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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.
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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.)
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Ishii K, Kazama Y, Hirano T, Fawcett JA, Sato M, Hirai MY, Sakai F, Shirakawa Y, Ohbu S, Abe T. Genomic view of heavy-ion-induced deletions associated with distribution of essential genes in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2024; 15:1352564. [PMID: 38693931 PMCID: PMC11061394 DOI: 10.3389/fpls.2024.1352564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/11/2024] [Indexed: 05/03/2024]
Abstract
Heavy-ion beam, a type of ionizing radiation, has been applied to plant breeding as a powerful mutagen and is a promising tool to induce large deletions and chromosomal rearrangements. The effectiveness of heavy-ion irradiation can be explained by linear energy transfer (LET; keV µm-1). Heavy-ion beams with different LET values induce different types and sizes of mutations. It has been suggested that deletion size increases with increasing LET value, and complex chromosomal rearrangements are induced in higher LET radiations. In this study, we mapped heavy-ion beam-induced deletions detected in Arabidopsis mutants to its genome. We revealed that deletion sizes were similar between different LETs (100 to 290 keV μm-1), that their upper limit was affected by the distribution of essential genes, and that the detected chromosomal rearrangements avoid disrupting the essential genes. We also focused on tandemly arrayed genes (TAGs), where two or more homologous genes are adjacent to one another in the genome. Our results suggested that 100 keV µm-1 of LET is enough to disrupt TAGs and that the distribution of essential genes strongly affects the heritability of mutations overlapping them. Our results provide a genomic view of large deletion inductions in the Arabidopsis genome.
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Affiliation(s)
- Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Radiation Measurement and Dose Assessment, Institute for Radiological Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Japan
| | - Tomonari Hirano
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jeffrey A. Fawcett
- RIKEN Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), Wako, Japan
| | - Muneo Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | | | - Yuki Shirakawa
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Sumie Ohbu
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science, Wako, Japan
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Hirano T, Murata M, Watarikawa Y, Hoshino Y, Abe T, Kunitake H. Distinctive development of embryo and endosperm caused by male gametes irradiated with carbon-ion beam. PLANT REPRODUCTION 2024:10.1007/s00497-024-00496-9. [PMID: 38332356 DOI: 10.1007/s00497-024-00496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE In Cyrtanthus mackenii, development of embryo and endosperm were differentially affected by fertilization of male gametes with DNA damage and mutations. Pollen irradiation with ionizing radiations has been applied in plant breeding and genetic research, and haploid plant induction has mainly been performed by male inactivation with high-dose irradiation. However, the fertilization process of irradiated male gametes and the early development of embryo and endosperm have not received much attention. Heavy-ion beams, a type of radiation, have been widely applied as effective mutagens for plants and show a high mutation rate even at low-dose irradiation. In this study, we analyzed the effects of male gametes of Cyrtanthus mackenii irradiated with a carbon-ion beam at low doses on fertilization. In immature seeds derived from the pollination of irradiated pollen grains, two types of embryo sacs were observed: embryo sac with a normally developed embryo and endosperm and embryo sac with an egg cell or an undivided zygote and an endosperm. Abnormalities in chromosome segregation, such as chromosomal bridges, were observed only in the endosperm nuclei, irrespective of the presence or absence of embryogenesis. Therefore, in Cyrtanthus, embryogenesis is strongly affected by DNA damage or mutations in male gametes. Moreover, various DNA contents were detected in the embryo and endosperm nuclei, and endoreduplication may have occurred in the endosperm nuclei. As carbon-ion irradiation causes chromosomal rearrangements even at low doses, pollen irradiation can be an interesting tool for studying double fertilization and mutation heritability.
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Affiliation(s)
- Tomonari Hirano
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan.
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Muneaki Murata
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Yurie Watarikawa
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
| | - Yoichiro Hoshino
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, 060-0811, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hisato Kunitake
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai Nishi, Miyazaki, 889-2192, Japan
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Yin Y, Cui D, Chi Q, Xu H, Guan P, Zhang H, Jiao T, Wang X, Wang L, Sun H. Reactive oxygen species may be involved in the distinctive biological effects of different doses of 12C 6+ ion beams on Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 14:1337640. [PMID: 38312361 PMCID: PMC10835405 DOI: 10.3389/fpls.2023.1337640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/31/2023] [Indexed: 02/06/2024]
Abstract
Introduction Heavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated by an increase in root and biomass, while 200 Gy irradiation significantly inhibited the growth of seedlings, causing a visible decrease in plant growth. Methods The Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels. Results and discussion Monte Carlo simulations revealed that high-dose irradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170 DEGs were present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cell wall homeostasis. Further GO enrichment of DEGs unique to 50 Gy and 200 Gy revealed 58 50Gy-exclusive DEGs were enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advances our insight into the biological effects of heavy ion irradiation and the underlying mechanisms.
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Affiliation(s)
- Yue Yin
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Dongjie Cui
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Qing Chi
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Hangbo Xu
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Panfeng Guan
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tao Jiao
- Asset Management Co., Ltd, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojie Wang
- School of Bioengineering, Xinxiang University, Xinxiang, China
| | - Lin Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hao Sun
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
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Wen X, Li J, Yang F, Zhang X, Li Y. Exploring the Effect of High-Energy Heavy Ion Beam on Rice Genome: Transposon Activation. Genes (Basel) 2023; 14:2178. [PMID: 38137000 PMCID: PMC10742395 DOI: 10.3390/genes14122178] [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: 10/30/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
High-energy heavy ion beams are a new type of physical mutagen that can produce a wide range of phenotypic variations. In order to understand the mechanism of high-energy heavy ion beams, we resequenced the whole genome of individual plants with obvious phenotypic variations in rice. The sequence alignment results revealed a large number of SNPs and InDels, as well as genetic variations related to grain type and heading date. The distribution of SNP and InDel on chromosomes is random, but they often occur in the up/downstream regions and the intergenic region. Mutagenesis can cause changes in transposons such as Dasheng, mPing, Osr13 and RIRE2, affecting the stability of the genome. This study obtained the major gene mutation types, discovered differentially active transposons, screened out gene variants related to phenotype, and explored the mechanism of high-energy heavy ion beam radiation on rice genes.
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Affiliation(s)
- Xiaoting Wen
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingpeng Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- Jilin Provincial Laboratory of Crop Germplasm Resources, Changchun 130299, China
| | - Fu Yang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
| | - Xin Zhang
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
| | - Yiwei Li
- Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (X.W.); (F.Y.); (X.Z.); (Y.L.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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Ogawa M, Tsuneizumi K, Abe T, Nozawa M. Testing immediate dosage compensation in Drosophila miranda via irradiation with heavy-ion beams. Genes Genet Syst 2023; 98:201-206. [PMID: 37779054 DOI: 10.1266/ggs.23-00100] [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] [Indexed: 10/03/2023] Open
Abstract
Many organisms with heteromorphic sex chromosomes possess a mechanism of dosage compensation (DC) in which X-linked genes are upregulated in males to mitigate the dosage imbalance between sexes and between chromosomes. However, how quickly the DC is established during evolution remains unknown. In this study, by irradiating Drosophila miranda male flies, which carry young sex chromosomes (the so-called neo-sex chromosomes), with heavy-ion beams, we induced deletions in the neo-Y chromosome to mimic the condition of Y-chromosome degeneration, in which functional neo-Y-linked genes are nonfunctionalized; furthermore, we tested whether their neo-X-linked gametologs were immediately upregulated. Because the males that received 2-Gy iron-ion beam irradiation exhibited lower fertility, we sequenced the genomes and transcriptomes of six F1 males derived from these males. Our pipeline identified 82 neo-Y-linked genes in which deletions were predicted in the F1 males. Only three of them showed a one-to-one gametologous relationship with the neo-X-linked genes. The candidate deletions in these three genes occurred in UTRs and did not seriously affect their expression levels. These observations indirectly suggest that DC was unlikely to have operated on the neo-X-linked genes immediately after the pseudogenization of their neo-Y-linked gametologs in D. miranda. Therefore, the dosage imbalance caused by deletions in the neo-Y-linked genes without paralogs may not have effectively been compensated, and individuals with such deletions could have exhibited lethality. Future studies on sex chromosomes at different ages will further reveal the relationship between the age of sex chromosomes and the stringency of DC.
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Affiliation(s)
- Masafumi Ogawa
- Department of Biological Sciences, Tokyo Metropolitan University
| | | | - Tomoko Abe
- Ion Beam Breeding Team, RIKEN Nishina Center for Accelerator-Based Science
| | - Masafumi Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University
- Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University
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Sasaki K, Tanaka T. Overcoming Difficulties in Molecular Biological Analysis through a Combination of Genetic Engineering, Genome Editing, and Genome Analysis in Hexaploid Chrysanthemum morifolium. PLANTS (BASEL, SWITZERLAND) 2023; 12:2566. [PMID: 37447127 DOI: 10.3390/plants12132566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/11/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023]
Abstract
Chrysanthemum is one of the most commercially important ornamental plants globally, of which many new varieties are produced annually. Among these new varieties, many are the result of crossbreeding, while some are the result of mutation breeding. Recent advances in gene and genome sequencing technology have raised expectations about the use of biotechnology and genome breeding to efficiently breed new varieties. However, some features of chrysanthemum complicate molecular biological analysis. For example, chrysanthemum is a hexaploid hyperploid plant with a large genome, while its genome is heterogeneous because of the difficulty of obtaining pure lines due to self-incompatibility. Despite these difficulties, an increased number of reports on transcriptome analysis in chrysanthemum have been published as a result of recent technological advances in gene sequencing, which should deepen our understanding of the properties of these plants. In this review, we discuss recent studies using gene engineering, genome editing, and genome analysis, including transcriptome analysis, to analyze chrysanthemum, as well as the current status of and future prospects for chrysanthemum.
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Affiliation(s)
- Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba 305-0852, Ibaraki, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8518, Ibaraki, Japan
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Feng Z, Du Y, Chen J, Chen X, Ren W, Wang L, Zhou L. Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean ( Glycine max (L.) Merr.). Int J Mol Sci 2023; 24:ijms24108825. [PMID: 37240171 DOI: 10.3390/ijms24108825] [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: 04/26/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M1 generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M2 families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M2 mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M2 generation, their stability was verified, and the genome mutation spectrum of M3 was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion-deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6.27%; meanwhile, the proportions were 0.04% and 4.04% when using gamma rays. A higher proportion of SVs were detected when using the carbon ion beam. The gene effects of missense mutations were greater under carbon-ion beam irradiation, and the gene effects of nonsense mutations were greater under gamma-ray irradiation, which meant that the changes in the amino acid sequences were different between the carbon-ion beam and gamma rays. Taken together, our results demonstrate that both carbon-ion beam and gamma rays are effective techniques for rapid mutation breeding in soybean. If one would like to obtain mutations with a low-frequency phenotype, low levels of background genomic mutations and mutations with a higher proportion of SVs, carbon-ion beams are the best choice.
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Affiliation(s)
- 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
| | - 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
| | - Jingmin 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
| | - 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
| | - Weibin Ren
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Wang
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Libin Zhou
- Biophysics Group, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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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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10
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Ahmad A, Akram W, Wang R, Shahzadi I, Umer M, Yasin NA, Wu T. Pathogenicity factors of Phytophthora melonis revealed by comparative proteomics. JOURNAL OF PLANT INTERACTIONS 2022; 17:183-197. [DOI: 10.1080/17429145.2021.2014581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 06/16/2023]
Affiliation(s)
- Aqeel Ahmad
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Waheed Akram
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
| | - Iqra Shahzadi
- Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Engineering Center of Natural Polymers-based Medical Materials, School of Resource and Environmental Science, Wuhan University, Wuhan, People’s Republic of China
| | - Muhammad Umer
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, People’s Republic of China
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
| | | | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences (IFA, GDAAS) / Vegetable Research Institute, Guangdong Academy of Agriculture Sciences / Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, People’s Republic of China
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11
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Wang J, Zhang Y, Zhou L, Yang F, Li J, Du Y, Liu R, Li W, Yu L. Ionizing Radiation: Effective Physical Agents for Economic Crop Seed Priming and the Underlying Physiological Mechanisms. Int J Mol Sci 2022; 23:ijms232315212. [PMID: 36499532 PMCID: PMC9737873 DOI: 10.3390/ijms232315212] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
To overcome various factors that limit crop production and to meet the growing demand for food by the increasing world population. Seed priming technology has been proposed, and it is considered to be a promising strategy for agricultural sciences and food technology. This technology helps to curtail the germination time, increase the seed vigor, improve the seedling establishment, and enhance the stress tolerance, all of which are conducive to improving the crop yield. Meanwhile, it can be used to reduce seed infection for better physiological or phytosanitary quality. Compared to conventional methods, such as the use of water or chemical-based agents, X-rays, gamma rays, electron beams, proton beams, and heavy ion beams have emerged as promising physics strategies for seed priming as they are time-saving, more effective, environmentally friendly, and there is a greater certainty for yield improvement. Ionizing radiation (IR) has certain biological advantages over other seed priming methods since it generates charged ions while penetrating through the target organisms, and it has enough energy to cause biological effects. However, before the wide utilization of ionizing priming methods in agriculture, extensive research is needed to explore their effects on seed priming and to focus on the underlying mechanism of them. Overall, this review aims to highlight the current understanding of ionizing priming methods and their applicability for promoting agroecological resilience and meeting the challenges of food crises nowadays.
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Affiliation(s)
- Jiaqi Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Zhang
- School of Biological Sciences, The University of Edinburgh, 57 George Square, Edinburgh EH89JU, UK
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fu Yang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jingpeng Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Yan Du
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruiyuan Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.L.); (L.Y.)
| | - Lixia Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730099, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (W.L.); (L.Y.)
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12
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Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:ijms231912053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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13
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Park H, Narasako Y, Abe T, Kunitake H, Hirano T. Comprehensive effects of heavy-ion beam irradiation on sweet potato ( Ipomoea batatas [L.] Lam.). PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:311-316. [PMID: 36349229 PMCID: PMC9592942 DOI: 10.5511/plantbiotechnology.22.0725a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 06/16/2023]
Abstract
Sweet potato is a major root crop with nutritious tuberous roots. The mechanism of tuberous root development has not yet been adequately elucidated. Genetic resources are required to develop the molecular understanding of sweet potato. Heavy-ion beams were applied to hexaploid sweet potato for an increase in genetic variation, after which the comprehensive effects of heavy-ion beam irradiation were investigated. In vitro cultured shoots with an axillary bud of 'Beniharuka' were irradiated with Ar-ions at a dose of 1-5 Gy and C-ions at a dose of 5-20 Gy, and three irradiated lines were separated from each irradiated shoot. The shoot regeneration was inhibited at high doses of each ion irradiation. Ar-ion irradiation had an especially high biological effect on shoot regeneration. A total of 335 lines were obtained, consisting of 104 and 231 lines derived from Ar- and C-ion irradiation, respectively. The change in the DNA content of the lines was analyzed by flow cytometry to evaluate the irradiation-induced damage to the DNA. The two lines demonstrated significant differences in the DNA content and changes at the chromosome level. The screening for the morphological mutants was conducted in the field. Some irradiated lines showed inhibited or no tuberous root phenotype as mutant candidates. Additionally, the high-yield mutant candidates were dominated by Ar-ion irradiation. It was indicated that heavy-ion beam mutagenesis is effective in broadening the range of the phenotypes corresponding to tuberous root formation in hexaploid sweet potato.
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Affiliation(s)
- Hyungjun Park
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Yosuke Narasako
- Kushima AoiFarm Co., 6564-12 Naru, Kushima-shi, Miyazaki 889-3531, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hisato Kunitake
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
| | - Tomonari Hirano
- Nishina Center for Accelerator-Based Science, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadainishi, Miyazaki-shi, Miyazaki 889-2192, Japan
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14
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Light Quality Modulates Photosynthesis and Antioxidant Properties of B. vulgaris L. Plants from Seeds Irradiated with High-Energy Heavy Ions: Implications for Cultivation in Space. PLANTS 2022; 11:plants11141816. [PMID: 35890451 PMCID: PMC9316636 DOI: 10.3390/plants11141816] [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: 06/24/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
Beta vulgaris L. is a crop selected for cultivation in Space for its nutritional properties. However, exposure to ionizing radiation (IR) can alter plant photosynthetic performance and phytochemical production in the extraterrestrial environment. This study investigated if plant growth under different light quality regimes (FL—white fluorescent; RGB—red–green–blue; RB—red–blue) modifies the photosynthetic behavior and bioactive compound synthesis of plants sprouted by dry seeds irradiated with carbon or titanium high-energy ions. The study evidenced that: (i) the plant response depends on the type of heavyion; (ii) control and C-ion-irradiated plants were similar for photosynthetic pigment content and PSII photochemical efficiency, regardless of the LQ regime; (iii) under FL, net photosynthesis (AN) and water use efficiency (iWUE) declined in C- and Ti-ion plants compared to control, while the growth of irradiated plants under RGB and RB regimes offset these differences; (iv) the interaction Ti-ion× RB improved iWUE, and stimulated the production of pigments, carbohydrates, and antioxidants. The overall results highlighted that the cultivation of irradiated plants under specific LQ regimes effectively regulates photosynthesis and bioactive compound amounts in leaf edible tissues. In particular, the interaction Ti-ion × RB improved iWUE and increased pigments, carbohydrates, and antioxidant content.
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15
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Random Mutagenesis as a Promising Tool for Microalgal Strain Improvement towards Industrial Production. Mar Drugs 2022; 20:md20070440. [PMID: 35877733 PMCID: PMC9318807 DOI: 10.3390/md20070440] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
Microalgae have become a promising novel and sustainable feedstock for meeting the rising demand for food and feed. However, microalgae-based products are currently hindered by high production costs. One major reason for this is that commonly cultivated wildtype strains do not possess the robustness and productivity required for successful industrial production. Several strain improvement technologies have been developed towards creating more stress tolerant and productive strains. While classical methods of forward genetics have been extensively used to determine gene function of randomly generated mutants, reverse genetics has been explored to generate specific mutations and target phenotypes. Site-directed mutagenesis can be accomplished by employing different gene editing tools, which enable the generation of tailor-made genotypes. Nevertheless, strategies promoting the selection of randomly generated mutants avoid the introduction of foreign genetic material. In this paper, we review different microalgal strain improvement approaches and their applications, with a primary focus on random mutagenesis. Current challenges hampering strain improvement, selection, and commercialization will be discussed. The combination of these approaches with high-throughput technologies, such as fluorescence-activated cell sorting, as tools to select the most promising mutants, will also be discussed.
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Hirano T, Kazama Y, Kunitake H, Abe T. Mutagenic Effects of Heavy-Ion Beam Irradiation to Plant Genome. CYTOLOGIA 2022. [DOI: 10.1508/cytologia.87.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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17
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Sato Y, Hirano T, Hayashi Y, Fukunishi N, Abe T, Kawano S. Screening for High-Growth Mutants in Sporophytes of Undaria pinnatifida Using Heavy-Ion Beam Irradiation. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoichi Sato
- Bio-Resources Business Development Division, Riken Food Co., Ltd
| | | | | | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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18
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Hirano T, Matsuyama Y, Hanada A, Hayashi Y, Abe T, Kunitake H. DNA Damage Response of Cyrtanthus mackenii Male Gametes Following Argon Ion Beam Irradiation. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Anna Hanada
- Faculty of Agriculture, University of Miyazaki
| | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
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19
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Morita R, Ichida H, Hayashi Y, Ishii K, Shirakawa Y, Usuda-Kogure S, Ichinose K, Hatashita M, Takagi K, Miura K, Kusajima M, Nakashita H, Endo T, Tojo Y, Okumoto Y, Sato T, Toriyama K, Abe T. Responsible Gene Analysis of Phenotypic Mutants Revealed the Linear Energy Transfer (LET)-Dependent Mutation Spectrum in Rice. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | - Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Science
| | | | | | | | | | | | - Kotaro Miura
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Miyuki Kusajima
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Hideo Nakashita
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Takashi Endo
- Miyagi Prefectural Furukawa Agricultural Experiment Station
| | | | | | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Science
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20
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Matsuta A, Mayuzumi T, Katano H, Hatashita M, Takagi K, Hayashi Y, Abe T, Murai K, Kazama Y. The Effect of Heavy-Ion Beams with High Linear Energy Transfer on Mutant Production in M 1 Generation of Torenia fournieri. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Ayaka Matsuta
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Takahiro Mayuzumi
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Hajime Katano
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | | | - Keiichi Takagi
- Research and Development Department, Wakasa Wan Energy Research Center
| | | | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN
| | - Koji Murai
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
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21
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Kobayashi T, Takahashi M, Nishijima R, Sugiyama R, Ishii K, Kawano S, Kazama Y. Effective Chromosomal Preparation Protocol for the Dioecious Plant Silene latifolia. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Taiki Kobayashi
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Masako Takahashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Ryo Nishijima
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
| | - Ryuji Sugiyama
- Botanical Garden, Faculty of Agriculture, Tokyo University of Agriculture
| | - Kotaro Ishii
- Nishina Center for Accelerator-Based Science, RIKEN
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Yusuke Kazama
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University
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22
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De Micco V, De Francesco S, Amitrano C, Arena C. Comparative Analysis of the Effect of Carbon- and Titanium-Ions Irradiation on Morpho-Anatomical and Biochemical Traits of Dolichos melanophthalmus DC. Seedlings Aimed to Space Exploration. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112272. [PMID: 34834635 PMCID: PMC8618800 DOI: 10.3390/plants10112272] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/28/2021] [Accepted: 10/21/2021] [Indexed: 05/11/2023]
Abstract
The realization of manned missions for space exploration requires the development of Bioregenerative Life Support Systems (BLSSs) to make human colonies self-sufficient in terms of resources. Indeed, in these systems, plants contribute to resource regeneration and food production. However, the cultivation of plants in space is influenced by ionizing radiation which can have positive, null, or negative effects on plant growth depending on intrinsic and environmental/cultivation factors. The aim of this study was to analyze the effect of high-LET (Linear Energy Transfer) ionizing radiation on seed germination and seedling development in eye bean. Dry seeds of Dolichos melanophthalmus DC. (eye bean) were irradiated with two doses (1 and 10 Gy) of C- and Ti-ions. Seedlings from irradiated seeds were compared with non-irradiated controls in terms of morpho-anatomical and biochemical traits. Results showed that the responses of eye bean plants to radiation are dose-specific and dependent on the type of ion. The information obtained from this study will be useful for evaluating the radio-resistance of eye bean seedlings, for their possible cultivation and utilization as food supplement in space environments.
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Affiliation(s)
- Veronica De Micco
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (S.D.F.); (C.A.)
- Correspondence:
| | - Sara De Francesco
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (S.D.F.); (C.A.)
| | - Chiara Amitrano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; (S.D.F.); (C.A.)
| | - Carmen Arena
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Napoli, Italy;
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), 80055 Portici, Italy
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23
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Double Mutant Analysis with the Large Flower Mutant, ohbana1, to Explore the Regulatory Network Controlling the Flower and Seed Sizes in Arabidopsis thaliana. PLANTS 2021; 10:plants10091881. [PMID: 34579413 PMCID: PMC8473154 DOI: 10.3390/plants10091881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/19/2022]
Abstract
Two growth processes, cell proliferation and expansion, determine plant species-specific organ sizes. A large flower mutant in Arabidopsis thaliana, ohbana1 (ohb1), was isolated from a mutant library. In the ohb1 flowers, post-mitotic cell expansion and endoreduplication of nuclear DNA were promoted. The whole-genome resequencing and genetic analysis results showed that the loss of function in MEDIATOR16 (MED16), a mediator complex subunit, was responsible for the large flower phenotypes exhibited by ohb1. A phenotypic analysis of the mutant alleles in MED16 and the double mutants created by crossing ohb1 with representative large flower mutants revealed that MED16 and MED25 share part of the negative petal size regulatory pathways. Furthermore, the double mutant analyses suggested that there were genetically independent pathways leading to cell size restrictions in the floral organs which were not related to the MED complex. Several double mutants also formed larger and heavier seeds than the wild type and single mutant plants, which indicated that MED16 was involved in seed size regulation. This study has revealed part of the size-regulatory network in flowers and seeds through analysis of the ohb1 mutant, and that the size-regulation pathways are partially different between floral organs and seeds.
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Light Spectral Composition Influences Structural and Eco-Physiological Traits of Solanum lycopersicum L. cv. 'Microtom' in Response to High-LET Ionizing Radiation. PLANTS 2021; 10:plants10081752. [PMID: 34451797 PMCID: PMC8399554 DOI: 10.3390/plants10081752] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/06/2021] [Accepted: 08/22/2021] [Indexed: 01/16/2023]
Abstract
This study evaluated if specific light quality (LQ) regimes (white fluorescent, FL; full-spectrum, FS; red-blue, RB) during plant growth modified morphological and photosynthetic traits of Solanum lycopersicum L. 'Microtom' plants irradiated at the dry seed stage with 25 Gy 48Ca ions (IR). The irradiation reduced plant size while it increased leaf dry matter content (LDMC) and relative water content (RWC) compared to the control. FS and RB light regimes determined a decrease of plant height and a rise of RWC compared to FL plants. The irradiation under FS and RB regimes favoured the development of dwarf plants and improved the leaf water status. Under the FL regime, irradiated plants showed reduced photosynthesis and stomatal conductance. The opposite behavior was observed in RB irradiated plants in which gas exchanges were significantly stimulated. RB regime enhanced Rubisco expression in irradiated plants also inducing anatomical and functional adjustments (i.e., increase of leaf thickness and incidence of intercellular spaces). Finally, 48Ca ions did not prevent fruit ripening and the achievement of the 'seed-to seed' cycle, irrespective of the LQ regime. Overall, the present study evidenced that RB light regime was the most effective in optimising growth and photosynthetic efficiency of 'Microtom' irradiated plants. These outcomes may help to develop proper cultivation protocols for the growth of dwarf tomato in Controlled Ecological Life Support Systems (CELSS).
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Sanjaya A, Kazama Y, Ishii K, Muramatsu R, Kanamaru K, Ohbu S, Abe T, Fujiwara MT. An Argon-Ion-Induced Pale Green Mutant of Arabidopsis Exhibiting Rapid Disassembly of Mesophyll Chloroplast Grana. PLANTS (BASEL, SWITZERLAND) 2021; 10:848. [PMID: 33922223 PMCID: PMC8145761 DOI: 10.3390/plants10050848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 01/13/2023]
Abstract
Argon-ion beam is an effective mutagen capable of inducing a variety of mutation types. In this study, an argon ion-induced pale green mutant of Arabidopsis thaliana was isolated and characterized. The mutant, designated Ar50-33-pg1, exhibited moderate defects of growth and greening and exhibited rapid chlorosis in photosynthetic tissues. Fluorescence microscopy confirmed that mesophyll chloroplasts underwent substantial shrinkage during the chlorotic process. Genetic and whole-genome resequencing analyses revealed that Ar50-33-pg1 contained a large 940 kb deletion in chromosome V that encompassed more than 100 annotated genes, including 41 protein-coding genes such as TYRAAt1/TyrA1, EGY1, and MBD12. One of the deleted genes, EGY1, for a thylakoid membrane-localized metalloprotease, was the major contributory gene responsible for the pale mutant phenotype. Both an egy1 mutant and F1 progeny of an Ar50-33-pg1 × egy1 cross-exhibited chlorotic phenotypes similar to those of Ar50-33-pg1. Furthermore, ultrastructural analysis of mesophyll cells revealed that Ar50-33-pg1 and egy1 initially developed wild type-like chloroplasts, but these were rapidly disassembled, resulting in thylakoid disorganization and fragmentation, as well as plastoglobule accumulation, as terminal phenotypes. Together, these data support the utility of heavy-ion mutagenesis for plant genetic analysis and highlight the importance of EGY1 in the structural maintenance of grana in mesophyll chloroplasts.
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Affiliation(s)
- Alvin Sanjaya
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Yusuke Kazama
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
- Faculty of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuoka-Kenjojima, Eiheiji, Yoshida, Fukui 910-1195, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Ryohsuke Muramatsu
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
| | - Kengo Kanamaru
- Faculty of Agriculture, Kobe University, Nada, Kobe, Hyogo 657-8501, Japan;
| | - Sumie Ohbu
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
| | - Makoto T. Fujiwara
- Faculty of Science and Technology, Sophia University, 7-1 Kioicho, Chiyoda, Tokyo 102-8554, Japan; (A.S.); (R.M.)
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (K.I.); (S.O.); (T.A.)
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Vilperte V, Boehm R, Debener T. A highly mutable GST is essential for bract colouration in Euphorbia pulcherrima Willd. Ex Klotsch. BMC Genomics 2021; 22:208. [PMID: 33757424 PMCID: PMC7988969 DOI: 10.1186/s12864-021-07527-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/12/2021] [Indexed: 01/24/2023] Open
Abstract
Background Mutation breeding is an extraordinary tool in plant breeding to increase the genetic variability, where mutations in anthocyanin biosynthesis are targets to generate distinctive phenotypes in ornamental species. In poinsettia, ionizing radiation is routinely applied in breeding programs to obtaining a range of colours, with nearly all pink and white varieties being obtained after γ- or X-ray mutagenesis of red varieties. In the present study we performed a thorough characterization of a potential mutagenesis target gene as the main responsible for the ‘white paradox’ in poinsettia. Results We identified a GST gene in poinsettia (Bract1) as an essential factor for the expression of anthocyanin-based red colouration of bracts, which presents a high phylogenetic similarity to known anthocyanin-related GSTs. Red poinsettia varieties and white mutants generated from these varieties by X-ray were analysed for polymorphisms related to the ‘white paradox’ in the species. A 4 bp mutation in a short repeat within the coding region of Bract1 is most likely responsible for the appearance of white phenotypes upon irradiation treatment. The polymorphism between wild-type and mutant alleles co-segregates with the phenotype in progeny from heterozygous red and white parents. Moreover, overexpression of Bract1 wild-type allele in Arabidopsis tt19 mutants restored the anthocyanin phenotype, while the Bract1 mutated allele showed to be non-functional. Conclusions The identified repeat seems to be highly unstable, since mutated plants can be easily detected among fewer than 200 shoots derived from 10 mutated plants. Our data indicate that particular short repeat sequences, similar to microsatellite sequences or so-called dynamic mutations, might be hot spots for genetic variability. Moreover, the identification of the Bract1 mutation fills a gap on the understanding on the molecular mechanism of colour formation in poinsettia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07527-z.
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Affiliation(s)
- Vinicius Vilperte
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.,Present address: KWS SAAT SE & Co. KGaA, 37574, Einbeck, Germany
| | - Robert Boehm
- Klemm + Sohn GmbH & Co., 70379, Stuttgart, KG, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, 30419, Hannover, Germany.
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Amritha PP, Shah JM. Can genetic engineering-based methods for gene function identification be eclipsed by genome editing in plants? A comparison of methodologies. Mol Genet Genomics 2021; 296:485-500. [PMID: 33751237 DOI: 10.1007/s00438-021-01769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Finding and explaining the functions of genes in plants have promising applications in crop improvement and bioprospecting and hence, it is important to compare various techniques available for gene function identification in plants. Today, the most popular technology among researchers to identify the functions of genes is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-based genome editing method. But by no means can we say that CRISPR/Cas9 is the go-to method for all purposes. It comes with its own baggage. Researchers will agree and have lived through at least seven more technologies deployed to find the functions of genes, which come under three umbrellas: 1. genetic engineering, 2. transient expression, and 3. chemical/physical mutagenesis. Each of the methods evolved when the previous one ran into an insurmountable problem. In this review, we compare the eight technologies against one another on 14 parameters. This review lays bare the pros and cons, and similarities and dissimilarities of various methods. Every method comes with its advantages and disadvantages. For example, the CRISPR/Cas9-based genome editing is an excellent method for modifying gene sequences, creating allelic versions of genes, thereby aiding the understanding of gene function. But it comes with the baggage of unwanted or off-target mutations. Then, we have methods based on random or targeted knockout of the gene, knockdown, and overexpression of the gene. Targeted disruption of genes is required for complete knockout of gene function, which may not be accomplished by editing. We have also discussed the strategies to overcome the shortcomings of the targeted gene-knockout and the CRISPR/Cas9-based methods. This review serves as a comprehensive guide towards the understanding and comparison of various technologies available for gene function identification in plants and hence, it will find application for crop improvement and bioprospecting related research.
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Affiliation(s)
- P P Amritha
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India.
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28
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Tojo H, Nakamura A, Ferjani A, Kazama Y, Abe T, Iida H. A Method Enabling Comprehensive Isolation of Arabidopsis Mutants Exhibiting Unusual Root Mechanical Behavior. FRONTIERS IN PLANT SCIENCE 2021; 12:646404. [PMID: 33747026 PMCID: PMC7966703 DOI: 10.3389/fpls.2021.646404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Root penetration into soils is fundamental for land plants to support their own aboveground parts and forage water and nutrients. To elucidate the molecular mechanisms underlying root mechanical penetration, mutants defective in this behavior need to be comprehensively isolated; however, established methods are currently scarce. We herein report a method to screen for these mutants of Arabidopsis thaliana and present their phenotypes. We isolated five mutants using this method, tentatively named creep1 to creep5, the primary roots of which crept over the surface of horizontal hard medium that hampered penetration by the primary root of the wild type, thereby forcing it to spring up on the surface and die. By examining root skewing, which is induced by a touch stimulation that is generated as the primary roots grow along a vertical impenetrable surface, the five creep mutants were subdivided into three groups, namely mutants with the primary root skewing leftward, those skewing rightward, and that growing dispersedly. While the majority of wild type primary roots skewed slightly leftward, nearly half of the primary roots of creep1 and creep5 skewed rightward as viewed from above. The primary roots of creep4 displayed scattered growth, while those of creep2 and creep3 showed a similar phenotype to the wild type primary roots. These results demonstrate the potential of the method developed herein to isolate various mutants that will be useful for investigating root mechanical behavior regulation not only in Arabidopsis, but also in major crops with economical value.
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Affiliation(s)
- Hiroshi Tojo
- Department of Biology, Tokyo Gakugei University, Koganei, Japan
| | - Aki Nakamura
- Department of Biology, Tokyo Gakugei University, Koganei, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei, Japan
| | - Yusuke Kazama
- Nishina Center for Accelerator-Based Science, RIKEN, Saitama, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, Saitama, Japan
| | - Hidetoshi Iida
- Department of Biology, Tokyo Gakugei University, Koganei, Japan
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Tsuneizumi K, Yamada M, Kim HJ, Ichida H, Ichinose K, Sakakura Y, Suga K, Hagiwara A, Kawata M, Katayama T, Tezuka N, Kobayashi T, Koiso M, Abe T. Application of heavy-ion-beam irradiation to breeding large rotifer. Biosci Biotechnol Biochem 2021; 85:703-713. [PMID: 33624778 DOI: 10.1093/bbb/zbaa094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022]
Abstract
In larviculture facilities, rotifers are generally used as an initial food source, while a proper size of live feeds to connect rotifer and Artemia associated with fish larval growth is needed. The improper management of feed size and density induces mass mortality and abnormal development of fish larvae. To improve the survival and growth of target larvae, this study applied carbon and argon heavy-ion-beam irradiation in mutation breeding to select rotifer mutants with larger lorica sizes. The optimal irradiation conditions of heavy-ion beam were determined with lethality, reproductivity, mutant frequency, and morphometric characteristics. Among 56 large mutants, TYC78, TYC176, and TYA41 also showed active population growth. In conclusion, (1) heavy-ion-beam irradiation was defined as an efficient tool for mutagenesis of rotifers and (2) the aforementioned 3 lines that have larger lorica length and active population growth may be used as a countermeasure of live feed size gap during fish larviculcure.
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Affiliation(s)
| | - Mieko Yamada
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
| | - Hee-Jin Kim
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroyuki Ichida
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
| | | | - Yoshitaka Sakakura
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Koushirou Suga
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Atsushi Hagiwara
- Institute of Integrated Science and Technology, Graduate School of Fisheries Science and Environmental Sciences, Nagasaki University, Nagasaki, Japan.,Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Miki Kawata
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Takashi Katayama
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Nobuhiro Tezuka
- Japan Sea National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Miyazu, Japan
| | - Takanori Kobayashi
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Japan
| | - Masahiko Koiso
- Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Ishigaki, Japan
| | - Tomoko Abe
- Nishina Center for Accelerator-Based Science, RIKEN, Wako, Japan
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Genotype-by-Sequencing Analysis of Mutations and Recombination in Pepper Progeny of Gamma-Irradiated Gametophytes. PLANTS 2021; 10:plants10010144. [PMID: 33445585 PMCID: PMC7827419 DOI: 10.3390/plants10010144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 11/17/2022]
Abstract
The irradiation of dry seeds is the most widely-used irradiation method for improving seed-propagated crops; however, the irradiation of other tissues also has useful effects. The irradiation of plant reproductive organs, rather than seeds, for mutation breeding has advantages, such as producing non-chimeric progeny. However, the mutation frequency and spectrum produced using this method have not been analyzed on a genome-wide level. We performed a genotype-by-sequencing analysis to determine the frequencies of single-base substitutions and small (1–2 bp) insertions and deletions in hot pepper (Capsicum annuum L.) plants derived from crosses using gamma-irradiated female or male gametophytes. The progeny of irradiated gametophytes showed similar or higher DNA mutation frequencies, which were dependent on the irradiation dose and irradiated tissue, and less biased single base substitutions than progeny of irradiated seeds. These characteristics were expected to be beneficial for development of mutation population with a high frequency of small DNA mutations and performing reverse-genetics-based mutation screening. We also examined the possible use of this irradiation method in manipulating the meiotic recombination frequency; however, no statistically significant increase was detected. Our results provide useful information for further research and breeding using irradiated gametophytes.
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31
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Salava H, Thula S, Mohan V, Kumar R, Maghuly F. Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects. Int J Mol Sci 2021; 22:E682. [PMID: 33445555 PMCID: PMC7827871 DOI: 10.3390/ijms22020682] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/31/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.
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Affiliation(s)
- Hymavathi Salava
- Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Sravankumar Thula
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic;
| | - Vijee Mohan
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA;
| | - Rahul Kumar
- Plant Translational Research Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500064, India;
| | - Fatemeh Maghuly
- Plant Functional Genomics, Institute of Molecular Biotechnology, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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32
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Lee SW, Kwon YJ, Baek I, Choi HI, Ahn JW, Kim JB, Kang SY, Kim SH, Jo YD. Mutagenic Effect of Proton Beams Characterized by Phenotypic Analysis and Whole Genome Sequencing in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:752108. [PMID: 34777430 PMCID: PMC8581144 DOI: 10.3389/fpls.2021.752108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 05/19/2023]
Abstract
Protons may have contributed to the evolution of plants as a major component of cosmic-rays and also have been used for mutagenesis in plants. Although the mutagenic effect of protons has been well-characterized in animals, no comprehensive phenotypic and genomic analyses has been reported in plants. Here, we investigated the phenotypes and whole genome sequences of Arabidopsis M2 lines derived by irradiation with proton beams and gamma-rays, to determine unique characteristics of proton beams in mutagenesis. We found that mutation frequency was dependent on the irradiation doses of both proton beams and gamma-rays. On the basis of the relationship between survival and mutation rates, we hypothesized that there may be a mutation rate threshold for survived individuals after irradiation. There were no significant differences between the total mutation rates in groups derived using proton beam or gamma-ray irradiation at doses that had similar impacts on survival rate. However, proton beam irradiation resulted in a broader mutant phenotype spectrum than gamma-ray irradiation, and proton beams generated more DNA structural variations (SVs) than gamma-rays. The most frequent SV was inversion. Most of the inversion junctions contained sequences with microhomology and were associated with the deletion of only a few nucleotides, which implies that preferential use of microhomology in non-homologous end joining was likely to be responsible for the SVs. These results show that protons, as particles with low linear energy transfer (LET), have unique characteristics in mutagenesis that partially overlap with those of low-LET gamma-rays and high-LET heavy ions in different respects.
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Affiliation(s)
- Sang Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Plant Science and Technology, Chung-Ang University, Anseong, South Korea
| | - Yu-Jeong Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- Department of Horticulture, Chonbuk National University, Jeonju-si, South Korea
| | - Inwoo Baek
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Hong-Il Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Jin-Baek Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Si-Yong Kang
- Department of Horticulture, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang Hoon Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
| | - Yeong Deuk Jo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, South Korea
- *Correspondence: Yeong Deuk Jo,
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Li X, Sun S, Yao J, Sun Z. Using Relaxation Time to characterize biological effects of different mutagens. Sci Rep 2020; 10:13941. [PMID: 32811881 PMCID: PMC7434921 DOI: 10.1038/s41598-020-70600-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/31/2020] [Indexed: 11/10/2022] Open
Abstract
All kinds of mutagenic factors may cause physiological, biochemical and genetic changes of all organisms. To characterize their characteristic biology effects, the concept of Relaxation Time (RT) was introduced for the first time, and the specific process was as follows. After mutation of organisms, the offsprings will be continuingly cultured (or cultivated) to the next generation (Rx). Once a biological effect began to show no significant difference compared to the untreated controls, the Rx was defined as the RT of the effect. In this paper, three kinds of mutagenic factors were selected to treat the seeds or seedlings of Astragalus sinicus L., subsequently, the corresponding RT was calibrated. The results showed that the RT was diverse not only among different biological effects but also among different mutagenic factors. For the RT of chemical mutagens and gamma rays, most of which are concentrated on R1, whereas the heavy ion beams have significant differences among different tracks. Among biological effects, the SOD activity and superoxide anion free radical content in the Peak region are more prominent, and their RT reaches R3 and R4, respectively. Thus, the RT may characterize the characteristic biological effects from differently mutagenic factors.
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Affiliation(s)
- Xinglin Li
- Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Shuguang Sun
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Jingxia Yao
- Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Zhengfeng Sun
- Tianjin University of Science and Technology, Tianjin, 300457, 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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35
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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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Chen X, Feng H, Du Y, Luo S, Li W, Yu L, Feng Z, Cui T, Zhou L. Genetic polymorphisms in mutagenesis progeny of Arabidopsis thaliana irradiated by carbon-ion beams and γ-rays irradiations. Int J Radiat Biol 2019; 96:267-275. [PMID: 31692404 DOI: 10.1080/09553002.2020.1688412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: Heavy-ion beams and γ-rays are popular physical mutagenesis to generate mutations in higher plants. It has been found that they show different mutation frequencies and spectrums of phenotype induction, however, the characteristics of heavy-ion beams on genetic polymorphism have not been clarified by comparing with γ-rays.Materials and methods: In the present study, seeds of Arabidopsis thaliana were exposed to carbon-ion beams (with linear energy transfer (LET) of 50 keV/μm) and γ-rays (with average LET of 0.2 keV/μm) irradiation. By using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analysis, the genetic polymorphism of both M1 and M3 plants were investigated, respectively.Results: Carbon-ion beams induced relatively higher polymorphism rate in both M1 and M3 generation than γ-rays: the polymorphism rates of M1 plants derived from carbon-ion beams irradiation are 12.87% (ISSR-C) and 9.01% (RAPD-C), while are 7.67% (ISSR-γ) and 1.45% (RAPD-γ) of plants derived from γ-rays. In M3 generation, the polymorphism rates of ISSR-C, RAPD-C, ISSR-γ, and RAPD-γ are 17.64%, 22.79%, 12.10%, and 2.82%, respectively.Conclusions: In summary, the exposure to carbon-ion beams and γ-rays lead to the change of genomic DNA of A. thaliana, which could be tested in M1 plants and M3 plants by ISSR and RAPD technology. So, both carbon-ion beams and γ-rays can induce variations of genetic polymorphisms in M1 plants and M3 plants. The genetic polymorphisms of M1 plants and M3 plants induced by carbon-ion beams are higher than γ-rays, indicating that heavy-ion beams irradiations mutation breeding is more advantageous than conventional ionizing radiations. Average molecular polymorphism of M1 plants is lower than M3 mutants, by nearly 4.77% (ISSR-C), 13.78% (RAPD-C), 4.43% (ISSR-γ), and 1.37% (RAPD-γ). We hope our study will provide basic information for understanding the effects of carbon-ion beams and γ-rays for plant mutation breeding.
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Affiliation(s)
- Xia Chen
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hui Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Yan Du
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Shanwei Luo
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Wenjian Li
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Lixia Yu
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Zhuo Feng
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Cui
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Libin Zhou
- Department of Biophysics, Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.,Baiyin Innovation Academy for Heavy Ion Bioindustry, Baiyin, China
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Krasovec M, Kazama Y, Ishii K, Abe T, Filatov DA. Immediate Dosage Compensation Is Triggered by the Deletion of Y-Linked Genes in Silene latifolia. Curr Biol 2019; 29:2214-2221.e4. [PMID: 31231053 PMCID: PMC6616318 DOI: 10.1016/j.cub.2019.05.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/27/2019] [Accepted: 05/24/2019] [Indexed: 11/28/2022]
Abstract
The loss of functional genes from non-recombining sex-specific chromosomes [1, 2], such as the Y chromosomes in mammals [3] or W chromosomes in birds [4], should result in an imbalance of gene products for sex-linked genes [5]. Different chromosome-wide systems that rebalance gene expression are known to operate in organisms with relatively old sex chromosomes [6]; e.g., Drosophila overexpress X-linked genes in males [7], while mammals shut down one of the X chromosomes in females [8]. It is not known how long it takes for a chromosome-wide dosage compensation system to evolve. To shed light on the early evolution of dosage compensation, we constructed a high-density Y-deletion map and used deletion mutants to manipulate gene dose and analyze gene expression in white campion (Silene latifolia), which evolved dioecy and sex chromosomes only 11 million years ago [9]. We demonstrate that immediate dosage compensation can be triggered by deletions in a large portion of the p arm of the Y chromosome. Our results indicate that dosage compensation in S. latifolia does not have to evolve gene by gene because a system to upregulate gene expression is already operating on part of the X chromosome, which likely represents an intermediate step in the evolution of a chromosome-wide dosage compensation system in this species.
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Affiliation(s)
- Marc Krasovec
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Yusuke Kazama
- RIKEN Nishina Center for Accelerator-Based Sciences, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center for Accelerator-Based Sciences, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Tomoko Abe
- RIKEN Nishina Center for Accelerator-Based Sciences, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.
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Xu D, Li Y, Yao Z, Yin Y, Feng H, Wei Z. Study on the Relationship between Seed Absorbed Dose and Seed Composition of 252Cf Neutron Source Irradiated Bean Seed. Sci Rep 2019; 9:9635. [PMID: 31270359 PMCID: PMC6610101 DOI: 10.1038/s41598-019-45829-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/29/2019] [Indexed: 12/03/2022] Open
Abstract
This study aims to further identify the biological effects of neutron-irradiated plants and provides insights into the mutation breeding of such plants. In this study, the neutron irradiation device designed by our institute was used to analyze the relationship between the seed components in different legume crops and their neutron absorption dose rate, fission gamma absorption dose rate, and induced gamma absorption dose rate. The results show that the effect sizes of the components on the neutron absorbed dose rate are as follows: ash > fat > moisture > carbohydrate > protein. The effect sizes of the components on the absorbed dose rate of fission gamma are as follows: ash > moisture > fat > carbohydrate > protein. There is a positive correlation between fission gamma absorbed dose rate and the weight of ash, water and fat, while a negative correlation with carbohydrate and protein. However, the linear relationship between each component and the absorbed dose rate of induced gamma is not significant, this needs to be identified by further researches. Based on the results of the present study, we conclude that the neutron absorbed dose can be calculated without taking into account the fat composition of bean crop seeds (except for soybean seeds) in the process of mutation breeding induced by radiation. In special cases where the accuracy requirement of the dose rate is not high, it is possible to use protein instead of legume crop seeds for neutron absorption dose calculations.
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Affiliation(s)
- Dapeng Xu
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China.
- Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China.
| | - Yingguo Li
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
- Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Ze'en Yao
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China.
- Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China.
| | - Yongzhi Yin
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
- Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zheng Wei
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000, China
- Engineering Research Center for Neutron Application Technology, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
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Arena C, Vitale E, Hay Mele B, Cataletto PR, Turano M, Simoniello P, De Micco V. Suitability of Solanum lycopersicum L. 'Microtom' for growth in Bioregenerative Life Support Systems: exploring the effect of high-LET ionising radiation on photosynthesis, leaf structure and fruit traits. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:615-626. [PMID: 30585676 DOI: 10.1111/plb.12952] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/20/2018] [Indexed: 05/09/2023]
Abstract
The realisation of manned space exploration requires the development of Bioregenerative Life Support Systems (BLSS). In such self-sufficient closed habitats, higher plants have a fundamental role in air regeneration, water recovery, food production and waste recycling. In the space environment, ionising radiation represents one of the main constraints to plant growth. In this study, we explore whether low doses of heavy ions, namely Ca 25 Gy, delivered at the seed stage, may induce positive outcomes on growth and functional traits in plants of Solanum lycopersicum L. 'Microtom'. After irradiation of seed, plant growth was monitored during the whole plant life cycle, from germination to fruit ripening. Morphological parameters, photosynthetic efficiency, leaf anatomical functional traits and antioxidant production in leaves and fruits were analysed. Our data demonstrate that irradiation of seeds with 25 Gy Ca ions does not prevent achievement of the seed-to-seed cycle in 'Microtom', and induces a more compact plant size compared to the control. Plants germinated from irradiated seeds show better photochemical efficiency than controls, likely due to the higher amount of D1 protein and photosynthetic pigment content. Leaves of these plants also had smaller cells with a lower number of chloroplasts. The dose of 25 Gy Ca ions is also responsible for positive outcomes in fruits: although developing a lower number of berries, plants germinated from irradiated seeds produce larger berries, richer in carotenoids, ascorbic acid and anthocyanins than controls. These specific traits may be useful for 'Microtom' cultivation in BLSS in space, in so far as the crew members could benefit from fresh food richer in functional compounds that can be directly produced on board.
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Affiliation(s)
- C Arena
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - E Vitale
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - B Hay Mele
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
| | - P R Cataletto
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - M Turano
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - P Simoniello
- Department of Science and Technology, University of Naples Pathenope, Centro Direzionale Isola C4, Naples, Italy
| | - V De Micco
- Department of Agricultural Sciences, University of Naples Federico II, Portici (Naples), Italy
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Kok EJ, Glandorf DC, Prins TW, Visser RG. Food and environmental safety assessment of new plant varieties after the European Court decision: Process-triggered or product-based? Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Frequency and Spectrum of Radiation-Induced Mutations Revealed by Whole-Genome Sequencing Analyses of Plants. QUANTUM BEAM SCIENCE 2019. [DOI: 10.3390/qubs3020007] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mutation breeding and functional genomics studies of mutant populations have made important contributions to plant research involving the application of radiation. The frequency and spectrum of induced mutations have long been regarded as the crucial determinants of the efficiency of the development and use of mutant populations. Systematic studies regarding the mutation frequency and spectrum, including genetic and genomic analyses, have recently resulted in considerable advances. These studies have consistently shown that the mutation frequency and spectrum are affected by diverse factors, including radiation type, linear energy transfer, and radiation dose, as well as the plant tissue type and condition. Moreover, the whole-genome sequencing of mutant individuals based on next-generation sequencing technologies has enabled the genome-wide quantification of mutation frequencies according to DNA mutation types as well as the elucidation of mutation mechanisms based on sequence characteristics. These studies will contribute to the development of a highly efficient and more controlled mutagenesis method relevant for the customized research of plants. We herein review the characteristics of radiation-induced mutations in plants, mainly focusing on recent whole-genome sequencing analyses as well as factors affecting the mutation frequency and spectrum.
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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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Yang G, Luo W, Zhang J, Yan X, Du Y, Zhou L, Li W, Wang H, Chen Z, Guo T. Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants. FRONTIERS IN PLANT SCIENCE 2019; 10:1514. [PMID: 31850019 PMCID: PMC6892775 DOI: 10.3389/fpls.2019.01514] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/31/2019] [Indexed: 05/19/2023]
Abstract
Physical mutagens, such as carbon-ion beams (CIBs) and gamma rays (GRs), induce mutations with high frequency at a relatively low dose and are more user-friendly and environment-friendly in mutation breeding. Previous studies showed that CIBs induced large sized deletions and insertions, and chromosomal rearrangements, whereas GRs induce shorter deletions and insertions, and more frequent base substitutions. However, the difference on the genomic level between CIB- and GR-induced mutations remains to be clarified. In the present study, we re-sequence six mutagenized lines derived from CIB irradiation and four mutagenized lines derived from GRs. A total of 283 and 381 variations are induced in these mutants by CIBs and GRs, respectively, including single base substitutions (SBSs), small insertion and deletions (InDels), multiple nucleotide variants (MNVs). SBSs are the most abundant type of mutation and single base transition is the main form for SBSs. CIB-induced InDels accounted for 25.44% of the total variations, while GR-induced InDels accounted for 17.85%. On the contrary, the frequency of MNVs induced by GRs was approximately 2.19 times that induced by CIBs, which indicates CIBs induced increased InDels, whereas GRs induced increased MNVs. Notably, multiple base deletions (≥5 bp) were induced at a much higher frequency by CIBs than by GRs. We also find mutations induced by CIBs and GRs are unevenly distributed on chromosomes. Unusual high-frequency (HF) and low-frequency (LF) mutation regions are discovered by analyzing mutations per 1Mb along the genome. The mutation frequency within the HF regions were significantly higher than the LF regions (P < 0.05). A large majority of SBSs, InDels, and MNVs induced by CIBs and GRs occurred in upstream and downstream regions. Our study compares difference of mutation profiles induced by the CIB irradiation and GR on rice genomes, and give some clues for understanding the mutagenesis mechanism of physical radiation and improving the mutagenesis efficiency.
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Affiliation(s)
- Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Wenlong Luo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Jian Zhang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Xiancheng Yan
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Yan Du
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Libin Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Wenjian Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, China
- *Correspondence: Tao Guo,
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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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Deoli NT, Hasenstein KH. Irradiation effects of MeV protons on dry and hydrated Brassica rapa seeds. LIFE SCIENCES IN SPACE RESEARCH 2018; 19:24-30. [PMID: 30482278 DOI: 10.1016/j.lssr.2018.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/27/2018] [Accepted: 08/15/2018] [Indexed: 06/09/2023]
Abstract
Although space radiation is a known risk for space travel and eventual colonization of Moon or Mars, relatively few data exist on radiation effects on potential crop plants. We studied Brassica rapa to assess the tolerance of seeds and seedlings to radiation by exposing dry and hydrated B. rapa seeds to 1, 2 and 3 MeV proton ions of various fluences and examined the effect on germination and root growth. Modeling penetration depth with SRIM code indicated that the applied energy was insufficient to penetrate the seeds; therefore, all energy was deposited into the tissue. Subsequent germination varied based on the incident ion energy and fluence (dose). Dry and hydrated seeds germinate after ion fluence (1013 ions cm-2) irradiation, but the germination percentage decreased with increasing fluence for ions that could penetrate the seed coat (> 1 MeV). Despite their greater volume and mass, hydrated seeds were more sensitive to irradiation than dry seeds. Damage of the seed coat after irradiation led to faster germination and initial seedling growth. Our results suggest that the seed coat represents a valuable natural radiation protection and that low energy protons, the prevailing solar radiation, are suitable for studying radiation effects in seeds and plants.
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Affiliation(s)
- Naresh T Deoli
- Louisiana Accelerator Center, University of Louisiana at Lafayette, Lafayette, LA, 70504-43600, USA
| | - Karl H Hasenstein
- Louisiana Accelerator Center, University of Louisiana at Lafayette, Lafayette, LA, 70504-43600, USA; Department of Biology, University of Louisiana at Lafayette, Lafayette, LA 70504-43602, USA.
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Ma L, Kazama Y, Hirano T, Morita R, Tanaka S, Abe T, Hatakeyama S. LET dependence on killing effect and mutagenicity in the model filamentous fungus Neurospora crassa. Int J Radiat Biol 2018; 94:1125-1133. [PMID: 30307372 DOI: 10.1080/09553002.2019.1524940] [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] [Indexed: 10/28/2022]
Abstract
PURPOSE To assess the unique biological effects of different forms of ionizing radiation causing DNA double-strand breaks (DSBs), we compared the killing effect, mutagenesis frequency, and mutation type spectrum using the model filamentous fungus Neurospora. MATERIALS AND METHODS Asexual spores of wild-type Neurospora and two DSB repair-deficient strains [one homologous recombination- and the other non-homologous end-joining (NHEJ) pathway-deficient] were irradiated with argon (Ar)-ion beams, ferrous (Fe)-ion beams, or X-rays. Relative biological effectiveness (RBE), forward mutation frequencies at the ad-3 loci, and mutation spectra at the ad-3B gene were determined. RESULTS The canonical NHEJ (cNHEJ)-deficient strain showed resistance to higher X-ray doses, while other strains showed dose-dependent sensitivity. In contrast, the killing effects of Ar-ion and Fe-ion beam irradiation were dose-dependent in all strains tested. The rank order of RBE was Ar-ion > Fe-ion > C-ion. Deletion mutations were the most common, but deletion size incremented with the increasing value of linear energy transfer (LET). CONCLUSIONS We found marked differences in killing effect of a cNHEJ-deficient mutant between X-ray and high-LET ion beam irradiations (Ar and Fe). The mutation spectra also differed between irradiation types. These differences may be due to the physical properties of each radiation and the repair mechanism of induced damage in Neurospora crassa. These results may guide the choice of irradiation beam to kill or mutagenize fungi for agricultural applications or further research.
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Affiliation(s)
- Liqiu Ma
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan.,b RIKEN Nishina Center , Saitama , Japan.,c Gunma University Heavy Ion Medical Center , Maebashi , Japan
| | | | - Tomonari Hirano
- b RIKEN Nishina Center , Saitama , Japan.,d Faculty of Agriculture , University of Miyazaki , Miyazaki , Japan
| | | | - Shuuitsu Tanaka
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan
| | - Tomoko Abe
- b RIKEN Nishina Center , Saitama , Japan
| | - Shin Hatakeyama
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan
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Kim WJ, Ryu J, Im J, Kim SH, Kang SY, Lee JH, Jo SH, Ha BK. Molecular characterization of proton beam-induced mutations in soybean using genotyping-by-sequencing. Mol Genet Genomics 2018; 293:1169-1180. [PMID: 29785615 DOI: 10.1007/s00438-018-1448-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/16/2018] [Indexed: 10/16/2022]
Abstract
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS). In total, 7453 single nucleotide polymorphisms (SNPs) were detected in the 20 M2 plants, compared with the two wild-type controls. The SNP frequency was 1/36,976 bp with proton beam irradiation at 118 Gy, and 1/32,945 bp at 239 Gy. Of these, 3569 SNPs were detected in genic regions. We observed that proton beam irradiation induced more substitutions than small insertion-deletions (INDELs). Based on the mutagenic effect of proton beam irradiation, the frequency of transition mutations was shown to be higher than that of transversions. The proton beam-induced SNPs were distributed uniformly in most of the chromosomes. Gene ontology (GO) analysis showed that there were many genes involved in protein metabolic process under biological process, intracellular membrane-bounded organelle under cellular component, and nucleic acid binding under molecular function. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing soybeans cultivars using mutation breeding.
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Affiliation(s)
- Woon Ji Kim
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Jaihyunk Ryu
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea
| | - Juhyun Im
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Sang Hun Kim
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea
| | - Si-Yong Kang
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongup, 56212, Korea
| | | | | | - Bo-Keun Ha
- Division of Plant Biotechnology, Chonnam National University, Gwangju, 61186, Korea.
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Sasaki N, Watanabe A, Asakawa T, Sasaki M, Hoshi N, Naito Z, Furusawa Y, Shimokawa T, Nishihara M. Biological effects of ion beam irradiation on perennial gentian and apple. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:249-257. [PMID: 31819730 PMCID: PMC6879364 DOI: 10.5511/plantbiotechnology.18.0612a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of new varieties of perennial plants generally requires lengthy and laborious procedures. In this study, we used ion beam irradiation mutagenesis in an attempt to accelerate the breeding process for perennial plants. We evaluated the biological effects of five ion beam sources (carbon, neon, argon, silicon, and iron) and neutron irradiation on Japanese gentian and apple. These treatments were applied at the National Institute of Radiological Sciences (NIRS) using the Heavy Ion Medical Accelerator in Chiba (HIMAC) and the Neutron-exposure Accelerator System for Biological Effect Experiments (NASBEE). Biological effects were observed in in vitro gentian plants after irradiation with ion beams at <10 Gy, whereas apple trees were less sensitive to ion beam irradiation. The growth of gentians in vitro was repressed by 3 Gy neutron irradiation, while that of grafted apple trees was not affected by 4 Gy neutron irradiation. During in vitro proliferation, seven pink-flowered lines were obtained from originally blue-flowered gentian after C and Ne ion beam irradiation treatments. Genomic and reverse transcription-PCR analyses of these lines suggested that the mutations occurred in the genomic region containing F3'5'H (encoding flavonoid 3',5'-hydroxylase). These results provide useful information for the mutagenesis and breeding of gentian, apple, and other perennial plants.
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Affiliation(s)
- Nobuhiro Sasaki
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Aiko Watanabe
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
| | - Tomonori Asakawa
- Iwate Agricultural Research Center, 20-1 Narita, Kitakami, Iwate 024-0003, Japan
| | - Makoto Sasaki
- Iwate Agricultural Research Center, 20-1 Narita, Kitakami, Iwate 024-0003, Japan
| | - Nobue Hoshi
- Iwate Agricultural Research Center, 20-1 Narita, Kitakami, Iwate 024-0003, Japan
| | - Zenbi Naito
- Iwate Agricultural Research Center, 20-1 Narita, Kitakami, Iwate 024-0003, Japan
| | - Yoshiya Furusawa
- National Institute of Radiological Sciences, National Institutes of Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba 263-8555, Japan
| | - Takashi Shimokawa
- National Institute of Radiological Sciences, National Institutes of Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba 263-8555, Japan
| | - Masahiro Nishihara
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003, Japan
- E-mail: Tel: +81-197-68-2911 Fax: +81-197-68-3881
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Kazama Y, Hirano T, Abe T, Matsunaga S. Chromosomal Rearrangement: From Induction by Heavy-Ion Irradiation to in Vivo Engineering by Genome Editing. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yusuke Kazama
- Mutation Genomics Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Tomonari Hirano
- Faculty of Agriculture, University of Miyazaki
- Ion Beam Breeding Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Tomoko Abe
- Ion Beam Breeding Team, Nishina Center for Accelerator-Based Science, RIKEN
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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Murata H, Abe T, Ichida H, Hayashi Y, Yamanaka T, Shimokawa T, Tahara K. Heavy-ion beam mutagenesis of the ectomycorrhizal agaricomycete Tricholoma matsutake that produces the prized mushroom "matsutake" in conifer forests. MYCORRHIZA 2018; 28:171-177. [PMID: 29164316 DOI: 10.1007/s00572-017-0810-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 11/09/2017] [Indexed: 06/07/2023]
Abstract
Tricholoma matsutake is an ectomycorrhizal agaricomycete that produces the prized mushroom "matsutake" in Pinaceae forests. Currently, there are no available cultivars or cultivation methods that produce fruiting bodies. Heavy-ion beams, which induce mutations through double-stranded DNA breaks, have been used widely for plant breeding. In the present study, we examined whether heavy-ion beams could be useful in isolating T. matsutake mutants. An argon-ion beam gave a suitable lethality curve in relation to irradiation doses, accelerating killing at 100-150 Gy. Argon-ion beam irradiation of the agar plate cultures yielded several transient mutants whose colony morphologies differed from that of the wild-type strain at the first screening, but which did not persist following culture transfer. It also generated a mutant whose phenotype remained stable after repeated culture transfers. The stable pleiotropic mutant not only exhibited a different colony morphology to the wild type, but also showed increased degradation of dye-linked water-insoluble amylose and cellulose substrates. Thus, heavy-ion beams may be useful for isolating mutants of T. matsutake, although precautions may be required to maintain the mutants, without phenotypic reversion, during repetitive culture of their mycelia.
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Affiliation(s)
- Hitoshi Murata
- Department of Mushroom Science and Forest Microbiology, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan.
| | - Tomoko Abe
- Ion Beam Breeding Team, RIKEN Nishina Center, Wako, Saitama, 351-0198, Japan
| | - Hiroyuki Ichida
- Ion Beam Breeding Team, RIKEN Nishina Center, Wako, Saitama, 351-0198, Japan
| | - Yoriko Hayashi
- Ion Beam Breeding Team, RIKEN Nishina Center, Wako, Saitama, 351-0198, Japan
| | - Takashi Yamanaka
- Department of Mushroom Science and Forest Microbiology, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
| | - Tomoko Shimokawa
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
| | - Ko Tahara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Matsunosato 1, Tsukuba, 305-8687, Japan
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