Department of Bioengineering Sciences

Division of Plant Genomics


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