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Ishii K, Kazama Y, Hirano T, Fawcett JA, Sato M, Hirai MY, Sakai F, Shirakawa Y, Ohbu S, Abe T. Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1352564. [PMID: 38693931 PMCID: PMC11061394 DOI: 10.3389/fpls.2024.1352564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/11/2024] [Indexed: 05/03/2024]
Abstract
Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome.
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Affiliation(s)
- Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Radiation Measurement and Dose Assessment, Institute for Radiological Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Japan
| | - Tomonari Hirano
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jeffrey A. Fawcett
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), Wako, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | | | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Sumie Ohbu
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
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2
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Hirano T, Murata M, Watarikawa Y, Hoshino Y, Abe T, Kunitake H. Distinctive development of embryo and endosperm caused by male gametes irradiated with carbon-ion beam. PLANT REPRODUCTION 2024:10.1007/s00497-024-00496-9. [PMID: 38332356 DOI: 10.1007/s00497-024-00496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE In Cyrtanthus mackenii, development of embryo and endosperm were differentially affected by fertilization of male gametes with DNA damage and mutations. Pollen irradiation with ionizing radiations has been applied in plant breeding and genetic research, and haploid plant induction has mainly been performed by male inactivation with high-dose irradiation. However, the fertilization process of irradiated male gametes and the early development of embryo and endosperm have not received much attention. Heavy-ion beams, a type of radiation, have been widely applied as effective mutagens for plants and show a high mutation rate even at low-dose irradiation. In this study, we analyzed the effects of male gametes of Cyrtanthus mackenii irradiated with a carbon-ion beam at low doses on fertilization. In immature seeds derived from the pollination of irradiated pollen grains, two types of embryo sacs were observed: embryo sac with a normally developed embryo and endosperm and embryo sac with an egg cell or an undivided zygote and an endosperm. Abnormalities in chromosome segregation, such as chromosomal bridges, were observed only in the endosperm nuclei, irrespective of the presence or absence of embryogenesis. Therefore, in Cyrtanthus, embryogenesis is strongly affected by DNA damage or mutations in male gametes. Moreover, various DNA contents were detected in the embryo and endosperm nuclei, and endoreduplication may have occurred in the endosperm nuclei. As carbon-ion irradiation causes chromosomal rearrangements even at low doses, pollen irradiation can be an interesting tool for studying double fertilization and mutation heritability.
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Affiliation(s)
- Tomonari Hirano
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan.
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Muneaki Murata
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Yurie Watarikawa
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Yoichiro Hoshino
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, 060-0811, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hisato Kunitake
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
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3
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Park H, Narasako Y, Abe T, Kunitake H, Hirano T. Comprehensive effects of heavy-ion beam irradiation on sweet potato ( Ipomoea batatas [L.] Lam.). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:311-316. [PMID: 36349229 PMCID: PMC9592942 DOI: 10.5511/plantbiotechnology.22.0725a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato is a major root crop with nutritious tuberous roots. The mechanism of tuberous root development has not yet been adequately elucidated. Genetic resources are required to develop the molecular understanding of sweet potato. Heavy-ion beams were applied to hexaploid sweet potato for an increase in genetic variation, after which the comprehensive effects of heavy-ion beam irradiation were investigated. In vitro cultured shoots with an axillary bud of 'Beniharuka' were irradiated with Ar-ions at a dose of 1-5 Gy and C-ions at a dose of 5-20 Gy, and three irradiated lines were separated from each irradiated shoot. The shoot regeneration was inhibited at high doses of each ion irradiation. Ar-ion irradiation had an especially high biological effect on shoot regeneration. A total of 335 lines were obtained, consisting of 104 and 231 lines derived from Ar- and C-ion irradiation, respectively. The change in the DNA content of the lines was analyzed by flow cytometry to evaluate the irradiation-induced damage to the DNA. The two lines demonstrated significant differences in the DNA content and changes at the chromosome level. The screening for the morphological mutants was conducted in the field. Some irradiated lines showed inhibited or no tuberous root phenotype as mutant candidates. Additionally, the high-yield mutant candidates were dominated by Ar-ion irradiation. It was indicated that heavy-ion beam mutagenesis is effective in broadening the range of the phenotypes corresponding to tuberous root formation in hexaploid sweet potato.
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Affiliation(s)
- Hyungjun Park
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Yosuke Narasako
- Kushima AoiFarm Co., 6564-12 Naru, Kushima-shi, Miyazaki 889-3531, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hisato Kunitake
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Tomonari Hirano
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
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4
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Ma L, Kong F, Sun K, Wang T, Guo T. From Classical Radiation to Modern Radiation: Past, Present, and Future of Radiation Mutation Breeding. Front Public Health 2022; 9:768071. [PMID: 34993169 PMCID: PMC8725632 DOI: 10.3389/fpubh.2021.768071] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Radiation mutation breeding has been used for nearly 100 years and has successfully improved crops by increasing genetic variation. Global food production is facing a series of challenges, such as rapid population growth, environmental pollution and climate change. How to feed the world's enormous human population poses great challenges to breeders. Although advanced technologies, such as gene editing, have provided effective ways to breed varieties, by editing a single or multiple specific target genes, enhancing germplasm diversity through mutation is still indispensable in modern and classical radiation breeding because it is more likely to produce random mutations in the whole genome. In this short review, the current status of classical radiation, accelerated particle and space radiation mutation breeding is discussed, and the molecular mechanisms of radiation-induced mutation are demonstrated. This review also looks into the future development of radiation mutation breeding, hoping to deepen our understanding and provide new vitality for the further development of radiation mutation breeding.
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Affiliation(s)
- Liqiu Ma
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing, China.,National Innovation Center of Radiation Application, Beijing, China
| | - Fuquan Kong
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing, China.,National Innovation Center of Radiation Application, Beijing, China
| | - Kai Sun
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangdong, China
| | - Ting Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangdong, China
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5
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Hirano T, Kazama Y, Kunitake H, Abe T. Mutagenic Effects of Heavy-Ion Beam Irradiation to Plant Genome. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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6
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Sato Y, Hirano T, Hayashi Y, Fukunishi N, Abe T, Kawano S. Screening for High-Growth Mutants in Sporophytes of Undaria pinnatifida Using Heavy-Ion Beam Irradiation. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoichi Sato
- Bio-Resources Business Development Division, Riken Food Co., Ltd
| | | | | | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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7
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Hirano T, Matsuyama Y, Hanada A, Hayashi Y, Abe T, Kunitake H. DNA Damage Response of Cyrtanthus mackenii Male Gametes Following Argon Ion Beam Irradiation. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Anna Hanada
- Faculty of Agriculture, University of Miyazaki
| | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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8
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Morita R, Ichida H, Hayashi Y, Ishii K, Shirakawa Y, Usuda-Kogure S, Ichinose K, Hatashita M, Takagi K, Miura K, Kusajima M, Nakashita H, Endo T, Tojo Y, Okumoto Y, Sato T, Toriyama K, Abe T. Responsible Gene Analysis of Phenotypic Mutants Revealed the Linear Energy Transfer (LET)-Dependent Mutation Spectrum in Rice. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | - Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science
| | | | | | | | | | | | - Kotaro Miura
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Miyuki Kusajima
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Hideo Nakashita
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Takashi Endo
- Miyagi Prefectural Furukawa Agricultural Experiment Station
| | | | | | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science
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9
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Matsuta A, Mayuzumi T, Katano H, Hatashita M, Takagi K, Hayashi Y, Abe T, Murai K, Kazama Y. The Effect of Heavy-Ion Beams with High Linear Energy Transfer on Mutant Production in M 1 Generation of Torenia fournieri. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ayaka Matsuta
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Takahiro Mayuzumi
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Hajime Katano
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | | | - Keiichi Takagi
- Research and Development Department, Wakasa Wan Energy Research Center
| | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
| | - Koji Murai
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
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10
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Double Mutant Analysis with the Large Flower Mutant, ohbana1, to Explore the Regulatory Network Controlling the Flower and Seed Sizes in Arabidopsis thaliana. PLANTS 2021; 10:plants10091881. [PMID: 34579413 PMCID: PMC8473154 DOI: 10.3390/plants10091881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022]
Abstract
Two growth processes, cell proliferation and expansion, determine plant species-specific organ sizes. A large flower mutant in Arabidopsis thaliana, ohbana1 (ohb1), was isolated from a mutant library. In the ohb1 flowers, post-mitotic cell expansion and endoreduplication of nuclear DNA were promoted. The whole-genome resequencing and genetic analysis results showed that the loss of function in MEDIATOR16 (MED16), a mediator complex subunit, was responsible for the large flower phenotypes exhibited by ohb1. A phenotypic analysis of the mutant alleles in MED16 and the double mutants created by crossing ohb1 with representative large flower mutants revealed that MED16 and MED25 share part of the negative petal size regulatory pathways. Furthermore, the double mutant analyses suggested that there were genetically independent pathways leading to cell size restrictions in the floral organs which were not related to the MED complex. Several double mutants also formed larger and heavier seeds than the wild type and single mutant plants, which indicated that MED16 was involved in seed size regulation. This study has revealed part of the size-regulatory network in flowers and seeds through analysis of the ohb1 mutant, and that the size-regulation pathways are partially different between floral organs and seeds.
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11
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Sanjaya A, Muramatsu R, Sato S, Suzuki M, Sasaki S, Ishikawa H, Fujii Y, Asano M, Itoh RD, Kanamaru K, Ohbu S, Abe T, Kazama Y, Fujiwara MT. Arabidopsis EGY1 Is Critical for Chloroplast Development in Leaf Epidermal Guard Cells. PLANTS (BASEL, SWITZERLAND) 2021; 10:1254. [PMID: 34205501 PMCID: PMC8235790 DOI: 10.3390/plants10061254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022]
Abstract
In Arabidopsis thaliana, the Ethylene-dependent Gravitropism-deficient and Yellow-green 1 (EGY1) gene encodes a thylakoid membrane-localized protease involved in chloroplast development in leaf mesophyll cells. Recently, EGY1 was also found to be crucial for the maintenance of grana in mesophyll chloroplasts. To further explore the function of EGY1 in leaf tissues, we examined the phenotype of chloroplasts in the leaf epidermal guard cells and pavement cells of two 40Ar17+ irradiation-derived mutants, Ar50-33-pg1 and egy1-4. Fluorescence microscopy revealed that fully expanded leaves of both egy1 mutants showed severe chlorophyll deficiency in both epidermal cell types. Guard cells in the egy1 mutant exhibited permanent defects in chloroplast formation during leaf expansion. Labeling of plastids with CaMV35S or Protodermal Factor1 (PDF1) promoter-driven stroma-targeted fluorescent proteins revealed that egy1 guard cells contained the normal number of plastids, but with moderately reduced size, compared with wild-type guard cells. Transmission electron microscopy further revealed that the development of thylakoids was impaired in the plastids of egy1 mutant guard mother cells, guard cells, and pavement cells. Collectively, these observations demonstrate that EGY1 is involved in chloroplast formation in the leaf epidermis and is particularly critical for chloroplast differentiation in guard cells.
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Affiliation(s)
- Alvin Sanjaya
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Ryohsuke Muramatsu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Shiho Sato
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Mao Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Shun Sasaki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Hiroki Ishikawa
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Yuki Fujii
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Makoto Asano
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
| | - Ryuuichi D Itoh
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe 657-8501, Japan
| | - Sumie Ohbu
- RIKEN Nishina Center, Wako, Saitama 351-0198, Japan
| | - Tomoko Abe
- RIKEN Nishina Center, Wako, Saitama 351-0198, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center, Wako, Saitama 351-0198, Japan
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji, Fukui 910-1195, Japan
| | - Makoto T Fujiwara
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Kioicho, Chiyoda, Tokyo 102-8554, Japan
- RIKEN Nishina Center, Wako, Saitama 351-0198, Japan
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12
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Sanjaya A, Kazama Y, Ishii K, Muramatsu R, Kanamaru K, Ohbu S, Abe T, Fujiwara MT. An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana. PLANTS (BASEL, SWITZERLAND) 2021; 10:848. [PMID: 33922223 PMCID: PMC8145761 DOI: 10.3390/plants10050848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 01/13/2023]
Abstract
Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.
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Affiliation(s)
- Alvin Sanjaya
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Ryohsuke Muramatsu
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan;
| | - Sumie Ohbu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Makoto T. Fujiwara
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
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13
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Tsuneizumi K, Yamada M, Kim HJ, Ichida H, Ichinose K, Sakakura Y, Suga K, Hagiwara A, Kawata M, Katayama T, Tezuka N, Kobayashi T, Koiso M, Abe T. Application of heavy-ion-beam irradiation to breeding large rotifer. Biosci Biotechnol Biochem 2021; 85:703-713. [PMID: 33624778 DOI: 10.1093/bbb/zbaa094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022]
Abstract
In larviculture facilities, rotifers are generally used as an initial food source, while a proper size of live feeds to connect rotifer and Artemia associated with fish larval growth is needed. The improper management of feed size and density induces mass mortality and abnormal development of fish larvae. To improve the survival and growth of target larvae, this study applied carbon and argon heavy-ion-beam irradiation in mutation breeding to select rotifer mutants with larger lorica sizes. The optimal irradiation conditions of heavy-ion beam were determined with lethality, reproductivity, mutant frequency, and morphometric characteristics. Among 56 large mutants, TYC78, TYC176, and TYA41 also showed active population growth. In conclusion, (1) heavy-ion-beam irradiation was defined as an efficient tool for mutagenesis of rotifers and (2) the aforementioned 3 lines that have larger lorica length and active population growth may be used as a countermeasure of live feed size gap during fish larviculcure.
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Affiliation(s)
| | - Mieko Yamada
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
| | - Hee-Jin Kim
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroyuki Ichida
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
| | | | - Yoshitaka Sakakura
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Koushirou Suga
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Atsushi Hagiwara
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan.,Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Miki Kawata
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Takashi Katayama
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Nobuhiro Tezuka
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Masahiko Koiso
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
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14
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Oono Y, Ichida H, Morita R, Nozawa S, Satoh K, Shimizu A, Abe T, Kato H, Hase Y. Genome sequencing of ion-beam-induced mutants facilitates detection of candidate genes responsible for phenotypes of mutants in rice. Mutat Res 2020; 821:111691. [PMID: 32171089 DOI: 10.1016/j.mrfmmm.2020.111691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 05/28/2023]
Abstract
Ion beams are physical mutagens used for plant and microbe breeding that cause mutations via a mechanism distinct from those of chemical mutagens or gamma rays. We utilized whole-exome sequencing of rice DNA in order to understand the properties of ion beam-induced mutations in a genome-wide manner. DNA libraries were constructed from selected carbon-ion-beam-induced rice mutants by capturing with a custom probes covering 66.3 M bases of nearly all exons and miRNAs predicted in the genome. A total of 56 mutations, including 24 single nucleotide variations, 23 deletions, and 5 insertions, were detected in five mutant rice lines (two dwarf and three early-heading-date mutants). The mutations were distributed among all 12 chromosomes, and the average mutation frequency in the M1 generation was estimated to be 2.7 × 10-7 per base. Many single base insertions and deletions were associated with homopolymeric repeats, whereas larger deletions up to seven base pairs were observed at polynucleotide repeats in the DNA sequences of the mutation sites. Of the 56 mutations, six were classified as high-impact mutations that caused a frame shift or loss of exons. A gene that was functionally related to the phenotype of the mutant was disrupted by a high-impact mutation in four of the five lines tested, suggesting that whole-exome sequencing of ion-beam-irradiated mutants could facilitate the detection of candidate genes responsible for the mutant phenotypes.
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Affiliation(s)
- Yutaka Oono
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan.
| | - Hiroyuki Ichida
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Ryouhei Morita
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Shigeki Nozawa
- Department of Research Planning and Promotion, QuBS, QST, Takasaki, Gunma, Japan
| | - Katsuya Satoh
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan
| | - Akemi Shimizu
- Radiation Breeding Division (RBD), Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Hitachi-ohmiya, Ibaraki, Japan
| | - Tomoko Abe
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Hiroshi Kato
- Radiation Breeding Division (RBD), Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Hitachi-ohmiya, Ibaraki, Japan
| | - Yoshihiro Hase
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan
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15
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Chen X, Feng H, Du Y, Luo S, Li W, Yu L, Feng Z, Cui T, Zhou L. Genetic polymorphisms in mutagenesis progeny of Arabidopsis thaliana irradiated by carbon-ion beams and γ-rays irradiations. Int J Radiat Biol 2019; 96:267-275. [PMID: 31692404 DOI: 10.1080/09553002.2020.1688412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: Heavy-ion beams and γ-rays are popular physical mutagenesis to generate mutations in higher plants. It has been found that they show different mutation frequencies and spectrums of phenotype induction, however, the characteristics of heavy-ion beams on genetic polymorphism have not been clarified by comparing with γ-rays.Materials and methods: In the present study, seeds of Arabidopsis thaliana were exposed to carbon-ion beams (with linear energy transfer (LET) of 50 keV/μm) and γ-rays (with average LET of 0.2 keV/μm) irradiation. By using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analysis, the genetic polymorphism of both M1 and M3 plants were investigated, respectively.Results: Carbon-ion beams induced relatively higher polymorphism rate in both M1 and M3 generation than γ-rays: the polymorphism rates of M1 plants derived from carbon-ion beams irradiation are 12.87% (ISSR-C) and 9.01% (RAPD-C), while are 7.67% (ISSR-γ) and 1.45% (RAPD-γ) of plants derived from γ-rays. In M3 generation, the polymorphism rates of ISSR-C, RAPD-C, ISSR-γ, and RAPD-γ are 17.64%, 22.79%, 12.10%, and 2.82%, respectively.Conclusions: In summary, the exposure to carbon-ion beams and γ-rays lead to the change of genomic DNA of A. thaliana, which could be tested in M1 plants and M3 plants by ISSR and RAPD technology. So, both carbon-ion beams and γ-rays can induce variations of genetic polymorphisms in M1 plants and M3 plants. The genetic polymorphisms of M1 plants and M3 plants induced by carbon-ion beams are higher than γ-rays, indicating that heavy-ion beams irradiations mutation breeding is more advantageous than conventional ionizing radiations. Average molecular polymorphism of M1 plants is lower than M3 mutants, by nearly 4.77% (ISSR-C), 13.78% (RAPD-C), 4.43% (ISSR-γ), and 1.37% (RAPD-γ). We hope our study will provide basic information for understanding the effects of carbon-ion beams and γ-rays for plant mutation breeding.
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Affiliation(s)
- Xia Chen
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yan Du
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Wenjian Li
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Zhuo Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Cui
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Libin Zhou
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Baiyin Innovation Academy for Heavy Ion Bioindustry, Baiyin, China
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16
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Frequency and Spectrum of Radiation-Induced Mutations Revealed by Whole-Genome Sequencing Analyses of Plants. QUANTUM BEAM SCIENCE 2019. [DOI: 10.3390/qubs3020007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutation breeding and functional genomics studies of mutant populations have made important contributions to plant research involving the application of radiation. The frequency and spectrum of induced mutations have long been regarded as the crucial determinants of the efficiency of the development and use of mutant populations. Systematic studies regarding the mutation frequency and spectrum, including genetic and genomic analyses, have recently resulted in considerable advances. These studies have consistently shown that the mutation frequency and spectrum are affected by diverse factors, including radiation type, linear energy transfer, and radiation dose, as well as the plant tissue type and condition. Moreover, the whole-genome sequencing of mutant individuals based on next-generation sequencing technologies has enabled the genome-wide quantification of mutation frequencies according to DNA mutation types as well as the elucidation of mutation mechanisms based on sequence characteristics. These studies will contribute to the development of a highly efficient and more controlled mutagenesis method relevant for the customized research of plants. We herein review the characteristics of radiation-induced mutations in plants, mainly focusing on recent whole-genome sequencing analyses as well as factors affecting the mutation frequency and spectrum.
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17
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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 : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:301-314. [PMID: 30584677 PMCID: PMC6850588 DOI: 10.1111/tpj.14213] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/20/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Heavy-ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost-efficient whole-exome sequencing procedure in rice, and its application to characterize an unselected population of heavy-ion beam-induced mutations. The bioinformatics pipeline identified single-nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy-ion beams at the population level. In total, 165 individual M2 lines derived from six irradiation conditions as well as eight pools from non-irradiated 'Nipponbare' controls were sequenced using the newly established target exome sequencing procedure. The characteristics and distribution of carbon-ion beam-induced mutations were analyzed in the absence of bias introduced by visual mutant selections. The average (±SE) number of mutations within the target exon regions was 9.06 ± 0.37 induced by 150 Gy irradiation of dry seeds. The mutation frequency changed in parallel to the irradiation dose when dry seeds were irradiated. The total number of mutations detected by sequencing unselected M2 lines was correlated with the conventional mutation frequency determined by the occurrence of morphological mutants. Therefore, mutation frequency may be a good indicator for sequencing-based determination of the optimal irradiation condition for induction of mutations.
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Affiliation(s)
- Hiroyuki Ichida
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Ryouhei Morita
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Yoriko Hayashi
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
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18
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Comparison of lipid productivity of Parachlorella kessleri heavy-ion beam irradiation mutant PK4 in laboratory and 150-L mass bioreactor, identification and characterization of its genetic variation. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.09.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Zhang M, Cao G, Guo X, Gao Y, Li W, Lu D. A Comet Assay for DNA Damage and Repair After Exposure to Carbon-Ion Beams or X-rays in Saccharomyces Cerevisiae. Dose Response 2018; 16:1559325818792467. [PMID: 30116170 PMCID: PMC6088507 DOI: 10.1177/1559325818792467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
Abstract
Ionizing radiation (IR) can result in serious genomic instability and genotoxicity by causing DNA damage. Carbon ion (CI) beams and X-rays are typical IRs and possess high-linear energy transfer (LET) and low-LET, respectively. In this article, a comet assay that was optimized by decreasing the electrophoresis time (8 minutes) and voltage (0.5 V/cm) was performed to elucidate and quantify the DNA damage induced by CI or X-rays radiation. Two quantitative methods for the comet assay, namely, comet score and olive tail moment, were compared, and the appropriate means and parameter values were selected for the present assay. The dose-effect relationship for CI or X-rays radiation and the DNA repair process were studied in yeast cells. These results showed that the quadratic function fitted the dose-effect relationship after CI or X-rays exposure, and the trend for the models fitted the dose-effect curves for various repair times was precisely described by the cubic function. A kinetics model was also creatively used to describe the process of DNA repair, and equations were calculated within repairable ranges that could be used to roughly evaluate the process and time necessary for DNA repair.
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Affiliation(s)
- Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou, China
| | - Guozhen Cao
- Department of Pharmacology, School of Preclinical Medicine of Xinjiang Medical University, Urumqi, China
| | - Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yue Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou, China
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20
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Kazama Y, Hirano T, Abe T, Matsunaga S. Chromosomal Rearrangement: From Induction by Heavy-Ion Irradiation to in Vivo Engineering by Genome Editing. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yusuke Kazama
- Mutation Genomics Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Tomonari Hirano
- Faculty of Agriculture, University of Miyazaki
- Ion Beam Breeding Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Tomoko Abe
- Ion Beam Breeding Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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21
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Hase Y, Satoh K, Kitamura S, Oono Y. Physiological status of plant tissue affects the frequency and types of mutations induced by carbon-ion irradiation in Arabidopsis. Sci Rep 2018; 8:1394. [PMID: 29362368 PMCID: PMC5780457 DOI: 10.1038/s41598-018-19278-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/09/2022] Open
Abstract
Ionizing radiation including heavy-ion beams has been widely used in mutation breeding. Dry seeds, seedlings, and cultured tissues are often used for mutagenesis; however, little is known about the differences in induced mutations among them. Here, we examined the characteristics of mutations using randomly chosen Arabidopsis M2 plants derived from dry seeds and seedlings irradiated with carbon ions. The mutation frequency was 1.4-1.9 times higher in dry-seed irradiation than in seedling irradiation. This difference was mainly due to the three-times higher frequency of insertions and deletions (InDels) in dry-seed irradiation than in seedling irradiation. This difference increased the proportion of mutations predicted to affect gene function among all mutations identified by whole genome re-sequencing. Our results demonstrate that the physiological status of plant tissue greatly affects the characteristics of mutations induced by ionizing radiation, and that dry seeds are more suitable materials than seedlings for inducing loss-of-function mutations. The results also showed that single base deletions often occurred in homopolymeric sequences, while InDels larger than 2-3 bp often occurred in or near polynucleotide-repeat or microhomologous sequences. Interestingly, microhomology was less commonly found around large deletions (≥50 bp), suggesting that the rejoining process differs depending on the deletion size.
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Affiliation(s)
- Yoshihiro Hase
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan.
| | - Katsuya Satoh
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Satoshi Kitamura
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Yutaka Oono
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
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22
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Kazama Y, Ishii K, Hirano T, Wakana T, Yamada M, Ohbu S, Abe T. Different mutational function of low- and high-linear energy transfer heavy-ion irradiation demonstrated by whole-genome resequencing of Arabidopsis mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:1020-1030. [PMID: 29024116 DOI: 10.1111/tpj.13738] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion irradiation is a powerful mutagen that possesses high linear energy transfer (LET). Several studies have indicated that the value of LET affects DNA lesion formation in several ways, including the efficiency and the density of double-stranded break induction along the particle path. We assumed that the mutation type can be altered by selecting an appropriate LET value. Here, we quantitatively demonstrate differences in the mutation type induced by irradiation with two representative ions, Ar ions (LET: 290 keV μm-1 ) and C ions (LET: 30.0 keV μm-1 ), by whole-genome resequencing of the Arabidopsis mutants produced by these irradiations. Ar ions caused chromosomal rearrangements or large deletions (≥100 bp) more frequently than C ions, with 10.2 and 2.3 per mutant genome under Ar- and C-ion irradiation, respectively. Conversely, C ions induced more single-base substitutions and small indels (<100 bp) than Ar ions, with 28.1 and 56.9 per mutant genome under Ar- and C-ion irradiation, respectively. Moreover, the rearrangements induced by Ar-ion irradiation were more complex than those induced by C-ion irradiation, and tended to accompany single base substitutions or small indels located close by. In conjunction with the detection of causative genes through high-throughput sequencing, selective irradiation by beams with different effects will be a powerful tool for forward genetics as well as studies on chromosomal rearrangements.
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Affiliation(s)
- Yusuke Kazama
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kotaro Ishii
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomonari Hirano
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki, Miyazaki, 889-2192, Japan
| | - Taeko Wakana
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mieko Yamada
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Sumie Ohbu
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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23
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Hu W, Li W, Chen J. Recent advances of microbial breeding via heavy-ion mutagenesis at IMP. Lett Appl Microbiol 2017; 65:274-280. [PMID: 28741678 DOI: 10.1111/lam.12780] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 12/12/2022]
Abstract
Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. SIGNIFICANCE AND IMPACT OF THE STUDY There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future.
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Affiliation(s)
- W Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - W Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - J Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
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24
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Hu W, Li W, Chen H, Liu J, Wang S, Chen J. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger. PLoS One 2017. [PMID: 28650980 PMCID: PMC5484496 DOI: 10.1371/journal.pone.0180120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.
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Affiliation(s)
- Wei Hu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
- * E-mail: (WH); (JC)
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Hao Chen
- College of food science and engineering, Gansu Agricultural University, Lanzhou city, Gansu Province, China
| | - Jing Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Shuyang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
| | - Jihong Chen
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou city, Gansu Province, China
- * E-mail: (WH); (JC)
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25
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Du Y, Luo S, Li X, Yang J, Cui T, Li W, Yu L, Feng H, Chen Y, Mu J, Chen X, Shu Q, Guo T, Luo W, Zhou L. Identification of Substitutions and Small Insertion-Deletions Induced by Carbon-Ion Beam Irradiation in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1851. [PMID: 29163581 PMCID: PMC5665000 DOI: 10.3389/fpls.2017.01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Heavy-ion beam irradiation is one of the principal methods used to create mutants in plants. Research on mutagenic effects and molecular mechanisms of radiation is an important subject that is multi-disciplinary. Here, we re-sequenced 11 mutagenesis progeny (M3) Arabidopsis thaliana lines derived from carbon-ion beam (CIB) irradiation, and subsequently focused on substitutions and small insertion-deletion (INDELs). We found that CIB induced more substitutions (320) than INDELs (124). Meanwhile, the single base INDELs were more prevalent than those in large size (≥2 bp). In details, the detected substitutions showed an obvious bias of C > T transitions, by activating the formation of covalent linkages between neighboring pyrimidine residues in the DNA sequence. An A and T bias was observed among the single base INDELs, in which most of these were induced by replication slippage at either the homopolymer or polynucleotide repeat regions. The mutation rate of 200-Gy CIB irradiation was estimated as 3.37 × 10-7 per site. Different from previous researches which mainly focused on the phenotype, chromosome aberration, genetic polymorphism, or sequencing analysis of specific genes only, our study revealed genome-wide molecular profile and rate of mutations induced by CIB irradiation. We hope our data could provide valuable clues for explaining the potential mechanism of plant mutation breeding by CIB irradiation.
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Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jiangyan Yang
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Tao Cui
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjian Li
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Feng
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuze Chen
- College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jinhu Mu
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xia Chen
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Libin Zhou
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- *Correspondence: Libin Zhou
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Morita R, Nakagawa M, Takehisa H, Hayashi Y, Ichida H, Usuda S, Ichinose K, Abe H, Shirakawa Y, Sato T, Fujiwara MT, Itoh RD, Abe T. Heavy-ion beam mutagenesis identified an essential gene for chloroplast development under cold stress conditions during both early growth and tillering stages in rice. Biosci Biotechnol Biochem 2016; 81:271-282. [PMID: 27804786 DOI: 10.1080/09168451.2016.1249452] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We isolated a cold sensitive virescent1 (csv1) mutant from a rice (Oryza sativa L.) population mutagenized by carbon ion irradiation. The mutant exhibited chlorotic leaves during the early growth stages, and produced normal green leaves as it grew. The growth of csv1 plants displayed sensitivity to low temperatures. In addition, the mutant plants that were transferred to low temperatures at the fifth leaf stage produced chlorotic leaves subsequently. Genetic and molecular analyses revealed translocation of a 13-kb genomic fragment that disrupted the causative gene (CSV1; LOC_Os05g34040). CSV1 encodes a plastid-targeted oxidoreductase-like protein conserved among land plants, green algae, and cyanobacteria. Furthermore, CSV1 transcripts were more abundant in immature than in mature leaves, and they did not markedly increase or decrease with temperature. Taken together, our results indicate that CSV1 supports chloroplast development under cold stress conditions, in both the early growth and tillering stages in rice.
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Affiliation(s)
- Ryouhei Morita
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Mayu Nakagawa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Hinako Takehisa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Yoriko Hayashi
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Hiroyuki Ichida
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Sachiko Usuda
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | | | - Hiroshi Abe
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Yuki Shirakawa
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
| | - Tadashi Sato
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan.,b Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
| | - Makoto T Fujiwara
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan.,c Faculty of Science and Technology , Sophia University , Tokyo , Japan
| | - Ryuuichi D Itoh
- d Faculty of Science , University of the Ryukyus , Nishihara, Japan
| | - Tomoko Abe
- a Nishina Center for Accelerator-Based Science, RIKEN, Wako , Japan
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Yamada K, Kazama Y, Mitra S, Marukawa Y, Arashida R, Abe T, Ishikawa T, Suzuki K. Production of a thermal stress resistant mutant Euglena gracilis strain using Fe-ion beam irradiation. Biosci Biotechnol Biochem 2016; 80:1650-6. [DOI: 10.1080/09168451.2016.1171702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Euglena gracilis is a common phytoplankton species, which also has motile flagellate characteristics. Recent research and development has enabled the industrial use of E. gracilis and selective breeding of this species is expected to further expand its application. However, the production of E. gracilis nuclear mutants is difficult because of the robustness of its genome. To establish an efficient mutation induction procedure for E. gracilis, we employed Fe-ion beam irradiation in the RIKEN RI beam factory. A decrease in the survival rate was observed with the increase in irradiation dose, and the upper limit used for E. gracilis selective breeding was around 50 Gy. For a practical trial of Fe-ion irradiation, we conducted a screening to isolate high-temperature-tolerant mutants. The screening yielded mutants that proliferated faster than the wild-type strain at 32 °C. Our results demonstrate the effectiveness of heavy-ion irradiation on E. gracilis selective breeding.
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Affiliation(s)
- Koji Yamada
- Euglena Co., Ltd., Tokyo, Japan
- JST, CREST, Tokyo, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-based Science, Saitama, Japan
| | | | | | | | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-based Science, Saitama, Japan
| | | | - Kengo Suzuki
- Euglena Co., Ltd., Tokyo, Japan
- JST, CREST, Tokyo, Japan
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Ishii K, Kazama Y, Hirano T, Hamada M, Ono Y, Yamada M, Abe T. AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana. Genes Genet Syst 2016; 91:229-233. [PMID: 27452041 DOI: 10.1266/ggs.15-00078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consuming process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator). Thus, all types of mutations such as base substitution, deletion, insertion, translocation and chromosomal rearrangement can be detected by AMAP. In addition, AMAP automatically distinguishes false positives by comparing lists of candidate mutations in sequenced mutants. We tested AMAP by inputting already analyzed read data derived from three individual Arabidopsis thaliana mutants and confirmed that all true mutations were included in the list of candidate mutations. The result showed that the number of false positives was reduced to 12% of that obtained in a previous analysis that lacked a process of reducing false positives. Thus, AMAP will accelerate not only the analysis of mutation induction by individual mutagens but also the process of forward genetics.
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Kazama Y, Ishii K, Aonuma W, Ikeda T, Kawamoto H, Koizumi A, Filatov DA, Chibalina M, Bergero R, Charlesworth D, Abe T, Kawano S. A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome. Sci Rep 2016; 6:18917. [PMID: 26742857 PMCID: PMC4705512 DOI: 10.1038/srep18917] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/01/2015] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.
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Affiliation(s)
- Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Wataru Aonuma
- Department of Integrated Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Tokihiro Ikeda
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroki Kawamoto
- Department of Integrated Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Ayako Koizumi
- Department of Integrated Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Margarita Chibalina
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Roberta Bergero
- Institute of Evolutionary Biology, University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK
| | - Deborah Charlesworth
- Institute of Evolutionary Biology, University of Edinburgh, School of Biological Sciences, Edinburgh EH9 3JT, UK
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shigeyuki Kawano
- Department of Integrated Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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Katano M, Takahashi K, Hirano T, Kazama Y, Abe T, Tsukaya H, Ferjani A. Suppressor Screen and Phenotype Analyses Revealed an Emerging Role of the Monofunctional Peroxisomal Enoyl-CoA Hydratase 2 in Compensated Cell Enlargement. FRONTIERS IN PLANT SCIENCE 2016; 7:132. [PMID: 26925070 PMCID: PMC4756126 DOI: 10.3389/fpls.2016.00132] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/25/2016] [Indexed: 05/02/2023]
Abstract
Efficient use of seed nutrient reserves is crucial for germination and establishment of plant seedlings. Mobilizing seed oil reserves in Arabidopsis involves β-oxidation, the glyoxylate cycle, and gluconeogenesis, which provide essential energy and the carbon skeletons needed to sustain seedling growth until photoautotrophy is acquired. We demonstrated that H(+)-PPase activity is required for gluconeogenesis. Lack of H(+)-PPase in fugu5 mutants increases cytosolic pyrophosphate (PPi) levels, which partially reduces sucrose synthesis de novo and inhibits cell division. In contrast, post-mitotic cell expansion in cotyledons was unusually enhanced, a phenotype called compensation. Therefore, it appears that PPi inhibits several cellular functions, including cell cycling, to trigger compensated cell enlargement (CCE). Here, we mutagenized fugu5-1 seeds with (12)C(6+) heavy-ion irradiation and screened mutations that restrain CCE to gain insight into the genetic pathway(s) involved in CCE. We isolated A#3-1, in which cell size was severely reduced, but cell number remained similar to that of original fugu5-1. Moreover, cell number decreased in A#3-1 single mutant (A#3-1sm), similar to that of fugu5-1, but cell size was almost equal to that of the wild type. Surprisingly, A#3-1 mutation did not affect CCE in other compensation exhibiting mutant backgrounds, such as an3-4 and fugu2-1/fas1-6. Subsequent map-based cloning combined with genome sequencing and HRM curve analysis identified enoyl-CoA hydratase 2 (ECH2) as the causal gene of A#3-1. The above phenotypes were consistently observed in the ech2-1 allele and supplying sucrose restored the morphological and cellular phenotypes in fugu5-1, ech2-1, A#3-1sm, fugu5-1 ech2-1, and A#3-1; fugu5-1. Taken together, these results suggest that defects in either H(+)-PPase or ECH2 compromise cell proliferation due to defects in mobilizing seed storage lipids. In contrast, ECH2 alone likely promotes CCE during the post-mitotic cell expansion stage of cotyledon development, probably by converting indolebutyric acid to indole acetic acid.
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Affiliation(s)
- Mana Katano
- Department of Biology, Tokyo Gakugei UniversityTokyo, Japan
| | | | - Tomonari Hirano
- Department of Biochemistry and Applied Biosciences, Miyazaki UniversityMiyazaki, Japan
| | | | | | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of TokyoTokyo, Japan
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei UniversityTokyo, Japan
- *Correspondence: Ali Ferjani,
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Abe T, Kazama Y, Hirano T. Ion Beam Breeding and Gene Discovery for Function Analyses Using Mutants. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/10619127.2015.1104130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Hirano T, Kazama Y, Ishii K, Ohbu S, Shirakawa Y, Abe T. Comprehensive identification of mutations induced by heavy-ion beam irradiation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:93-104. [PMID: 25690092 DOI: 10.1111/tpj.12793] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/25/2015] [Accepted: 02/05/2015] [Indexed: 05/06/2023]
Abstract
Heavy-ion beams are widely used for mutation breeding and molecular biology. Although the mutagenic effects of heavy-ion beam irradiation have been characterized by sequence analysis of some restricted chromosomal regions or loci, there have been no evaluations at the whole-genome level or of the detailed genomic rearrangements in the mutant genomes. In this study, using array comparative genomic hybridization (array-CGH) and resequencing, we comprehensively characterized the mutations in Arabidopsis thaliana genomes irradiated with Ar or Fe ions. We subsequently used this information to investigate the mutagenic effects of the heavy-ion beams. Array-CGH demonstrated that the average number of deleted areas per genome were 1.9 and 3.7 following Ar-ion and Fe-ion irradiation, respectively, with deletion sizes ranging from 149 to 602,180 bp; 81% of the deletions were accompanied by genomic rearrangements. To provide a further detailed analysis, the genomes of the mutants induced by Ar-ion beam irradiation were resequenced, and total mutations, including base substitutions, duplications, in/dels, inversions, and translocations, were detected using three algorithms. All three resequenced mutants had genomic rearrangements. Of the 22 DNA fragments that contributed to the rearrangements, 19 fragments were responsible for the intrachromosomal rearrangements, and multiple rearrangements were formed in the localized regions of the chromosomes. The interchromosomal rearrangements were detected in the multiply rearranged regions. These results indicate that the heavy-ion beams led to clustered DNA damage in the chromosome, and that they have great potential to induce complicated intrachromosomal rearrangements. Heavy-ion beams will prove useful as unique mutagens for plant breeding and the establishment of mutant lines.
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Affiliation(s)
- Tomonari Hirano
- Innovation Center, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Cao G, Zhang M, Miao J, Li W, Wang J, Lu D, Xia J. Effects of X-ray and carbon ion beam irradiation on membrane permeability and integrity in Saccharomyces cerevisiae cells. JOURNAL OF RADIATION RESEARCH 2015; 56:294-304. [PMID: 25599994 PMCID: PMC4380059 DOI: 10.1093/jrr/rru114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/02/2014] [Accepted: 11/05/2014] [Indexed: 05/20/2023]
Abstract
Saccharomyces cerevisiae has served as a eukaryotic model in radiation biology studies of cellular responses to ionizing radiation (IR). Research in this field has thus far mainly been focused on DNA strand breaks, DNA base damage, or inhibition of protein activity. However, the effects of IR on S. cerevisiae cell membranes have barely been studied. Here, we investigated the changes in the permeability and integrity of S. cerevisiae cell membranes induced by high-linear energy transfer carbon ion (CI) beam or low-linear energy transfer X-ray. After CI exposure, protein elution and nucleotide diffusion were more pronounced than after X-ray treatment at the same doses, although these features were most prevalent following irradiation doses of 25-175 Gy. Flow cytometry of forward scatter light versus side scatter light and double-staining with fluorescein diacetate and propidium iodide showed that CI and X-ray irradiation significantly affected S. cerevisiae cell membrane integrity and cellular enzyme activity compared with untreated control cells. The extent of lesions in CI-irradiated cells, which exhibited markedly altered morphology and size, was greater than that in X-ray-irradiated cells. The relationships between permeabilized cells, esterase activity, and non-viable cell numbers furthermore indicated that irradiation-induced increases in cell permeabilization and decreases in esterase activity are dependent on the type of radiation and that these parameters correspond well with cell viability. These results also indicate that the patterns of cell inactivity due to X-ray or CI irradiation may be similar in terms of cell membrane damage.
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Affiliation(s)
- Guozhen Cao
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China School of Pharmacy, Lanzhou University, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Jianshun Miao
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Jufang Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
| | - Jiefang Xia
- Institute of Modern Physics, Chinese Academy of Sciences, Lan zhou 730000, China School of Pharmacy, Lanzhou University, Lan zhou 730000, China Key Laboratory of Microbial Resources Exploition and Application, Lan zhou 730000, China
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Maeda S, Gunji S, Hanai K, Hirano T, Kazama Y, Ohbayashi I, Abe T, Sawa S, Tsukaya H, Ferjani A. The conflict between cell proliferation and expansion primarily affects stem organogenesis in Arabidopsis. PLANT & CELL PHYSIOLOGY 2014; 55:1994-2007. [PMID: 25246492 DOI: 10.1093/pcp/pcu131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Plant shoot organs such as stems, leaves and flowers are derived from specialized groups of stem cells organized at the shoot apical meristem (SAM). Organogenesis involves two major processes, namely cell proliferation and differentiation, whereby the former contributes to increasing the cell number and the latter involves substantial increases in cell volume through cell expansion. Co-ordination between the above processes in time and space is essential for proper organogenesis. To identify regulatory factors involved in proper organogenesis, heavy-ion beam-irradiated de-etiolated (det) 3-1 seeds have been used to identify striking phenotypes in the A#26-2; det3-1 mutant. In addition to the stunted plant stature mimicking det3-1, the A#26-2; det3-1 mutant exhibited stem thickening, increased floral organ number and a fruit shape reminiscent of clavata (clv) mutants. DNA sequencing analysis demonstrated that A#26-2; det3-1 harbors a mutation in the CLV3 gene. Importantly, A#26-2; det3-1 displayed cracks that randomly occurred on the main stem with a frequency of approximately 50%. Furthermore, the double mutants clv3-8 det3-1, clv1-4 det3-1 and clv2-1 det3-1 consistently showed stem cracks with frequencies of approximately 97, 38 and 35%, respectively. Cross-sections of stems further revealed an increase in vascular bundle number, cell number and size in the pith of clv3-8 det3-1 compared with det3-1. These findings suggest that the stem inner volume increase due to clv mutations exerts an outward mechanical stress; that in a det3-1 background (defective in cell expansion) resulted in cracking of the outermost layer of epidermal cells.
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Affiliation(s)
- Saori Maeda
- Department of Biology, Tokyo Gakugei University, Koganei-shi, 184-8501 Japan These authors contributed equally to this work
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei-shi, 184-8501 Japan These authors contributed equally to this work
| | - Kenya Hanai
- Department of Biology, Tokyo Gakugei University, Koganei-shi, 184-8501 Japan These authors contributed equally to this work
| | - Tomonari Hirano
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Iwai Ohbayashi
- Department of Biology, Tokyo Gakugei University, Koganei-shi, 184-8501 Japan
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Chuo-ku, 860-8555 Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, 113-0033 Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei-shi, 184-8501 Japan
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Kazama Y, Hirano T, Nishihara K, Ohbu S, Shirakawa Y, Abe T. Effect of high-LET Fe-ion beam irradiation on mutation induction in Arabidopsis thaliana. Genes Genet Syst 2014; 88:189-97. [PMID: 24025247 DOI: 10.1266/ggs.88.189] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Heavy-ion beams are powerful mutagens. They cause a broad spectrum of mutation phenotypes with high efficiency even at low irradiation doses and short irradiation times. These mutagenic effects are due to dense ionisation in a localised region along the ion particle path. Linear energy transfer (LET; keV·μm(-1)), which represents the degree of locally deposited energy, is an important parameter in heavy-ion mutagenesis. For high LET radiation above 290 keV∙μm(-1), however, neither the mutation frequency nor the molecular nature of the mutations has been fully characterised. In this study, we investigated the effect of Fe-ion beams with an LET of 640 keV∙μm(-1) on both the mutation frequency and the molecular nature of the mutations. Screening of well-characterised mutants (hy and gl) revealed that the mutation frequency was lower than any other ion species with low LET. We investigated the resulting mutations in the 4 identified mutants. Three mutants were examined by employing PCR-based methods, one of which had 2-bp deletion, another had 178 bp of tandemly duplication, and other one had complicated chromosomal rearrangements with variable deletions in size at breakpoints. We also detected large deletions in the other mutant by using array comparative genomic hybridisation. From the results of the analysis of the breakpoints and junctions of the detected deletions, it was revealed that the mutants harboured chromosomal rearrangements in their genomes. These results indicate that Fe-ion irradiation tends to cause complex mutations with low efficiency. We conclude that Fe-ion irradiation could be useful for inducing chromosomal rearrangements or large deletions.
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Du Y, Li W, Yu L, Chen G, Liu Q, Luo S, Shu Q, Zhou L. Mutagenic effects of carbon-ion irradiation on dry Arabidopsis thaliana seeds. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2014; 759:28-36. [DOI: 10.1016/j.mrgentox.2013.07.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/07/2013] [Accepted: 07/08/2013] [Indexed: 11/30/2022]
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Abe T, Kazama Y, Nishi M, Nagayoshi S. New agricultural products from Kyushu with high competitiveness in global market. ACTA ACUST UNITED AC 2014. [DOI: 10.1270/jsbbr.16.67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Tomoko Abe
- RIKEN Innovation Center,
- RIKEN Nishina Center
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Ota S, Matsuda T, Takeshita T, Yamazaki T, Kazama Y, Abe T, Kawano S. Phenotypic spectrum of Parachlorella kessleri (Chlorophyta) mutants produced by heavy-ion irradiation. BIORESOURCE TECHNOLOGY 2013; 149:432-438. [PMID: 24135567 DOI: 10.1016/j.biortech.2013.09.079] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 06/02/2023]
Abstract
Heavy-ion mutagenesis is a technology used for effective production of genetic mutants. This study demonstrates that algal breeding using a unicellular alga, Parachlorella kessleri, by heavy-ion mutagenesis can improve lipid yield in laboratory experiments. The primary screening yielded 23 mutants among which a secondary screening yielded 7 strains, which were subjected to phenotypic assays. P. kessleri strains produced by heavy-ion radiation spanned a broad spectrum of phenotypes that differed in lipid content and fatty acid profiles. Starch grain morphology was distinctively altered in one of the mutants. The growth of strain PK4 was comparable to that of the wild type under stress-free culture conditions, and the mutant also produced large quantities of lipids, a combination of traits that may be of commercial interest. Thus, heavy-ion irradiation is an effective mutagenic agent for microalgae and may have potential in the production of strains with gain-of-function phenotypes.
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Affiliation(s)
- Shuhei Ota
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; Japan Science and Technology Agency, CREST, Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Hirano T, Takagi K, Hoshino Y, Abe T. DNA damage response in male gametes of Cyrtanthus mackenii during pollen tube growth. AOB PLANTS 2013; 5:plt004. [PMID: 23550213 PMCID: PMC3583183 DOI: 10.1093/aobpla/plt004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 01/16/2013] [Indexed: 05/09/2023]
Abstract
Male gametophytes of plants are exposed to environmental stress and mutagenic agents during the double fertilization process and therefore need to repair the DNA damage in order to transmit the genomic information to the next generation. However, the DNA damage response in male gametes is still unclear. In the present study, we analysed the response to DNA damage in the generative cells of Cyrtanthus mackenii during pollen tube growth. A carbon ion beam, which can induce DNA double-strand breaks (DSBs), was used to irradiate the bicellular pollen, and then the irradiated pollen grains were cultured in a liquid culture medium. The male gametes were isolated from the cultured pollen tubes and used for immunofluorescence analysis. Although inhibitory effects on pollen tube growth were not observed after irradiation, sperm cell formation decreased significantly after high-dose irradiation. After high-dose irradiation, the cell cycle progression of generative cells was arrested at metaphase in pollen mitosis II, and phosphorylated H2AX (γH2AX) foci, an indicator of DSBs, were detected in the majority of the arrested cells. However, these foci were not detected in cells that were past metaphase. Cell cycle progression in irradiated generative cells is regulated by the spindle assembly checkpoint, and modification of the histones surrounding the DSBs was confirmed. These results indicate that during pollen tube growth generative cells can recognize and manage genomic lesions using DNA damage response pathways. In addition, the number of generative cells with γH2AX foci decreased with culture prolongation, suggesting that the DSBs in the generative cells are repaired.
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Affiliation(s)
- Tomonari Hirano
- Innovation Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Advanced Science and Technology, Tokyo Denki University, 5 Senjyu-Asahicho, Adachi, Tokyo 120-8551, Japan
| | - Keiichi Takagi
- Research and Development Department, Wakasa Wan Energy Research Center, 64-52-1 Nagatani, Tsuruga, Fukui 914-0192, Japan
| | - Yoichiro Hoshino
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo 060-0811, Japan
| | - Tomoko Abe
- Innovation Center, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Corresponding author's e-mail address:
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Kazama Y, Fujiwara MT, Takehisa H, Ohbu S, Saito H, Ichida H, Hayashi Y, Abe T. Characterization of a heavy-ion induced white flower mutant of allotetraploid Nicotiana tabacum. PLANT CELL REPORTS 2013; 32:11-9. [PMID: 22930364 DOI: 10.1007/s00299-012-1336-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/09/2012] [Accepted: 08/09/2012] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE : We characterized a white flower mutant of allotetraploid N. tabacum as a DFR-deficient mutant; one copy of DFR has a cultivar-specific frameshift, while the other was deleted by heavy-ion irradiation. In most plants, white-flowered mutants have some kind of deficiency or defect in their anthocyanin biosynthetic pathway. Nicotiana tabacum normally has pink petals, in which cyanidin is the main colored anthocyanidin. When a relevant gene in the cyanidin biosynthetic pathway is mutated, the petals show a white color. Previously, we generated white-flowered mutants of N. tabacum by heavy-ion irradiation, which is accepted as an effective mutagen. In this study, we determined which gene was responsible for the white-flowered phenotype of one of these mutants, cv. Xanthi white flower 1 (xwf1). Southern blot analysis using a DNA fragment of the dihydroflavonol 4-reductase (DFR) gene as a probe showed that the xwf1 mutant lacked signals that were present in wild-type genomic DNAs. Sequence analysis demonstrated that one copy of the DFR gene (NtDFR2) was absent from the genome of the xwf1 mutant. The other copy of the DFR gene (NtDFR1) contained a single-base deletion resulting in a frameshift mutation, which is a spontaneous mutation in cv. Xanthi. Introduction of NtDFR2 cDNA into the petal limbs of xwf1 by particle bombardment resulted in production of the pink-colored cells, whereas introduction of NtDFR1 cDNA did not. These results indicate that xwf1 is a DFR-deficient mutant. One copy of NtDFR1 harbors a spontaneous frameshift mutation, while the other copy of NtDFR2 was deleted by heavy-ion beam irradiation.
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Affiliation(s)
- Yusuke Kazama
- RIKEN Innovation Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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