1
|
Ling Y, Zhang Y, Huang M, Guo T, Yang G. Genome-Wide Profile of Mutations Induced by Carbon Ion Beam Irradiation of Dehulled Rice Seeds. Int J Mol Sci 2024; 25:5195. [PMID: 38791234 PMCID: PMC11121050 DOI: 10.3390/ijms25105195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
As a physical mutagen, carbon ion beam (CIB) irradiation can induce high-frequency mutation, which is user-friendly and environment-friendly in plant breeding. In this study, we resequenced eight mutant lines which were screened out from the progeny of the CIB-irradiated dehulled rice seeds. Among these mutants, CIB induced 135,535 variations, which include single base substitutions (SBSs), and small insertion and deletion (InDels). SBSs are the most abundant mutation, and account for 88% of all variations. Single base conversion is the main type of SBS, and the average ratio of transition and transversion is 1.29, and more than half of the InDels are short-segmented mutation (1-2 bp). A total of 69.2% of the SBSs and InDels induced by CIBs occurred in intergenic regions on the genome. Surprisingly, the average mutation frequency in our study is 9.8 × 10-5/bp and much higher than that of the previous studies, which may result from the relatively high irradiation dosage and the dehulling of seeds for irradiation. By analyzing the mutation of every 1 Mb in the genome of each mutant strain, we found some unusual high-frequency (HF) mutation regions, where SBSs and InDels colocalized. This study revealed the mutation mechanism of dehulled rice seeds by CIB irradiation on the genome level, which will enrich our understanding of the mutation mechanism of CIB radiation and improve mutagenesis efficiency.
Collapse
Affiliation(s)
- Ying Ling
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Y.Z.); (M.H.)
| | - Yuming Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Y.Z.); (M.H.)
| | - Ming Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Y.Z.); (M.H.)
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Y.Z.); (M.H.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517000, China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (Y.L.); (Y.Z.); (M.H.)
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Satoh K, Hoshino W, Hase Y, Kitamura S, Hayashi H, Furuta M, Oono Y. Lethal and mutagenic effects of different LET radiations on Bacillus subtilis spores. Mutat Res 2023; 827:111835. [PMID: 37562181 DOI: 10.1016/j.mrfmmm.2023.111835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023]
Abstract
New, useful microorganism resources have been generated by ionizing radiation breeding technology. However, the mutagenic effects of ionizing radiation on microorganisms have not been systematically clarified. For a deeper understanding and characterization of ionizing radiation-induced mutations in microorganisms, we investigated the lethal effects of seven different linear energy transfer (LET) radiations based on the survival fraction (SF) and whole-genome sequencing analysis of the mutagenic effects of a dose resulting in an SF of around 1% in Bacillus subtilis spores. Consequently, the lower LET radiations (gamma [surface LET: 0.2 keV/µm] and 4He2+ [24 keV/µm]) showed low lethality and high mutation frequency (MF), resulting in the major induction of single-base substitutions. Whereas higher LET radiations (12C5+ [156 keV/µm] and 12C6+ [179 keV/µm]) showed high lethality and low MF, resulting in the preferential induction of deletion mutations. In addition, 12C6+ (111) ion beams likely possess characteristics of both low- and high-LET radiations simultaneously. A decrease in the relative biological effectiveness and an evaluation of the inactivation cross section indicated that 20Ne8+ (468 keV/µm) and 40Ar13+ (2214 keV/µm) ion beams had overkill effects. In conclusion, in the mutation breeding of microorganisms, it should be possible to regulate the proportions, types, and frequencies of induced mutations by selecting an ionizing radiation of an appropriate LET in accordance with the intended purpose.
Collapse
Affiliation(s)
- Katsuya Satoh
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan.
| | - Wataru Hoshino
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan; Faculty of Engineering, Maebashi Institute of Technology, 460-1 Kamisadori, Maebashi, Gunma 371-0816, Japan
| | - Yoshihiro Hase
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Satoshi Kitamura
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Hidenori Hayashi
- Faculty of Engineering, Maebashi Institute of Technology, 460-1 Kamisadori, Maebashi, Gunma 371-0816, Japan
| | - Masakazu Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
| | - Yutaka Oono
- Department of Quantum-Applied Biosciences, Takasaki Institute for Advanced Quantum Science, Foundational Quantum Technology Research Directorate, National Institutes for Quantum Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| |
Collapse
|
5
|
Ren W, Wang H, Du Y, Li Y, Feng Z, Zhou X, Kang G, Shu Q, Guo T, Guo H, Yu L, Jin W, Yang F, Li J, Ma J, Li W, Xu C, Chen X, Liu X, Yang C, Liu L, Zhou L. Multi-generation study of heavy ion beam-induced mutations and agronomic trait variations to accelerate rice breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1213807. [PMID: 37416884 PMCID: PMC10322207 DOI: 10.3389/fpls.2023.1213807] [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: 04/28/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
Heavy ion beam (HIB) is an effective physical mutagen that has been widely used in plant mutational breeding. Systemic knowledge of the effects caused by different HIB doses at developmental and genomic levels will facilitate efficient breeding for crops. Here we examined the effects of HIB systematically. Kitaake rice seeds were irradiated by ten doses of carbon ion beams (CIB, 25 - 300 Gy), which is the most widely used HIB. We initially examined the growth, development and photosynthetic parameters of the M1 population and found that doses exceeding 125 Gy caused significant physiological damages to rice. Subsequently, we analyzed the genomic variations in 179 M2 individuals from six treatments (25 - 150 Gy) via whole-genome sequencing (WGS). The mutation rate peaks at 100 Gy (2.66×10-7/bp). Importantly, we found that mutations shared among different panicles of the same M1 individual are at low ratios, validating the hypothesis that different panicles may be derived from different progenitor cells. Furthermore, we isolated 129 mutants with distinct phenotypic variations, including changes in agronomic traits, from 11,720 M2 plants, accounting for a 1.1% mutation rate. Among them, about 50% possess stable inheritance in M3. WGS data of 11 stable M4 mutants, including three lines with higher yields, reveal their genomic mutational profiles and candidate genes. Our results demonstrate that HIB is an effective tool that facilitates breeding, that the optimal dose range for rice is 67 - 90% median lethal dose (LD50), and that the mutants isolated here can be further used for functional genomic research, genetic analysis, and breeding.
Collapse
Affiliation(s)
- Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinhui Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Guisen Kang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingyao Shu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Huijun Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixia Yu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenjie Jin
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Fu Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jingpeng Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Jianzhong Ma
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Wenjian Li
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chaoli Xu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenan Yang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Luxiang Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Zou M, Tong S, Zou T, Wang X, Wu L, Wang J, Guo T, Xiao W, Wang H, Huang M. A new method for mutation inducing in rice by using DC electrophoresis bath and its mutagenic effects. Sci Rep 2023; 13:6707. [PMID: 37185291 PMCID: PMC10126576 DOI: 10.1038/s41598-023-33742-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Mutation breeding is a significant means of increasing breeding efficiency and accelerating breeding process. In present study, we explored a new method for mutations inducing in rice (Oryza sativa L.) by using direct current electrophoresis bath (DCEB). The results showed that 20 mM NaCl solution is the optimal buffer, and the mortality of rice seeds followed an upward trend with increasing voltage and processing time of DCEB. By exploring the mutagenic effects of γ-irradiation and DCEB on seed vigor and physiological damages, we found that the physiological damages induced by DCEB on seed vigor were significant compared with that by γ-irradiation. We screened two mutants with low filled grain percentage and one mutant with abnormal hull from the M2 generations. These three mutants were confirmed to be authentic mutants based on 48 SSR markers followed by the protocol NY/T 1433-2014. Whole-genome resequencing detected a total of 503 and 537 polymorphisms in the two mutants, respectively, and the DCEB mutagenesis induced mainly InDel variants, while the exon region of mutant genes occupied a large proportion, especially the SNP variants, which occupied about 20% of the mutation sites in the exon region.
Collapse
Affiliation(s)
- Minmin Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Sun Tong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ting Zou
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xinyi Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Linxuan Wu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jiafeng Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Tao Guo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Wuming Xiao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Hui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Ming Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| |
Collapse
|
8
|
Hase Y, Satoh K, Kitamura S. Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 14:1149083. [PMID: 37089645 PMCID: PMC10117944 DOI: 10.3389/fpls.2023.1149083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
The molecular nature of mutations induced by ionizing radiation and chemical mutagens in plants is becoming clearer owing to the availability of high-throughput DNA sequencing technology. However, few studies have compared the induced mutations between different radiation qualities and between different irradiated materials with the same analysis method. To compare mutation induction between dry-seeds and seedlings irradiated with carbon ions and gamma rays in Arabidopsis, in this study we detected the mutations induced by seedling irradiation with gamma rays and analyzed the data together with data previously obtained for the other irradiation treatments. Mutation frequency at the equivalent dose for survival reduction was higher with gamma rays than with carbon ions, and was higher with dry-seed irradiation than with seedling irradiation. Carbon ions induced a higher frequency of deletions (2-99 bp) than gamma rays in the case of dry-seed irradiation, but this difference was less evident in the case of seedling irradiation. This result supported the inference that dry-seed irradiation under a lower water content more clearly reflects the difference in radiation quality. However, the ratio of rearrangements (inversions, translocations, and deletions larger than 100 bp), which are considered to be derived from the rejoining of two distantly located DNA breaks, was significantly higher with carbon ions than gamma rays irrespective of the irradiated material. This finding suggested that high-linear energy transfer radiation induced closely located DNA damage, irrespective of the water content of the material, that could lead to the generation of rearrangements. Taken together, the results provide an overall picture of radiation-induced mutation in Arabidopsis and will be useful for selection of a suitable radiation treatment for mutagenesis.
Collapse
|
9
|
Li B, Zhao L, Zhang S, Cai H, Xu L, An B, Wang R, Liu G, He Y, Jiao C, Liu L, Xu Y. The Mutational, Epigenetic, and Transcriptional Effects Between Mixed High-Energy Particle Field (CR) and 7Li-Ion Beams (LR) Radiation in Wheat M 1 Seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:878420. [PMID: 35646033 PMCID: PMC9131052 DOI: 10.3389/fpls.2022.878420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Ionizing radiation (IR) is an effective approach for mutation breeding. Understanding the mutagenesis and transcriptional profiles induced by different mutagens is of great significance for improving mutation breeding efficiency. Here, using RNA sequencing and methylation-sensitive amplification polymorphism (MSAP) approaches, we compared the genetic variations, epigenetics, and transcriptional responses induced by the mixed high-energy particle field (CR) and 7Li-ion beam (LR) radiation in M1 seedlings of two wheat genotypes (Yangmai 18 and Yangmai 20). The results showed that, in both wheat genotypes, CR displayed significantly a higher mutation efficiency (1.79 × 10-6/bp) than that by LR (1.56 × 10-6/bp). The induced mutations were not evenly distributed across chromosomes and varied across wheat genotypes. In Y18 M1, the highest number of mutations were detected on Chr. 6B and Chr. 6D, whilst in Y20 M1, Chr. 7A and Chr. 3A had the highest mutations. The transcript results showed that total of 4,755 CR-regulated and 1,054 LR-regulated differentially expressed genes (DEGs) were identified in the both genotypes. Gene function enrichment analysis of DEGs showed that these DEGs overlapped or diverged in the cascades of molecular networks involved in "phenylpropanoid biosynthesis" and "starch and sucrose metabolism" pathways. Moreover, IR type specific responses were observed between CR an LR irradiation, including specific TFs and response pathways. MSAP analysis showed that DNA methylation level increased in LR treatment, while decreased at CR. The proportion of hypermethylation was higher than that of hypomethylation at LR, whereas a reverse pattern was observed at CR, indicating that DNA methylation plays critical roles in response to IR irradiation. All these results support that the response to different IRs in wheat includes both common and unique pathways, which can be served as a useful resource to better understand the mechanisms of responses to different IRs in other plants.
Collapse
Affiliation(s)
- Bo Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Centre for the Industrialization of Major Grain Crops, Yangtze University, Jingzhou, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuo Zhang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Haiya Cai
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Le Xu
- Hubei Collaborative Innovation Centre for the Industrialization of Major Grain Crops, Yangtze University, Jingzhou, China
| | - Bingzhuang An
- Hubei Collaborative Innovation Centre for the Industrialization of Major Grain Crops, Yangtze University, Jingzhou, China
| | - Rong Wang
- Hubei Collaborative Innovation Centre for the Industrialization of Major Grain Crops, Yangtze University, Jingzhou, China
| | - Gang Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yonggang He
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chunhai Jiao
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanhao Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Frequency and Spectrum of Mutations Induced by Gamma Rays Revealed by Phenotype Screening and Whole-Genome Re-Sequencing in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23020654. [PMID: 35054839 PMCID: PMC8775868 DOI: 10.3390/ijms23020654] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/26/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Genetic variations are an important source of germplasm diversity, as it provides an allele resource that contributes to the development of new traits for plant breeding. Gamma rays have been widely used as a physical agent for mutation creation in plants, and their mutagenic effect has attracted extensive attention. However, few studies are available on the comprehensive mutation profile at both the large-scale phenotype mutation screening and whole-genome mutation scanning. In this study, biological effects on M1 generation, large-scale phenotype screening in M2 generation, as well as whole-genome re-sequencing of seven M3 phenotype-visible lines were carried out to comprehensively evaluate the mutagenic effects of gamma rays on Arabidopsis thaliana. A total of 417 plants with visible mutated phenotypes were isolated from 20,502 M2 plants, and the phenotypic mutation frequency of gamma rays was 2.03% in Arabidopsis thaliana. On average, there were 21.57 single-base substitutions (SBSs) and 11.57 small insertions and deletions (InDels) in each line. Single-base InDels accounts for 66.7% of the small InDels. The genomic mutation frequency was 2.78 × 10−10/bp/Gy. The ratio of transition/transversion was 1.60, and 64.28% of the C > T events exhibited the pyrimidine dinucleotide sequence; 69.14% of the small InDels were located in the sequence with 1 to 4 bp terminal microhomology that was used for DNA end rejoining, while SBSs were less dependent on terminal microhomology. Nine genes, on average, were predicted to suffer from functional alteration in each re-sequenced line. This indicated that a suitable mutation gene density was an advantage of gamma rays when trying to improve elite materials for one certain or a few traits. These results will aid the full understanding of the mutagenic effects and mechanisms of gamma rays and provide a basis for suitable mutagen selection and parameter design, which can further facilitate the development of more controlled mutagenesis methods for plant mutation breeding.
Collapse
|
13
|
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
| | | |
Collapse
|
14
|
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
| |
Collapse
|
15
|
Hashimoto K, Kazama Y, Ichida H, Abe T, Murai K. Einkorn Wheat ( Triticum monococcum) Mutant Extra-Early Flowering 4, Generated by Heavy-Ion Beam Irradiation, Has a Deletion of the LIGHT-REGULATED WD1 Homolog. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.297] [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)
| | - Yusuke Kazama
- Graduate School of Bioscience, Fukui Prefectural University
| | | | - Tomoko Abe
- RIKEN, Nishina Center for Accelerator-Based Science
| | - Koji Murai
- Graduate School of Bioscience, Fukui Prefectural University
| |
Collapse
|
16
|
Du Y, Luo S, Zhao J, Feng Z, Chen X, Ren W, Liu X, Wang Z, Yu L, Li W, Qu Y, Liu J, Zhou L. Genome and transcriptome-based characterization of high energy carbon-ion beam irradiation induced delayed flower senescence mutant in Lotus japonicus. BMC PLANT BIOLOGY 2021; 21:510. [PMID: 34732128 PMCID: PMC8564971 DOI: 10.1186/s12870-021-03283-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Flower longevity is closely related to pollen dispersal and reproductive success in all plants, as well as the commercial value of ornamental plants. Mutants that display variation in flower longevity are useful tools for understanding the mechanisms underlying this trait. Heavy-ion beam irradiation has great potential to improve flower shapes and colors; however, few studies are available on the mutation of flower senescence in leguminous plants. RESULTS A mutant (C416) exhibiting blossom duration eight times longer than that of the wild type (WT) was isolated in Lotus japonicus derived from carbon ion beam irradiation. Genetic assays supported that the delayed flower senescence of C416 was a dominant trait controlled by a single gene, which was located between 4,616,611 Mb and 5,331,876 Mb on chromosome III. By using a sorting strategy of multi-sample parallel genome sequencing, candidate genes were narrowed to the gene CUFF.40834, which exhibited high identity to ethylene receptor 1 in other model plants. A physiological assay demonstrated that C416 was insensitive to ethylene precursor. Furthermore, the dynamic changes of phytohormone regulatory network in petals at different developmental stages was compared by using RNA-seq. In brief, the ethylene, jasmonic acid (JA), and salicylic acid (SA) signaling pathways were negatively regulated in C416, whereas the brassinosteroid (BR) and cytokinin signaling pathways were positively regulated, and auxin exhibited dual effects on flower senescence in Lotus japonicus. The abscisic acid (ABA) signaling pathway is positively regulated in C416. CONCLUSION So far, C416 might be the first reported mutant carrying a mutation in an endogenous ethylene-related gene in Lotus japonicus, rather than through the introduction of exogenous genes by transgenic techniques. A schematic of the flower senescence of Lotus japonicus from the perspective of the phytohormone regulatory network was provided based on transcriptome profiling of petals at different developmental stages. This study is informative for elucidating the molecular mechanism of delayed flower senescence in C416, and lays a foundation for candidate flower senescence gene identification in Lotus japonicus. It also provides another perspective for the improvement of flower longevity in legume plants by heavy-ion beam.
Collapse
Affiliation(s)
- Yan Du
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Shanwei Luo
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Jian Zhao
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730000, People's Republic of China
| | - Zhuo Feng
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xia Chen
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Xiao Liu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Zhuanzi Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Lixia Yu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Wenjian Li
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
| | - Ying Qu
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China
| | - Jie Liu
- Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100000, People's Republic of China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100000, People's Republic of China.
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, 730900, People's Republic of China.
| |
Collapse
|
17
|
Zhang J, Peng Z, Liu Q, Yang G, Zhou L, Li W, Wang H, Chen Z, Guo T. Time Course Analysis of Genome-Wide Identification of Mutations Induced by and Genes Expressed in Response to Carbon Ion Beam Irradiation in Rice ( Oryza sativa L.). Genes (Basel) 2021; 12:genes12091391. [PMID: 34573373 PMCID: PMC8469171 DOI: 10.3390/genes12091391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Heavy-ion irradiation is a powerful mutagen and is widely used for mutation breeding. In this study, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) techniques, we comprehensively characterized these dynamic changes caused by mutations at three time points (48, 96, and 144 h after irradiation) and the expression profiles of rice seeds irradiated with C ions at two doses. Subsequent WGS analysis revealed that more mutations were detected in response to 40 Gy carbon ion beam (CIB) irradiation than 80 Gy of CIB irradiation at the initial stage (48 h post-irradiation). In the mutants generated from both irradiation doses, single-base substitutions (SBSs) were the most frequent type of mutation induced by CIB irradiation. Among the mutations, the predominant ones were C:T and A:G transitions. CIB irradiation also induced many short InDel mutations. RNA-seq analysis at the three time points showed that the number of differentially expressed genes (DEGs) was highest at 48 h post-irradiation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the DEGs showed that the "replication and repair" pathway was enriched specifically 48 h post-irradiation. These results indicate that the DNA damage response (DDR) and the mechanism of DNA repair tend to quickly start within the initial stage (48 h) after irradiation.
Collapse
Affiliation(s)
- Jian Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Ziai Peng
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Qiling Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (L.Z.); (W.L.)
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China; (L.Z.); (W.L.)
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (Z.P.); (Q.L.); (G.Y.); (H.W.); (Z.C.)
- Correspondence: ; Tel./Fax: +86-20-3860-4903
| |
Collapse
|
18
|
Zheng Y, Li S, Huang J, Fu H, Zhou L, Furusawa Y, Shu Q. Identification and characterization of inheritable structural variations induced by ion beam radiations in rice. Mutat Res 2021; 823:111757. [PMID: 34271440 DOI: 10.1016/j.mrfmmm.2021.111757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 12/01/2022]
Abstract
High energy ion beams are effective physical mutagens for mutation induction in plants. Due to their high linear energy transfer (LET) property, they are known to generate single nucleotide variations (SNVs) and insertion/deletions (InDels, <50 bp) as well as structural variations (SVs). However, due to the technical difficulties to identify SVs, studies on ion beam induced SVs by genome sequencing have so far been limited in numbers and inadequate in nature, and knowledge of SVs is scarce with regards to their characteristics. In the present study, we identified and validated SVs in six M4 plants (designated as Ar_50, Ar_100, C_150, C_200, Ne_50 and Ne_100 according to ion beam types and irradiation doses), two each induced by argon (40Ar18+), carbon (12C6+) and neon (20Ne10+) ion beams and performed in depth analyses of their characteristics. In total, 22 SVs were identified and validated, consisting of 11 deletions, 1 duplication, and 4 intra-chromosomal and 6 inter-chromosomal translocations. There were several SVs larger than 1 kbp. The SVs were distributed across the whole genome with an aggregation with SNVs and InDels only in the Ne_50 mutants. An enrichment of a 11-bp wide G-rich DNA motif 'GAAGGWGGRGG' was identified around the SV breakpoints. Three mechanisms might be involved in the SV formation, i.e., the expansion of tandem repeats, transposable element insertion, and non-allelic homologous recombination. Put together, the present study provides a preliminary view of SVs induced by Ar, C and Ne ion beam radiations, and as a pilot study, it contributes to our understanding of how SVs might form after ion beam irradiation in rice.
Collapse
Affiliation(s)
- Yunchao Zheng
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China; Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
| | - Jianzhong Huang
- Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Haowei Fu
- Jiaxing Academy of Agricultural Science, Jiaxing, Zhejiang, 314016, China.
| | - Libin Zhou
- Biophysics Group, Biomedical Research Center, Institute of Modern Physics, Chinese Academy of Science, Lanzhou, 730000, China.
| | - Yoshiya Furusawa
- Department of Basic Medical Sciences for Radiation Damages, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba, 263-8555, Japan.
| | - Qingyao Shu
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
19
|
Udagawa H, Ichida H, Takeuchi T, Abe T, Takakura Y. Highly Efficient and Comprehensive Identification of Ethyl Methanesulfonate-Induced Mutations in Nicotiana tabacum L. by Whole-Genome and Whole-Exome Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:671598. [PMID: 34140964 PMCID: PMC8204250 DOI: 10.3389/fpls.2021.671598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Tobacco (Nicotiana tabacum L.) is a complex allotetraploid species with a large 4.5-Gb genome that carries duplicated gene copies. In this study, we describe the development of a whole-exome sequencing (WES) procedure in tobacco and its application to characterize a test population of ethyl methanesulfonate (EMS)-induced mutations. A probe set covering 50.3-Mb protein coding regions was designed from a reference tobacco genome. The EMS-induced mutations in 19 individual M2 lines were analyzed using our mutation analysis pipeline optimized to minimize false positives/negatives. In the target regions, the on-target rate of WES was approximately 75%, and 61,146 mutations were detected in the 19 M2 lines. Most of the mutations (98.8%) were single nucleotide variants, and 95.6% of them were C/G to T/A transitions. The number of mutations detected in the target coding sequences by WES was 93.5% of the mutations detected by whole-genome sequencing (WGS). The amount of sequencing data necessary for efficient mutation detection was significantly lower in WES (11.2 Gb), which is only 6.2% of the required amount in WGS (180 Gb). Thus, WES was almost comparable to WGS in performance but is more cost effective. Therefore, the developed target exome sequencing, which could become a fundamental tool in high-throughput mutation identification, renders the genome-wide analysis of tobacco highly efficient.
Collapse
Affiliation(s)
- Hisashi Udagawa
- Leaf Tobacco Research Center, Japan Tobacco Inc., Oyama, Japan
| | - Hiroyuki Ichida
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | | | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | | |
Collapse
|
20
|
Guo H, Du Q, Xie Y, Xiong H, Zhao L, Gu J, Zhao S, Song X, Islam T, Liu L. Identification of Rice Blast Loss-of-Function Mutant Alleles in the Wheat Genome as a New Strategy for Wheat Blast Resistance Breeding. Front Genet 2021; 12:623419. [PMID: 34093638 PMCID: PMC8170139 DOI: 10.3389/fgene.2021.623419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Blast is caused by the host-specific lineages of the fungus Magnaporthe oryzae and is the most important destructive disease in major crop plants, including rice and wheat. The first wheat blast outbreak that occurred in Bangladesh in 2016 and the recent epidemic in Zambia were caused by the M. oryzae Triticum (MoT) pathotype, a fungal lineage belonging to M. oryzae. Although a few reported wheat cultivars show modest resistance to MoT, the patterns of genetic variation and diversity of this pathotype make it crucial to identify additional lines of resistant wheat germplasm. Nearly 40 rice blast resistant and susceptible genes have so far been cloned. Here, we used BLAST analysis to locate two rice blast susceptible genes in the wheat reference genome, bsr-d1 and bsr-k1, and identified six identical homologous genes located on subgenomes A, B, and D. We uncovered a total of 171 single nucleotide polymorphisms (SNPs) in an ethyl methanesulfonate (EMS)-induced population, with mutation densities ranging from 1/1107.1 to 1/230.7 kb through Targeting Induced Local Lesions IN Genomes (TILLING) by sequencing. These included 81 SNPs located in exonic and promoter regions, and 13 coding alleles that are predicted to have severe effects on protein function, including two pre-mature mutants that might affect wheat blast resistance. The loss-of-function alleles identified in this study provide insights into new wheat blast resistant lines, which represent a valuable breeding resource.
Collapse
Affiliation(s)
- Huijun Guo
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qidi Du
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongdun Xie
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiyun Song
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Luxiang Liu
- National Engineering Laboratory for Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
21
|
Du Y, Hase Y, Satoh K, Shikazono N. Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining. JOURNAL OF RADIATION RESEARCH 2020; 61:639-647. [PMID: 32766789 PMCID: PMC7482170 DOI: 10.1093/jrr/rraa059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/01/2020] [Accepted: 07/14/2020] [Indexed: 05/03/2023]
Abstract
To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70-/- and AtLig4-/-). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70-/- mutant was slightly more sensitive than the AtLig4-/- mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11-30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3-4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.
Collapse
Affiliation(s)
- Yan Du
- Biophysics Group, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, PR China
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Yoshihiro Hase
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
- Corresponding author. Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan. Tel: +81-27-346-9032; Fax: +81-27-346-9688;
| | - Katsuya Satoh
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| | - Naoya Shikazono
- Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 1233 Watanuki, Takasaki, Gunma 370-1292, Japan
| |
Collapse
|
22
|
Tabassum R, Dosaka T, Ichida H, Morita R, Ding Y, Abe T, Katsube-Tanaka T. FLOURY ENDOSPERM11-2 encodes plastid HSP70-2 involved with the temperature-dependent chalkiness of rice (Oryza sativa L.) grains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:604-616. [PMID: 32215974 DOI: 10.1111/tpj.14752] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 02/01/2020] [Accepted: 03/10/2020] [Indexed: 05/23/2023]
Abstract
The frequent occurrence of chalky rice (Oryza sativa L.) grains becomes a serious problem as a result of climate change. The molecular mechanism underlying chalkiness is largely unknown, however. In this study, the temperature-sensitive floury endosperm11-2 (flo11-2) mutant was isolated from ion beam-irradiated rice of 1116 lines. The flo11-2 mutant showed significantly higher chalkiness than the wild type grown under a mean temperature of 28°C, but similar levels of chalkiness to the wild type grown under a mean temperature of 24°C. Whole-exome sequencing of the flo11-2 mutant showed three causal gene candidates, including Os12g0244100, which encodes the plastid-localized 70-kDa heat shock protein 2 (cpHSP70-2). The cpHSP70-2 of the flo11-2 mutant has an amino acid substitution on the 259th aspartic acid with valine (D259V) in the conserved Motif 5 of the ATPase domain. Transgenic flo11-2 mutants that express the wild-type cpHSP70-2 showed significantly lower chalkiness than the flo11-2 mutant. Moreover, the accumulation level of cpHSP70-2 was negatively correlated with the chalky ratio, indicating that cpHSP70-2 is a causal gene for the chalkiness of the flo11-2 mutant. The intrinsic ATPase activity of recombinant cpHSP70-2 was lower by 23% at Vmax for the flo11-2 mutant than for the wild type. The growth of DnaK-defective Escherichia coli cells complemented with DnaK with the D201V mutation (equivalent to the D259V mutation) was severely reduced at 37°C, but not in the wild-type DnaK. The results indicate that the lowered cpHSP70-2 function is involved with the chalkiness of the flo11-2 mutant.
Collapse
Affiliation(s)
- Rehenuma Tabassum
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, 606-8502, Japan
- Department of Crop Botany and Tea Production Technology, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Tokinori Dosaka
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Hiroyuki Ichida
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama, 351-0198, Japan
| | - Ryouhei Morita
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama, 351-0198, Japan
| | - Yifan Ding
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, 606-8502, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Saitama, 351-0198, Japan
| | | |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Mutagenic Effect of Three Ion Beams on Rice and Identification of Heritable Mutations by Whole Genome Sequencing. PLANTS 2020; 9:plants9050551. [PMID: 32357388 PMCID: PMC7284785 DOI: 10.3390/plants9050551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
High-energy ion beams are known to be an effective and unique type of physical mutagen in plants. However, no study on the mutagenic effect of argon (Ar) ion beam radiation on rice has been reported. Genome-wide studies on induced mutations are important to comprehend their characteristics for establishing knowledge-based protocols for mutation induction and breeding, which are still very limited in rice. The present study aimed to investigate the mutagenic effect of three ion beams, i.e., Ar, carbon (C) and neon (Ne) on rice and identify and characterize heritable induced mutations by the whole genome sequencing of six M4 plants. Dose-dependent damage effects were observed on M1 plants, which were developed from ion beam irradiated dry seeds of two indica (LH15, T23) and two japonica (DS551, DS48) rice lines. High frequencies of chlorophyll-deficient seedlings and male-sterile plants were observed in all M2 populations (up to ~30% on M1 plant basis); plants from the seeds of different panicles of a common M1 plant appeared to have different mutations; the whole genome-sequencing demonstrated that there were 236–453 mutations in each of the six M4 plants, including single base substitutions (SBSs) and small insertion/deletions (InDels), with the number of SBSs ~ 4–8 times greater than that of InDels; SBS and InDel mutations were distributed across different genomic regions of all 12 chromosomes, however, only a small number of mutations (0–6) were present in exonic regions that might have an impact on gene function. In summary, the present study demonstrates that Ar, C and Ne ion beam radiation are all effective for mutation induction in rice and has revealed at the genome level the characteristics of the mutations induced by the three ion beams. The findings are of importance to the efficient use of ion beam radiation for the generation and utilization of mutants in rice.
Collapse
|
25
|
Hase Y, Satoh K, Seito H, Oono Y. Genetic Consequences of Acute/Chronic Gamma and Carbon Ion Irradiation of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:336. [PMID: 32273879 PMCID: PMC7113374 DOI: 10.3389/fpls.2020.00336] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/06/2020] [Indexed: 05/19/2023]
Abstract
Gamma rays are the most frequently used ionizing radiation in plant mutagenesis; however, few studies are available on the characteristics of mutations at a genome-wide level. Here, we quantitatively and qualitatively characterized the mutations induced by acute/chronic gamma ray irradiation in Arabidopsis. The data were then compared with those previously obtained for carbon ion irradiation. In the acute irradiation of dry seeds at the same effective survival dose, gamma rays and carbon ions differed substantially, with the former inducing a significantly greater number of total mutation events, while the number of gene-affecting mutation events did not differ between the treatments. This may result from the gamma rays predominantly inducing single-base substitutions, while carbon ions frequently induced deletions ≥2 bp. Mutation accumulation lines prepared by chronic gamma irradiation with 100-500 mGy/h in five successive generations showed higher mutation frequencies per dose compared with acute irradiation of dry seeds. Chronic gamma ray irradiation may induce larger genetic changes compared with acute gamma ray irradiation. In addition, the transition/transversion ratio decreased as the dose rate increased, suggesting that plants responded to very low dose rates of gamma rays (∼1 mGy/h), even though the overall mutation frequency did not increase. These data will aid our understanding of the effects of radiation types and be useful in selecting suitable radiation treatments for mutagenesis.
Collapse
|
26
|
Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice ( Oryza sativa L.) Using Whole-Genome Resequencing. G3-GENES GENOMES GENETICS 2019; 9:3743-3751. [PMID: 31519747 PMCID: PMC6829151 DOI: 10.1534/g3.119.400555] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gamma-rays are the most widely used mutagenic radiation in plant mutation breeding, but detailed characteristics of mutated DNA sequences have not been clarified sufficiently. In contrast, newly introduced physical mutagens, e.g., heavy-ion beams, have attracted geneticists’ and breeders’ interest and many studies on their mutation efficiency and mutated DNA characteristics have been conducted. In this study, we characterized mutations induced by gamma rays and carbon(C)-ion beams in rice (Oryza sativa L.) mutant lines at M5 generation using whole-genome resequencing. On average, 57.0 single base substitutions (SBS), 17.7 deletions, and 5.9 insertions were detected in each gamma-ray-irradiated mutant, whereas 43.7 single SBS, 13.6 deletions, and 5.3 insertions were detected in each C-ion-irradiated mutant. The structural variation (SV) analysis detected 2.0 SVs (including large deletions or insertions, inversions, duplications, and reciprocal translocations) on average in each C-ion-irradiated mutant, while 0.6 SVs were detected on average in each gamma-ray-irradiated mutant. Furthermore, complex SVs presumably having at least two double-strand breaks (DSBs) were detected only in C-ion-irradiated mutants. In summary, gamma-ray irradiation tended to induce larger numbers of small mutations than C-ion irradiation, whereas complex SVs were considered to be the specific characteristics of the mutations induced by C-ion irradiation, which may be due to their different radiation properties. These results could contribute to the application of radiation mutagenesis to plant mutation breeding.
Collapse
|