation. Biologia plantarum. 58: 641-648.
  8. Reuscher S., Akiyama M., Mori C., Aoki K., Shibata D. and Shiratake K. (2013) Genome-wide identification and expression analysis of aquaporins in tomato. PLoS ONE. 8: e79052.
  9. Nashima K., Shimizu T., Nishitani C., Yamamoto T., Takahashi H., Nakazono M., Itai A., Isuzugawa K., Hanada T., Takashina T., Matsumoto S., Otagaki S., Oikawa A. and Shiratake K. (2013) Microarray analysis of gene expression patterns during fruit development in European pear (Pyrus communis). Scientia Horticulturae. 164: 466–473.
  10. Umemura H., Otagaki S., Wada M., Kondo S. and Matsumoto S. (2013) Expression and functional analysis of a novel MYB gene, MdMYB110a_JP, responsible for red flesh, not skin color in apple fruit. Planta 238: 65-76.


  FAX: +81-52-789-4029
Prof. KAWAKITA, Kazuhito D. Agr. kkawakit@
Assoc. Prof. TAKEMOTO, Daigo D. Agr. dtakemo@
Des. Assoc. Prof. CHIBA, Sotaro D. Agr. chiba@
Asst. Prof. SATO, Ikuo D. Agr. isato@

Our research group focuses on the molecular mechanisms of plant disease resistances against fungal and oomycete pathogens. We are working in particular on interaction between oomycete pathogen Phytophthora infestans and Solanaceae species. To elucidate the molecular and cellular basis of the plant-microbe interactions, we are aiming to identify and characterize genes involved in effective defense responses. Especially, we are tiring to understand the role of reactive oxygen species (ROS) and nitric oxide (NO) in disease resistance.
We also investigate the symbiotic interaction between perennial ryegrass and endophytic fungi Epichloë festucae. Recent studies have shown that the infection of this symbiotic fungi improves plant tolerance to a range of biotic and abiotic stresses, including drought, disease, and animal herbivory.
The ultimate goal of our research is to develop strategies to prevent plant diseases through the better understanding of the molecular basis of plant-microbe interactions.

The recent research projects are as follows:

  1. Characterization of genes involved in NO production in plant disease resistance.
  2. Purification and characterization of elicitors derived form P. infestans.
  3. Identification of proteins modified by NO in disease resistance.
  4. Imaging of plant-microbe interactions with GFP and modified fluorescence proteins.
  5. Identification and characterization of the genes from symbiotic fungi required initiating and maintaining mutualistic association with host plant.

Recent publications:

  1. Takemoto D., Rafiqi M., Hurley U., Lawrence G.J., Bernoux M., Hardham A.R., Ellis J.G., Dodds P.N. and Jones D.A. (2012) N-Terminal motifs in some plant disease resistance proteins function in membrane attachment and contribute to disease resistance. Mol. Plant-Microbe Interact. 25: 379-392.
  2. Takemoto D., Kamakura S., Saikia S., Becker Y., Wrenn R., Tanaka A., Sumimoto H. and Scott B. (2011) Polarity proteins Bem1 and Cdc24 are components of the filamentous fungal NADPH oxidase complex. Proc. Nat. Acad. Sci. USA 108: 2861-2866.
  3. Shibata Y., Kawakita K. and Takemoto D. (2011) SGT1 and HSP90 are essential for age-related non-host resistance of Nicotiana benthamiana against the oomycete pathogen Phytophthora infestans. Physiol. Mol. Plant Pathol. 75: 120-128.
  4. Shibata Y., Kawakita K. and Takemoto D. (2010) Age-related resistance of Nicotiana benthamiana against hemibiotrophic pathogen Phytophthora infestans requires both ethylene- and salicylic acid-mediated signaling pathways. Mol. Plant-Microbe Interact. 23: 1130-1142.
  5. Uruma S., Shibata Y., Takemoto D. and Kawakita K. (2009) N,N-dimethylsphingosine, an inhibitor of sphingosine kinase, induces phytoalexin production and hypersensitive cell death of Solanaceae plants without generation of reactive oxygen species. J. Gen. Plant Pathol. In press.
  6. Kato H., Asai S., Yamamoto-Katou A., Yoshioka H., Doke N. and Kawakita K. (2008) Involvement of NbNOA1 in NO production and defense responses in INF1-treated Nicotiana benthamiana. J. Gen. Plant Pathol. 74: 15-23.
  7. Yamamizo C., Doke N., Yoshioka H. and Kawakita K. (2007) Involvement of mitogen-activated protein kinase in the induction of StrbohC and StrbohD genes in response to pathogen signals in potato. J. Gen. Plant Pathol. 73: 304-313.
  8. Takemoto D., Tanaka A., and Scott B. (2006) A p67Phox-like regulator recruited to control hyphal branching in a fungal-plant mutualistic symbiosis. Plant Cell 18: 2807-2821.
  9. Yamamoto-Katou, A., Katou, S., Yoshioka, H., Doke, N. and Kawakita, K. (2006) Nitrate reductase is responsible for elicitin-induced nitric oxide production in Nicotiana benthamiana. Plant Cell Physiol. 47: 726-735.
  10. Saito, S., Yamamoto-Katou, A., Yoshioka, H., Doke, N. and Kawakita, K. (2006) Peroxynitrite generation and tyrosine nitration in defense responses in tobacco BY-2 cells. Plant Cell Physiol. 47: 689-697.


  FAX: +81-52-789-4283
Assoc. Prof. YOSHIOKA, Hirofumi D. Agr. hyoshiok@

The main focus of our research is to understand the molecular mechanisms of plant immune system in plant-pathogen interactions. One of our goals is to produce genetically engineered plants showing disease resistance in such a way as to reduce the use of environmentally damaging fungicides.

Current themes:

  1. Regulatory mechanisms of NADPH oxidase and role of ROS in plant immunity.
  2. Regulatory mechanisms of NO production and its role in plant immunity.
  3. Downstream signaling pathway of defense-related MAP kinase cascades.
  4. Production of transgenic potato plants showing resistance to Phytophthora infestans.
  5. Signaling pathway of host-selective toxin produced by a plant pathogenic fungus.
  6. Defense mechanisms between herbivore and plant interactions.

Selected publications:

  1. Kobayashi, M., Ohura, I., Kawakita, K., Yokota, N., Fujiwara, M., Shimamoto, K., Doke, N. and Yoshioka, H. (2007) Calcium-dependent protein kinases regulate production of reactive oxygen species by potato NADPH oxidase. Plant Cell 19, 1065-1080.
  2. Asai, S., Ohta, K. and Yoshioka, H. (2008) MAPK signaling regulates nitric oxide and NADPH oxidase-dependent oxidative bursts in Nicotiana benthamiana. Plant Cell 20, 1390-1406.
  3. Ishihama, N., Yamada, R., Yoshioka, M., Katou, S. and Yoshioka, H. (2011) Phosphorylation of the Nicotiana benthamiana WRKY8 transcription factor by MAPK functions in the defense response. Plant Cell 23, 1153-1170.
  4. Kobayashi, M., Yoshioka, M., Asai, S., Nomura, H., Kuchimura, K., Mori, H., Doke, N. and Yoshioka, H. (2012) StCDPK5 confers resistance to late blight pathogen but increases susceptibility to early blight pathogen in potato via reactive oxygen species burst. New Phytol. 196, 223-237.
  5. Nomura, H., Komori, T., Uemura, S., Kanda, Y., Shimotani, K., Nakai, K., Furuichi, T., Takebayashi, K., Sugimoto, T., Sano, S., Suwastika, I.N., Fukusaki, E., Yoshioka, H., Nakahira, Y. and Shiina, T. (2012) Chloroplast-mediated activation of plant immune signalling in Arabidopsis. Nature Commun. 3, 926.
  6. Asai, S., Ichikawa, T., Nomura, H., Kobayashi, M., Kamiyoshihara, Y., Mori, H., Kadota, Y., Zipfel, C., Jones, J.D.G. and Yoshioka, H. (2013) The variable domain of a plant calcium-dependent protein kinase (CDPK) confers subcellular localization and substrate recognition for NADPH oxidase. J. Biol. Chem. 288, 14332-14340.
  7. Yamaguchi, K., Yamada, K., Ishikawa, K., Yoshimura, S., Hayashi, N., Uchihashi, K., Ishihama, N., Kishi-Kaboshi, M., Takahashi, A., Tsuge, S., Ochiai, H., Tada, Y., Shimamoto, K., Yoshioka, H. and Kawasaki, T. (2013) A receptor-like cytoplasmic kinase targeted by a plant pathogen effector is directly phosphorylated by the chitin receptor and mediates rice immunity. Cell Host Microbe 13, 347-357.
  8. Mase, K., Ishihama, N., Mori, H., Takahashi, H., Kaminaka, H., Kodama, M. and Yoshioka, H. (2013) Ethylene responsive AP2/ERF transcription factor MACD1 participates in phytotoxin-triggered programmed cell death. Mol. Plant-Microbe Interact. 26, 868-879.
  9. Le Roux, C., Huet, G., Jauneau, A., Camborde, L., Trémousaygue, D., Kraut, A., Zhou, B., Levaillant, M., Adachi, H., Yoshioka, H., Raffaele, S., Berthomé, R., Couté, Y., Parker, J.E. and Deslandes, L. (2015) A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell 161, 1074-1088.
  10. Adachi, H., Nakano, T., Miyagawa, N., Ishihama, N., Yoshioka, M., Katou, Y., Yaeno, T., Shirasu, K. and Yoshioka, H. (2015) WRKY transcription factors phosphorylated by MAPK regulate a plant immune NADPH oxidase in Nicotiana benthamiana. Plant Cell 27, 2645-2663.


Tel: +81-561-38-4473
Assoc. Prof. DOI Kazuyuki Ph. D (Agronomy) kdoi@
Asst. Prof. NISHIUCHI Shunsaku Ph. D (Agronomy) s_nishi@

The plot for rice nested association mapping population. The population consists of >2000 lines from >20 cross combinations and all lines are genotyped by using NGS. Genotype (DNA) and trait information are combined and statistically analyzed for discovering useful genes.

Our research focuses on the plant genetic diversity, the interactions betweenplant and their environments, and the application of our research findings to improve agricultural productivity and raise labor efficiency, especially in rice and its production. The genomic sequence of rice greatly facilitated the molecular cloning of rice genes, discovered from both mutants and naturally occurring variation. This enabled us to know the genetic variation in the nucleotide sequence level. Our target is to develop genetic methods and materials for discovering and utilizing the potential useful genes hidden in germplasm collections. Recently we are interested in the use of next-generation DNA sequencer and field informatics (small devices for data correction) for large-scale genetic analysis.

Recent Publications:

  1. Kurokawa Y., T. Noda, Y. Yamagata, R. Angeles-Shim, H. Sunohara, K. Uehara, T. Furuta, K. Nagai, K.K. Jena, H. Yasui, A. Yoshimura, M. Ashikari and K. Doi (2015) Construction of a versatile SNP array for pyramiding useful genes of rice. Plant Sci. doi:10.1016/j.plantsci.2015.09.008
  2. Shiono K., M. Ando, S. Nishiuchi, H. Takahashi, K. Watanabe, M. Nakamura, Y. Matsuo, N. Yasuno, U. Yamanouchi, M. Fujimoto, H. Takanashi, K. Ranathunge, R. Franke, N. Shitan, N.K. Nishizawa, I. Takamure, M. Yano, N. Tsutsumi, L. Schreiber, K. Yazaki, M. Nakazono and K. Kato (2014) RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). Plant Journal, 80: 40-51
  3. Wada, T., H. Yasui, T. Inoue, M. Tsubone, T. Ogata, K. Doi, A. Yoshimura and Y. Matsue (2013) Validation of QTLs for eating quality of japonica rice ‘Koshihikari’ using backcross inbred lines. Plant Prod. Sci. 16: 131-140.
  4. Nishiuchi S., T. Yamauchi, H. Takahashi, L. Kotula and M. Nakazono (2012) Mechanisms for coping with submergence and waterlogging in rice. Rice, 5, 2.
  5. N. Takano-Kai, K. Doi and A. Yoshimura (2011) GS3 participates in stigma exsertion as well as seed length in rice. Breed. Sci. 61: 244-250.
  6. A. Yoshimura, H. Nagayama, Sobrizal, T. Kurakazu, P.L. Sanchez, K. Doi, Y. Yamagata and H. Yasui (2010) Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng. Breed. Sci. 60: 597-603.
  7. D. Fujita, K. Doi, A. Yoshimura and H. Yasui (2010) A major QTL for resistance to green rice leafhopper (Nephotettix cincticeps Uhler) derived from African rice (Oryza glaberrima Steud.). Breed. Sci. 60: 336-341.
  8. M. Ikeda, Y. Hirose, T. Takashi, Y. Shibata, T. Yamamura, T. Komura, K. Doi, M. Ashikari, M. Matsuoka and H. Kitano (2010) Analysis of rice panicle traits and detection of QTLs using an image analyzing method. Breed. Sci. 60: 55-64.
  9. Y. Yamagata, E. Yamamoto, K. Aya, K.T. Win, K. Doi, Sobrizal, T. Ito, H. Kanamori, J. Wu, T. Matsumoto, M. Matsuoka, M. Ashikari, A. Yoshimura (2010) Mitochondrial gene in the nuclear genome induces reproductive barrier in rice. Proc. Natl. Acad. Sci. U.S.A. 107: 1494-1499.
  10. N. Takano-Kai, H. Jiang, T. Kubo, M. Sweeney, T. Matsumoto, H. Kanamori, B. Padhukasahasram, C. Bustamante, A. Yoshimura, K. Doi and S. McCouch (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182: 1323-1334.


  FAX: +81-52-789-4042
Prof. SHOGENJI, shinichi D. Agr. ashogen@
Assoc. Prof. TAKESHITA, Hironobu D. Agr. awa@
Asst. Prof. MIURA, Satoshi M. Agr. miuranet@

Socioeconomic science of food production concerns the economic and managerial aspects of agriculture and rural resources. Agricultural production systems are studied with stress on the compatibility of ecological balance and vitality of rural society. Those must be efficient in the sense not only of the market systems but also of non-monetary systems such as shadow works and communal cooperation. For this purpose, studies are carried out on relations between natural and historical characteristics of agriculture in a region and the relation between a nation and the world economy.

Main investigating topics currently are listed below:

  1. Relations between national food situation and structural change in agriculture
  2. Economy and ecology towards sustainable agriculture
  3. Rural resources management towards sustainable development

Recent Publications:

  1. Kazunori Awaji (2012) The Development of Renewable Energy in Germany. Noson to Toshi wo Musubu, 62(2), 23-35.
  2. Kazunori Awaji (2012) Feed and Animal Products: Two Certification Systems. Dairyman, 62(4), 40-41
  3. Kazunori Awaji (2011) Utilization of the out grading agricultural products for feed. Japanese Journal of Farm Management, 49(3), 37-42.
  4. Isao KITO, Kazunori AWAJI, Satoshi MIURA (2011) Large Scale Rice Farm’s Strategy for Weed Working in Hilly and Mountainous Area. Japanese Journal of Farm Management, 49(3), 67-72.
  5. Shinichi Shogenji (2011) A Community-Based Model of Rural Recovery, The Tokyo Foundation (website).
  6. Shinich Shogenji (2010) Role of consumer Co-ops in the Japanese Food System. The Consumer Co-operative Institute of Japan eds., Toward Contemporary Co-operative Studies, 207-222.
  7. Yusuke Ozaki, Keigo Anmen, Kazunori Awaji, Satohi Miura (2010) A Study on Self-utilization of Bioethanol. Journal of Rural Economics (Special Issue 2010), 199-203.
  8. Takuya Miyano, Kazunori Awaji, Satohi Miura (2010) Significance and Issue on Sale of Byproduct and Transport of Unhulled Feed Rice. Journal of Rural Economics (Special Issue 2010), 121-125.
  9. Isao Kito, Kazunori Awaji, Satoshi Miura (2010) Cost and Strategy of weeding Work in a Large Scale Rice Farm. Journal of Rural Economics (Special Issue 2010), 62-68.
  10. Isao KITO, Kazunori AWAJI, Satoshi MIURA (2010) Evaluation of Weeding Work Cost on Paddy Field Levees in the Hillside. Japanese Journal of Farm Management, 48(1), 67-72.


  FAX: +81-52-789-5214
Prof. ASHIKARI, Motoyuki D. Agr. ashi@
Asst. Prof. NAGAI, Keisuke D. Agr. nagai.k@

Research theme
Habitat expansion is an important adaptational strategy of living organisms to survive unfavorable environments. However, overcoming adverse environmental conditions is not easy for plants due their sedentary nature. To overcome this constraint, plants evolve and gain new functions to fit in severely inhospitable environments and survive adverse conditions.
In understanding the different adaptational responses of plants to adverse environments, the production and analysis of loss-of-function mutants have been an essential tool. In the case of rice, for example, many mutants have been identified. However, insights into the possible multitude of traits present in many species of rice have been limited instead to the study of characters that are present in rice cultivars. In 10,000 years of crop domestication, cultivars have evolved through human selection of crops for important agronomic characters including non-shattering (i.e. of grains), high production and non-dormancy. Due to such focus of selection, many important characters including stress tolerance and disease resistance that are present in wild species have been lost. Particularly in rice, many wild species have important and unique characters that cultivars do not have. It is on this fact that I founded my belief that rice cultivars are mutants and the wild rice species are wild types.
The genus Oryza has 24 species (22 wild rice species + 2 cultivated species) distributed all over Asia, North Africa, South Africa and Australia. Each of the 22 wild rice species has its own adaptation to its native environment. Comparison of wild rice species and cultivars can provide us with insights into the unique characters present in wild rice but not in the cultivars. To date, several important characters that confer fitness to adverse conditions in wild rice have been identified. Some of these characters use plant hormone signaling for adaptation. Our laboratory aims at elucidating the mechanistic role of plant hormones in the environmental adaptation and survival of plants.

Representative papers

Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E. R., Qian, Q., Kitano, H. and Matsuoka, M. (2005) Cytokinin oxidase regulates rice grain production. Science 309, (5735) 741-745.
Ueguchi-Tanaka*, M., Ashikari*, M., Nakajima, M*., Itoh, H., Katoh, E., Kobayashi, M., Chow, T.-Y., Hsing, Y. C., Kitano, H., Yamaguchi, I. and Matsuoka, M. (2005) GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437, (7059) 693-698. *:Equal contribution
Sasaki, A., Itoh, H., Gomi, K., Ueguchi-Tanaka, M., Ishiyama, K., Kobayashi, M., Jeong, D.H., An, G., Kitano, H., Ashikari, M. and Matsuoka, M. (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299, (5614) 1896-1898.
Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G. S., Kitano, H. and Matsuoka, M. (2002) A mutant gibberellin-synthesis gene in rice. Nature 416, (6882) 701-702.

Lab. Members

Professor: Motoyuki Ashikari
Postdoc: Kotaro Miura
Postdoc: Yoko Hattori
Postdoc: Xianjun Song
Ph.D student (D3): Kenji Asano
Ph.D student (D2): Eiji Yamamoto
Ph.D student (D1): Rosalyn Shim
MS student (M2): Keisuke Nagai
MS student (M1): Chihiro Sato
Undergraduate student: Shizuka Furukawa
Undergraduate student: Atsushi Matsubara
Technical staff: Midori Ito
Technical staff: Kiyomi Sakata


Prof. MATSUOKA, Makoto D. Agr. makoto@
Assoc. Prof. SAZUKA, Takashi D. Sci. sazuka@

<Research theme>
The compact nature of the rice genome provides a distinct advantage in gene isolation and genomic sequencing in contrast to other cereal crops. Further, the rice genome shows apparent syntenies with many other cereal crops, such as wheat, barley, and maize. These syntenies suggest that rice genomics has implications not only for rice genetic studies and breeding but also for other crops. For these reasons, rice has been selected as a target species for genome research by a number of groups, and finally the International Rice Genome Sequencing Project (IRGSP) was launched in 1998 with ten countries participating (Sasaki and Burr, 2000). In 2004, IRGSP declared the completion of whole sequence of rice genome, which provides us very powerful information for studying rice biology. Taking this advantage and also other advantages on rice biology, such as tagging libraries, transformation techniques, and full-length cDNA clones, we have been studying biosynthesis and signal transduction mechanisms of gibberellin (GA) from the viewpoint of molecular breeding.
Because dwarf characteristics are favored in plant breeding, many rice dwarf mutants have been identified and some have been used in analysis of GA. The sd1 mutant is a good example that rice GA-related mutants contribute the progress on basic science and breeding program. This mutant enabled a dramatic increase in rice yield and significant contribution to global food security in the 1960s, which is referred to as the “green revolution” (Khush 1999). We identified the SD1 gene and revealed that that gene encodes GA20 oxidase catalyzing the late steps for GA biosynthesis (Nature, 2002). We have also performed large screening of dwarf mutants concerning GA, and have used them to analyze the biosynthetic and signal transduction pathways for these hormones (e.g. PNAS, 2000; Plant Cell, 2000, 2003, 2005; Science, 2003; Nature, 2005).
As most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations, we have also performed the QTL analysis of some important agronomical traits in order to use these QTL genes for rice molecular breeding. We have developed a high-throughput genome typing system. Using this system, we showed that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailor-made crop improvement (Science, 2005; Trend Plant Sci, 2006).

<Representative papers>

  1. Hirano, K., Asano, K., Tsuji, H., Kawamura, M., Mori, H., Kitano, H., Ueguchi-Tanaka, M. and Matsuoka M. (2010) Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice. Plant Cell 22, (8) 2680-2696.
  2. Asano, K., Yamasaki, M., Taku, S., Miur,a K., Katagir,i S., Ito, T., Do, K., Wu, J., Ebana, K., Matsumoto, T., Innan, H., Kitano, H., Ashikari, M., Matsuoka M. (2011) Artificial selection for a green revolution gene during japonica rice domestication. Proc. Natl .Acad. Sci. U S A 108, (27) 11034-11039.
  3. Hirano, K., Kouketu, E., Katoh, H., Aya, K., Ueguchi-Tanaka, M., Matsuoka M. (2012) The suppressive function of the rice DELLA protein SLR1 is dependent on its transcriptional activation activity. Plant J. 71, (3) 443-453.
  4. Tanaka, J., Yano K., Aya, K., Hirano, K., Takehara, S., Koketsu, E., Ordonio, RL., Park, SH., Nakajima, M., Ueguchi-Tanaka, M., Matsuoka M. (2014) Antheridiogen determines sex in ferns via a spatiotemporally split gibberellin synthesis pathway. Science. 2014 Oct 24;346(6208):469-473. doi: 10.1126/science.1259923.
  5. Yano, K., Aya, K., Hirano, K., Ordonio, RL., Ueguchi-Tanaka, M., Matsuoka M.  (2015) Comprehensive Gene Expression Analysis of Rice Aleurone Cells: Probing the Existence of an Alternative Gibberellin Receptor(s). Plant Physiol. 2015 Feb;167(2):531-544. doi: 10.1104/pp.114.247940. Epub 2014 Dec 15.

<Lab. Members>

Professor: Makoto Matsuoka
Associate Professor: Takashi Sazuka
Postdoc: Akihiro Fujii
Ph.D student (D3): Tsuyoshi Tanaka
Ph.D student (D3): Kenji Yano
MS student (M2): Takahiro Iida
MS student (M2): Keijirou Kurami
MS student (M2): Hideyuki Takeuchi
MS student (M2): Kenshirou Nakamura
MS student (M2): Miki Yamaguchi
MS student (M1): Hu Li
MS student (M1): Keiichi Nakagawa
MS student (M1): Tamon Wada
Undergraduate student: Shinnosuke Okamura


  FAX: +81-52-789-5226
Prof. KITANO, Hidemi D. Agr. hdkitano@
Assoc. Prof. UEGUCHI-TANAKA, Miyako D. Agr. mueguchi@

Fig. 1 Branching pattern of the ear

Fig.2 Structure of GID1

<Research theme>
Our laboratory, targeting rice—one of the three major cereals in the world—, is developing, collecting and preserving resources useful in research as well as conducting research to elucidate, at the molecular level, the biological mechanism of expressed phenotype of various rice mutants, with the aim of applying the findings to rice production. Also, we collaborate with relevant research fields and institutions within and outside the university and have recently embarked on the research on the development of high-yield rice that would realize increased food production and stable food supply in the world.
(1) Development, collection and preservation of bio-resources for research
Mutants are useful for efficiently conducting genetic and biological research in plants. Our laboratory has been preparing for future research by creating, collecting and preserving thousands of mutant lines, many of which are morphological mutants in rice. Some of these stock mutants were published in the National Bio-Resource Project (2002–06) of the Ministry of Education, Culture, Sports, Science and Technology. We also have participated in the second term of the project since 2007 and have mainly been involved in research on the character assessment in wild rice.
(2) Search for and utilization of genes that control ear type
The ear of rice has a complex structure consisting of many branches. The number of grains—one of the yield components in rice—is believed to be controlled by the branching pattern of the ear (Fig.1). Focusing on the ear-branching structure of high-yield rice varieties, we have been searching for useful genes that control the branching pattern using the hybrids of varieties with significantly different ear types by quantitative trait loci (QLT) analysis.
(3) New strategy for designing of next-generation plant growth regulators
Gibberellins (GAs) are a large family of tetracyclic diterpenoid plant hormones that induce a wide range of plant growth responses. Our recent work using the X-ray analysis revealed that GA receptor, GID1, has the structure which resembles the hormone-sensitive lipases (HSLs), and its GA-binding pocket corresponds to the substrate-binding site of HSLs (Fig.2). Therefore, compounds which can interact with the GA-binding pocket could be good candidates for next-generation plant growth regulators. We are focusing on screening such compound from the chemical compound library based on the interacting activity with GID1.

<Representative papers>

Shimada, A., Ueguchi-Tanaka, M., Nakatsu, T., Nakajima, M., Naoe, Y., Ohmiya, H., Kato, H. and Matsuoka, M. (2008) Structural basis for gibberellin recognition by its receptor GID1. Nature 456, (7221) 520-523.
Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E. R., Qian, Q., Kitano, H. and Matsuoka, M. (2005) Cytokinin oxidase regulates rice grain production. Science 309, (5735) 741-745.
Ueguchi-Tanaka, M., Ashikari, M., Nakajima, M., Itoh, H., Katoh, E., Kobayashi, M., Chow, T.-Y., Hsing, Y. C., Kitano, H., Yamaguchi, I. and Matsuoka, M. (2005) GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437, (7059) 693-698.
Sasaki, A., Itoh, H., Gomi, K., Ueguchi-Tanaka, M., Ishiyama, K., Kobayashi, M., Jeong, D.H., An, G., Kitano, H., Ashikari, M. and Matsuoka, M. (2003) Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science 299, (5614) 1896-1898.
Sasaki, A., Ashikari, M., Ueguchi-Tanaka, M., Itoh, H., Nishimura, A., Swapan, D., Ishiyama, K., Saito, T., Kobayashi, M., Khush, G. S., Kitano, H. and Matsuoka, M. (2002) A mutant gibberellin-synthesis gene in rice. Nature 416, (6882) 701-702.

<Lab. Members>

Professor: Hidemi Kitano
Associate Professor: Miyako Ueguchi-Tanaka
Postdoc: Takuya Yamamura
Ph.D student (D3): Mayuko Ikeda
MS student (M1): Takaaki Hirai
undergraduate student (B4): Toshiya Nakano


  FAX: +81-52-789-4232
Prof. EHARA, Hiroshi Ph. D. ehara@
Assoc. Prof. MAKIHARA, Daigo D. Agr. makihara@


  FAX: +81-52-789-4240
Assoc. Prof. ITO, Kasumi D. Agr. kasumito@
Assoc. Prof. INUKAI, Yoshiaki D. Agr. inukaiy@


  FAX: +81-52-789-4232
Prof. EHARA, Hiroshi Ph. D. ehara@
Assoc. Prof. MAKIHARA, Daigo D. Agr. makihara@


  FAX: +81-52-789-4240
Assoc. Prof. ITO, Kasumi D. Agr. kasumito@
Assoc. Prof. INUKAI, Yoshiaki D. Agr. inukaiy@