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RIKEN Nishina Center for Accelerator-Based Science Plant Genome Evolution Research Team

Team Leader: Hiroyuki Ichida (Ph.D.)

Research Summary

Hiroyuki Ichida(Ph.D.)

Coevolved since the prehistoric period, plant and microbes have been indispensable in our daily lives. Heavy-ion beams produce a wide variety of mutations from small, single nucleotide substitutions to large inter-chromosomal rearrangements in plant and microbial genomes, thus artificially accelerating the process of evolution. We develop and operate a highly efficient genome analysis platform with cutting-edge sequencing technologies, analyze mutants’ genomes in different organisms, and establish the theory and practical applications of “mutagenesis 2.0” to contribute to the future of plant and microbial breeding.

Main Research Fields

  • Biology

Related Research Fields

  • Agricultural Sciences
  • Informatics
  • Environmental Science
  • Complex Systems
  • Biological Sciences
  • Genome biology
  • Applied microbiology
  • Science in genetics and breeding


  • Heavy-ion beam
  • Genome sequencing technology
  • Bioinformatics
  • DNA repair
  • Microbial breeding

Selected Publications

  • 1. Tabassum, R., Dosaka, T., Ichida, H., Morita, R., Ding, Y., Abe, T., and Katsube-Tanaka, T.:
    "FLOURY ENDOSPERM11–2 encodes plastid HSP70-2 involved with temperature dependent chalkiness of rice (Oryza sativa L.) grains"
    The Plant Journal, 103, 604–616, 2020.
  • 2. Oono, Y., Ichida, H., Morita, R., Nozawa, S, Satoh, K., Shimizu, A., Abe, T., Kato, H., and Hase, Y.:
    "Genome sequencing of ion-beam-induced mutants facilitates detection of candidate genes responsible for phenotypes of mutants in rice"
    Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 821, 111691, 2020.
  • 3. Morita, R.*, Ichida, H.*, Ishii, K., Hayashi, Y., Abe, H., Shirakawa, Y., Ichinose, K., Tsuneizumi, K., Kazama, T., Toriyama, K., Sato, T., and Abe, T.:
    "LONG GRAIN 1: a novel gene that regulates grain length in rice"
    Molecular Breeding, 39, article number 135 (8 pp), 2019.
  • 4. Ichida, H., Morita, R., Shirakawa, Y., Hayashi Y., Abe, T.:
    "Targeted exome sequencing of unselected heavy-ion beam-irradiated populations reveals less-biased mutation characteristics in the rice genome"
    The Plant Journal, 98, 301–314, 2019.
  • 5. Ichida, H. and Abe, T.:
    "An improved and robust method to efficiently deplete repetitive elements from complex plant genomes"
    Plant Science, 280, 455–460, 2019.
  • 6. Murata, H., Abe, T., Ichida, H., Hayashi, Y., Yamanaka, T., Shimokawa, T., and Tahara, K.:
    "Heavy-ion beam mutagenesis of the ectomycorrhizal agaricomycete Tricholoma matsutake that produces the prized mushroom ’matsutake' in conifer forests"
    Mycorrhiza, 28, 171–177, 2018.
  • 7. Yamamoto, Y.Y., Ichida, H., Hieno, A., Daich, O., Tokizawa, M., Nomoto, M., Tada, Y., Kusunoki, K., Koyama, H., and Hayami, N.:
    "Prediction of bipartite transcriptional regulatory elements using transcriptome data of Arabidopsis"
    DNA Research, 24, 271–278, 2017.
  • 8. Sato, Y., Hirano, T., Ichida, H., Murakami, M., Fukunishi, N., Abe, T., and Kawano, S.:
    "Morphological and physiological differences among cultivation lines of Undaria pinnatifida in a common garden experiment using a tank culture system"
    Journal of Applied Phycology, 29, 2287–2295, 2017.
  • 9. Ichida, H. and Long, S.R.:
    "LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression"
    Nucleic Acids Research, 44, 5045–5053, 2016.
  • 10. Ichida, H., Matsuyama, T., Ryuto, H., Hayashi, Y., Fukunishi, N., Abe, T., and Koba, T.:
    "Molecular characterization of microbial mutations induced by ion beam irradiation"
    Mutation Research, 639, 101–107, 2008.

Related Links

Lab Members

Principal investigator

Hiroyuki Ichida
Team Leader

Core members

Kotaro Ishii
Contract Researcher

Contact Information

Bioscience Building, S-304
2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Email: ichida [at] riken.jp