VI. RNC ACTIVITIESRIKEN Accel. Prog. Rep. 54 (2021)

Accelerator Applications Research Division
Beam Mutagenesis Group
Plant Genome Evolution Research Team
1. Abstract

Established in May 2018 and succeed in October 2020, the plant genome evolution research team studies the eﬀect of heavyion induced mutations on plant and microbial phenotypes. Chromosome rearrangements including translocations, inversions, anddeletions are thought to play an important role in evolution and have a greater potential to achieve large phenotypic changes. However,this potential has not been fully investigated due to the lack of an eﬀective method to induce and analyze complexed mutations.
We employ the population genomics approach with robust molecular biology and bioinformatics techniques to characterize genomic
mutations in model and non-model plant and microbial species, and create the future of mutation breeding.

2. Major Research Subjects(1) Study on the eﬀect of chromosomal rearrangements on plant genomes and phenotypes(2) Genomics-based approach to revolutionize the mutagenesis in model and non-model plants and microbes

3. Summary of Research Activity(1) Study on the eﬀect of chromosomal rearrangements on plant genomes and phenotypes
We have established an eﬃcient bioinformatics pipeline named AMAP, an automated mutation analysis pipeline, and have used
it for genome-wide analysis of chromosome rearrangements and other mutations in various organisms. In Arabidopsis, we isolated ashort-petiole mutant, Ar55-as1, from Ar-beam irradiated population at a dose of 50 Gy with an LET of 290 keV/µm. We showed that
this mutant has no typical base substitutions, deletions, and insertions that were linked to the mutant’s phenotype, but has chromosomal
rearrangements in the genome. Genetic linkage analysis showed that the short-petiole phenotype and the presence or absence of theinversion on chromosome 2 was completely linked in M3 generation, indicating that this inversion is responsible for the phenotype.
The Ar55-as1 mutant will serve as a good model to investigate the eﬀects on gene expressions by chromosomal rearrangements.
We previously isolated a high oil-production mutant of Parachlorella kessleri, a starch and oil-producing unicellular green algae,by C-beam irradiations. The eﬀect on chromosomal rearrangements by Ar- and Fe-beams was quantitatively evaluated by cytologicalobservations and high-throughput sequencing. As the result, Fe-beam irradiation at a dose of 75 Gy caused dramatic increase offragmented chromosomes: 14 percent of the population had more than 30 chromosomes right after the irradiation and three percent of
the population still remained more than 20 chromosomes after four consecutive cultures, although the wild-type P. kessleri cells have
only seven A- and three B-chromosomes. We performed whole-genome sequencing in two mutants, and the results indicated that one
mutant, Fe75-1-3H had chromosomal rearrangements with 10 junction regions, and the other, Ar75-1-2C, had a novel chromosomal
terminus by the result from a translocation.
(2) Genomics-based approach to revolutionize the mutagenesis in model and non-model plants and microbes
Recent advances in genome sequencing and bioinformatics technology enabled us to obtain a genome-wide view of the induced
mutations in unselected populations. We chose baker’s yeast and a legume Lotus japonicus as model systems, irradiated diﬀerent dosesof carbon-ion beams to these organisms, and determined the dose-survival correlation. We isolated a semi-dwarf L. japonicus mutant,identified the responsible mutation by whole-genome sequencing, and started to characterize the phenotypic traits of this mutant. Thesemi-dwarf L. japonicus mutant is suitable for high-density cultivation in laboratory environment and may serve as an eﬃcient model
platform for legume-Rhizobium symbiosis.

Members
Team Leader
Tomoko ABE (～2020.09)

Hiroyuki ICHIDA (2020.10～)

Contract Researcher
Kotaro ISHIIVisiting Scientists
Ali FERJANI (Tokyo Gakugei Univ.)

Yusuke KAZAMA (Fukui Prefectural Univ.)

Part-time Worker
Yusaku NISHIMIYA (Administrative Part-time Worker II)

List of Publications & Presentations
Publications[Original Papers]- 291 -VI. RNC ACTIVITIESRIKEN Accel. Prog. Rep. 54 (2021)

Y. Oono, H. Ichida, R. Morita, S. Nozawa, K. Satoh, A. Shimizu, T. Abe, H. Kato, and Y. Hase, “Genome sequencing of ion-beaminduced mutants facilitates detection of candidate genes responsible for phenotypes of mutants in rice,” Mutat. Res. Fund. Mol. Mech.
Mutagen.821, 111691 (2020).
R. Tabassum, T. Dosaka, H. Ichida, R. Morita, Y. Ding, T. Abe, and T. Katsube-Tanaka, “FLOURY ENDOSPERM11-2 encodes plastid
HSP70-2 involved with the temperature-dependent chalkiness of rice (Oryza sativa L.) grains,” Plant J. 103, 604–616 (2020).
H. Murata, S. Nakano, T. Yamanaka, T. Shimokawa, T. Abe, H. Ichida, Y. Hayashi, and K. Tahara, “Argon-ion beam induced mutantsof the ectomycorrhizal agaricomycete Tricholoma matsutake defective in β-1,4-endoglucanase activity promote the seedling growth ofPinus densiflora in vitro,” Botany 99, 139–149 (2020). DOI:10.1139/cjb-2020-0076 .

Presentations[Domestic Conferences/Workshops]
市田裕之, 阿部知子, 「オープンソースな変異タイピング手法の開発とイネをモデルとした概念実証」, 日本育種学会 第 137 回講演会, 東京都文京区 (東京大学), 2020 年 3 月 28 日.
橋本佳澄, 西浦愛子, 上田純平, 風間裕介, 阿部知子, 市田裕之, 村井耕二, 「2 倍体ヒトツブコムギにおける重イオンビーム照射による超極早生変異体 extra early-flowering 4 の原因遺伝子の同定」, 同上.
森田竜平, 市田裕之, 石井公太郎, 林依子, 安部弘, 白川侑希, 一瀬勝紀, 常泉和秀, 風間智彦, 鳥山欽哉, 佐藤雅志, 阿部知子, 「イネ長粒変異体 lin1 の単離および原因遺伝子同定」, 同上.
石井公太郎, 大部澄江, 白川侑希, 阿部知子, 「全ゲノム変異解析による重イオンビームの高頻度な変異誘発線量区の推定」, 同上.
Y. Ding (口頭発表), T. Katsube-Tanaka, H. Ichida, R. Morita, and T. Abe, “Studies on chalkiness of the rice cultivar ‘Kinmaze’ underheat stress,” 日本作物学会第 250 回講演会, オンライン開催, 2020 年 9 月 3–4 日.
蝶野真喜子 (ポスター発表), 藤田雅也, 神山紀子, 松中仁, 氷見英子, 市田裕之, 阿部知子, 川上直人, 「粒の赤みが弱い新規コムギ変異体の農業特性」, 日本育種学会 第 138 回講演会, オンライン開催, 2020 年 10 月 10–11 日.
藤田悠生 (ポスター発表), 市田裕之, 風間智彦, 阿部知子, 鳥山欽哉, 「インディカイネ品種 Lebed に由来する雄性不稔遺伝子とその抑制遺伝子の解析」, 同上.
石井公太郎 (口頭発表), 風間裕介, 浅野円花, 阿部知子, 河野重行, 「Ar・Fe イオンビーム照射によって生じるクロレラ染色体の断片化と染色体再編成」, 同上.
橋本佳澄 (ポスター発表), 西浦愛子, 風間裕介, 市田裕之, 阿部知子, 村井耕二, 「重イオンビーム照射によって作出された超極早生
コムギ変異体 extra early-flowering 4（exe4）の花成関連遺伝子の発現解析」, 第 15 回ムギ類研究会, オンライン開催, 2020 年 12月 26 日.

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