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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.
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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
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Liu J, Zhao G, Geng J, Geng Z, Dou H, Liu X, An Z, Zhang H, Wang Y. Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton. FRONTIERS IN PLANT SCIENCE 2023; 14:1056662. [PMID: 36875607 PMCID: PMC9978701 DOI: 10.3389/fpls.2023.1056662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were "hotspot" mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.
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Affiliation(s)
- Jianguang Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Jinpeng Geng
- School of Science, Hebei University of Technology, Tianjin, China
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Haikuan Dou
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Xu Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Zetong An
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Shijiazhuang, China
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Hirao AS, Watanabe Y, Hasegawa Y, Takagi T, Ueno S, Kaneko S. Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156224. [PMID: 35644386 DOI: 10.1016/j.scitotenv.2022.156224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M2) progeny derived from 12 first generation (M1) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.
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Affiliation(s)
- Akira S Hirao
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648, Japan
| | - Yoshito Watanabe
- Fukushima Project Headquarters, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan; Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima, Japan.
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Zhang X, Yang F, Ma H, Li J. Evaluation of the Saline–Alkaline Tolerance of Rice (Oryza sativa L.) Mutants Induced by Heavy-Ion Beam Mutagenesis. BIOLOGY 2022; 11:biology11010126. [PMID: 35053124 PMCID: PMC8773086 DOI: 10.3390/biology11010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 01/06/2023]
Abstract
Simple Summary Soil salinization is one of the important obstacles restricting agricultural development. Cultivating new varieties of saline–alkaline-tolerant rice can increase the yield of rice. It is possible to minimize breeding costs and shorten the breeding period through heavy ion beam irradiation mutation breeding. Our research evaluated and screened saline–alkaline-tolerant rice mutants induced by heavy ion beams. The results show that heavy ion beam radiation is an effective method for breeding new saline–alkaline-tolerant rice cultivars, and the selected mutant lines have excellent production performance under saline–alkaline stress. Our research results provide new theoretical and practical insights that can be used to help develop new saline–alkaline-tolerant rice cultivars. Abstract Soil salinity is a widespread and important abiotic factor impeding rice production by adversely affecting seed germination, seedling growth, and plant productivity. In this study, the rice cultivar TH899 was treated with 200 Gy of heavy-ion beam irradiation, and 89 mutant lines with stable phenotypes were selected using the pedigree method based on continuous assessment over six years. The seed germination performance of these mutants was tested under different saline–alkaline concentrations. Five highly tolerant lines were further evaluated in a series of experiments at the seedling stage and in the field. During the seedling stage, the reduction of seedling length, root length, fresh weight, and dry weight were dramatically lower in these five mutants than those in TH899 under saline–alkali stress. The K+/Na+ ratio was higher in these five mutants than in TH899. In the field experiment, the grain yield of mutant lines was higher than that of TH899. In addition, the grain yield of mutant line M89 was higher than that of the local cultivar in actual production. These mutant lines are expected to increase grain yield in soda saline–alkaline regions in northeast China.
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Affiliation(s)
- Xin Zhang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.Z.); (F.Y.); (H.M.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.Z.); (F.Y.); (H.M.)
| | - Hongyuan Ma
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.Z.); (F.Y.); (H.M.)
| | - Jingpeng Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.Z.); (F.Y.); (H.M.)
- Correspondence:
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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.
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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.
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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.
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Xiong H, Guo H, Xie Y, Gu J, Zhao L, Zhao S, Ding Y, Kong F, Sui L, Liu L. Comparative transcriptome analysis of two common wheat varieties induced by 7Li-ion beam irradiation reveals mutation hotspot regions and associated pathways. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2019.108650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Oono Y, Ichida H, Morita R, Nozawa S, Satoh K, Shimizu A, Abe T, Kato H, Hase Y. Genome sequencing of ion-beam-induced mutants facilitates detection of candidate genes responsible for phenotypes of mutants in rice. Mutat Res 2020; 821:111691. [PMID: 32171089 DOI: 10.1016/j.mrfmmm.2020.111691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/07/2020] [Accepted: 02/17/2020] [Indexed: 05/28/2023]
Abstract
Ion beams are physical mutagens used for plant and microbe breeding that cause mutations via a mechanism distinct from those of chemical mutagens or gamma rays. We utilized whole-exome sequencing of rice DNA in order to understand the properties of ion beam-induced mutations in a genome-wide manner. DNA libraries were constructed from selected carbon-ion-beam-induced rice mutants by capturing with a custom probes covering 66.3 M bases of nearly all exons and miRNAs predicted in the genome. A total of 56 mutations, including 24 single nucleotide variations, 23 deletions, and 5 insertions, were detected in five mutant rice lines (two dwarf and three early-heading-date mutants). The mutations were distributed among all 12 chromosomes, and the average mutation frequency in the M1 generation was estimated to be 2.7 × 10-7 per base. Many single base insertions and deletions were associated with homopolymeric repeats, whereas larger deletions up to seven base pairs were observed at polynucleotide repeats in the DNA sequences of the mutation sites. Of the 56 mutations, six were classified as high-impact mutations that caused a frame shift or loss of exons. A gene that was functionally related to the phenotype of the mutant was disrupted by a high-impact mutation in four of the five lines tested, suggesting that whole-exome sequencing of ion-beam-irradiated mutants could facilitate the detection of candidate genes responsible for the mutant phenotypes.
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Affiliation(s)
- Yutaka Oono
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan.
| | - Hiroyuki Ichida
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Ryouhei Morita
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Shigeki Nozawa
- Department of Research Planning and Promotion, QuBS, QST, Takasaki, Gunma, Japan
| | - Katsuya Satoh
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan
| | - Akemi Shimizu
- Radiation Breeding Division (RBD), Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Hitachi-ohmiya, Ibaraki, Japan
| | - Tomoko Abe
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Saitama, Japan
| | - Hiroshi Kato
- Radiation Breeding Division (RBD), Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), Hitachi-ohmiya, Ibaraki, Japan
| | - Yoshihiro Hase
- Department of Radiation-Applied Biology Research, Takasaki Advanced Radiation Research Institute (TARRI), Quantum Beam Science Research Directorate (QuBS), National Institutes for Quantum and Radiological Science and Technology (QST), Takasaki, Gunma, Japan
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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.
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Ichida H, Morita R, Shirakawa Y, Hayashi Y, Abe T. Targeted exome sequencing of unselected heavy-ion beam-irradiated populations reveals less-biased mutation characteristics in the rice genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:301-314. [PMID: 30584677 PMCID: PMC6850588 DOI: 10.1111/tpj.14213] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/20/2018] [Accepted: 12/18/2018] [Indexed: 05/19/2023]
Abstract
Heavy-ion beams have been widely utilized as a novel and effective mutagen for mutation breeding in diverse plant species, but the induced mutation spectrum is not fully understood at the genome scale. We describe the development of a multiplexed and cost-efficient whole-exome sequencing procedure in rice, and its application to characterize an unselected population of heavy-ion beam-induced mutations. The bioinformatics pipeline identified single-nucleotide mutations as well as small and large (>63 kb) insertions and deletions, and showed good agreement with the results obtained with conventional polymerase chain reaction (PCR) and sequencing analyses. We applied the procedure to analyze the mutation spectrum induced by heavy-ion beams at the population level. In total, 165 individual M2 lines derived from six irradiation conditions as well as eight pools from non-irradiated 'Nipponbare' controls were sequenced using the newly established target exome sequencing procedure. The characteristics and distribution of carbon-ion beam-induced mutations were analyzed in the absence of bias introduced by visual mutant selections. The average (±SE) number of mutations within the target exon regions was 9.06 ± 0.37 induced by 150 Gy irradiation of dry seeds. The mutation frequency changed in parallel to the irradiation dose when dry seeds were irradiated. The total number of mutations detected by sequencing unselected M2 lines was correlated with the conventional mutation frequency determined by the occurrence of morphological mutants. Therefore, mutation frequency may be a good indicator for sequencing-based determination of the optimal irradiation condition for induction of mutations.
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Affiliation(s)
- Hiroyuki Ichida
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Ryouhei Morita
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Yoriko Hayashi
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator‐Based ScienceWakoSaitama351‐0198Japan
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11
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Guo X, Zhang M, Gao Y, Cao G, Yang Y, Lu D, Li W. A genome-wide view of mutations in respiration-deficient mutants of Saccharomyces cerevisiae selected following carbon ion beam irradiation. Appl Microbiol Biotechnol 2019; 103:1851-1864. [PMID: 30661110 DOI: 10.1007/s00253-019-09626-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/10/2018] [Accepted: 12/16/2018] [Indexed: 12/15/2022]
Abstract
Mitochondrial dysfunction in Saccharomyces cerevisiae was selected as a marker of ion penetration following carbon ion beam (CIB) irradiation. Respiration-deficient mutants were screened. Following confirmation of negligible spontaneous mutation, eight genetically stable S. cerevisiae respiration-deficient mutant strains and a control strain were resequenced with ~ 200-fold read depth. Strategies were established to identify and validate the particular mutations induced by CIB irradiation. In the nuclear genome, CIB irradiation mainly caused base substitutions and some small (< 100 bp) insertions/deletions (indels), which were widely distributed across the chromosomes. Although mitochondrial dysfunction was selected as a screening marker, variants in the nuclear genome were detected at a high frequency (10-7) relative to spontaneous mutations (10-9). The transition to transversion ratio for base substitutions was 0.746, which was less than that of spontaneous mutations. In the mitochondrial genome, there were very large deletions including substantial gene areas, resulting in extremely low read coverage. Meanwhile, every mutant possessed a distinctive mutation pattern, for both the nuclear and the mitochondrial genome. Nuclear genomes contained scanty mitochondrial respiration-related genes that were potentially affected by verified mutations, suggesting that variants in the mitochondrial genome may be the main drivers of respiratory deficiencies. Our study confirmed the previous finding that heavy ion beam (HIB) irradiation mainly induces substantial base substitutions and some small indels but also yielded some novel findings, in particular, novel structural variants in the mitochondrial genomes. These data will enhance the understanding of HIB-induced damage and mutations and aid in the HIB-based microbial mutation breeding.
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Affiliation(s)
- Xiaopeng Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Miaomiao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China
| | - Yue Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guozhen Cao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Department of Pharmacology, School of Preclinical Medicine of Xinjiang Medical University, Urumqi, 830011, China
| | - Yang Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou, 730050, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China.
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Gansu Key Laboratory of Microbial Resources Exploition and Application, Lanzhou, 730000, China.
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12
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Wang L, Ma R, Yin Y, Jiao Z. Antioxidant response of Arabidopsis thaliana seedlings to oxidative stress induced by carbon ion beams irradiation. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2018; 195:1-8. [PMID: 30237078 DOI: 10.1016/j.jenvrad.2018.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/25/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Due to the fact that carbon ion beams irradiation as an important type of ionizing radiation can potentially cause oxidative stress in plants, it is significant to evaluate the antioxidant response of plants to carbon ion beams radiation. Therefore, the objective of this study is to investigate the effects of carbon ion beams irradiation on oxidative stress induced by reactive oxygen species (ROS) and antioxidant response in Arabidopsis thaliana seedlings by irradiating the dry seeds at various doses of carbon ion beams (0, 50, 100, 150 and 200 Gy) and measuring the plant growth parameters, ROS and malondialdehyde (MDA) levels, activities of antioxidant systems and antioxidant-related gene expression. The results showed that 50-Gy carbon ion beam irradiation exhibited stimulatory effects on germination index, root length and fresh weight in Arabidopsis seedlings, while high-dose irradiation (100-200 Gy) inhibited plant growth. Moreover, the production rate of superoxide anion radical, hydroxyl radical generation activity, hydrogen peroxide and MDA contents in Arabidopsis seedlings were obviously increased with the irradiation dose. Additionally, the antioxidant enzyme activities (superoxide dismutase, catalase and peroxidase) and non-enzymatic antioxidant contents (ascorbate and glutathione) in 50-Gy irradiated seedlings were apparently higher than control. Notably, transcriptional analysis displayed that 50-Gy carbon ion beams irradiation could enhance the expression of antioxidant-related genes in Arabidopsis seedlings. These results suggest that the improved activities of antioxidant systems induced by moderate ROS levels play important roles in growth promotion of Arabidopsis seedlings caused by low-dose carbon ion beams irradiation.
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Affiliation(s)
- Lin Wang
- Henan Key Laboratory of Ion-beam Bioengineering, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruonan Ma
- Henan Key Laboratory of Ion-beam Bioengineering, Zhengzhou University, Zhengzhou, 450052, China
| | - Yue Yin
- Henan Key Laboratory of Ion-beam Bioengineering, Zhengzhou University, Zhengzhou, 450052, China
| | - Zhen Jiao
- Henan Key Laboratory of Ion-beam Bioengineering, Zhengzhou University, Zhengzhou, 450052, China.
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13
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Liu L, Hu W, Li WJ, Wang SY, Lu D, Tian XJ, Mao YQ, Liu J, Chen JH. Heavy-ion mutagenesis significantly enhances enduracidin production by Streptomyces fungicidicus. Eng Life Sci 2018; 19:112-120. [PMID: 32624993 DOI: 10.1002/elsc.201800109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/09/2018] [Accepted: 11/16/2018] [Indexed: 11/11/2022] Open
Abstract
To improve fermentative production of enduracidin, heavy-ion beams generated by the Heavy Ion Research Facility in Lanzhou (HIRFL), China, were employed for the first time to generate mutations in Streptomyces fungicidicus. Initial screening detected 44 positive mutants with larger inhibition zone, which were subsequently tested based on flask fermentation. Finally, 20 mutants showed 20% increase in enduracidin production, when compared with the original strain. Among them, enduracidin production by the three mutants (M13, M30, and M34) was significantly higher than that by the original strain. In particular, mutant M30 exhibited highest enduracidin production, which was 114% higher than that obtained with the original strain. Following culture optimization, the maximal enduracidin yield obtained by M30 reached 918.5 mg/L in 10 days, which was 34% higher than that noted in the control.
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Affiliation(s)
- Lu Liu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Wei Hu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Wen-Jian Li
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Shu-Yang Wang
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Dong Lu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Xue-Jiao Tian
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Yan-Qin Mao
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China.,University of Chinese Academy of Sciences Beijing P. R. China
| | - Jing Liu
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
| | - Ji-Hong Chen
- Institute of Modern Physics Chinese Academy of Sciences Lanzhou P. R. China
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