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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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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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Chen X, Du Y, Luo S, Qu Y, Jin W, Liu S, Wang Z, Liu X, Feng Z, Qin B, Zhou L. Physiological and Transcriptomic Analyses Reveal the Effects of Carbon-Ion Beam on Taraxacum kok-saghyz Rodin Adventitious Buds. Int J Mol Sci 2023; 24:ijms24119287. [PMID: 37298239 DOI: 10.3390/ijms24119287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/23/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Taraxacum kok-saghyz Rodin (TKS) has great potential as an alternative natural-rubber (NR)-producing crop. The germplasm innovation of TKS still faces great challenges due to its self-incompatibility. Carbon-ion beam (CIB) irradiation is a powerful and non-species-specific physical method for mutation creation. Thus far, the CIB has not been utilized in TKS. To better inform future mutation breeding for TKS by the CIB and provide a basis for dose-selection, adventitious buds, which not only can avoid high levels of heterozygosity, but also further improve breeding efficiency, were irradiated here, and the dynamic changes of the growth and physiologic parameters, as well as gene expression pattern were profiled, comprehensively. The results showed that the CIB (5-40 Gy) caused significant biological effects on TKS, exhibiting inhibitory effects on the fresh weight and the number of regenerated buds and roots. Then,15 Gy was chosen for further study after comprehensive consideration. CIB-15 Gy resulted in significant oxidative damages (hydroxyl radical (OH•) generation activity, 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity and malondialdehyde (MDA) content) and activated the antioxidant system (superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX)) of TKS. Based on RNA-seq analysis, the number of differentially expressed genes (DEGs) peaked at 2 h after CIB irradiation. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that DNA-replication-/repair- (mainly up-regulated), cell-death- (mainly up-regulated), plant-hormone- (auxin and cytokinin, which are related to plant morphogenesis, were mainly down-regulated), and photosynthesis- (mainly down-regulated) related pathways were involved in the response to the CIB. Furthermore, CIB irradiation can also up-regulate the genes involved in NR metabolism, which provides an alternative strategy to elevate the NR production in TKS in the future. These findings are helpful to understand the radiation response mechanism and further guide the future mutation breeding for TKS by the CIB.
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Affiliation(s)
- Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanwei Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ying Qu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Jin
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Shizhong Liu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
| | - Zhuanzi Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bi Qin
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou 571101, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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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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