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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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2
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Nishizawa‐Yokoi A, Toki S. A piggyBac-mediated transgenesis system for the temporary expression of CRISPR/Cas9 in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1386-1395. [PMID: 33529430 PMCID: PMC8313132 DOI: 10.1111/pbi.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/27/2021] [Indexed: 05/03/2023]
Abstract
Targeted mutagenesis via CRISPR/Cas9 is now widely used, not only in model plants but also in agriculturally important crops. However, in vegetative crop propagation, CRISPR/Cas9 expression cassettes cannot be segregated out in the resulting progenies, but must nevertheless be eliminated without leaving unnecessary sequences in the genome. To this end, we designed a piggyBac-mediated transgenesis system for the temporary expression of CRISPR/Cas9 in plants. This system allows integration into the host genome of piggyBac carrying both CRISPR/Cas9 and positive selection marker expression cassettes from an extrachromosomal double-stranded transfer DNA (dsT-DNA), with subsequent excision of the transgenes by the re-transposition of piggyBac from the host genome after successful induction of targeted mutagenesis via CRISPR/Cas9. Here, we demonstrate that the transgenesis system via piggyBac transposition from T-DNA works to deliver transgenes in rice. Following positive-negative selection to exclude transgenic cells randomly transformed with T-DNA, piggyBac-mediated transgenesis from the extrachromosomal dsT-DNA was successful in ca. 1% of transgenic callus lines. After temporary expression of CRISPR/Cas9 within piggyBac, we confirmed, in a proof-of-concept experiment, that piggyBac could be excised precisely from the genome via the stably transformed transposase PBase. Even after excision of piggyBac, CRISPR/Cas9-induced targeted mutations could be detected in the endogenous gene in regenerated rice plants. These results suggest that our piggyBac-mediated transgenesis system will be a valuable tool in establishing efficient CRISPR/Cas9-mediated targeted mutagenesis in vegetatively propagated crops.
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Affiliation(s)
- Ayako Nishizawa‐Yokoi
- Plant Genome Engineering Research UnitInstitute of Agrobiological SciencesNational Agriculture and Food research Organization (NARO)TsukubaJapan
- Japan Science and Technology Agency (JST)Precursory Research for Embryonic Science and Technology (PRESTO)KawaguchiJapan
| | - Seiichi Toki
- Plant Genome Engineering Research UnitInstitute of Agrobiological SciencesNational Agriculture and Food research Organization (NARO)TsukubaJapan
- Kihara Institute for Biological ResearchYokohama City UniversityYokohamaJapan
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Ariga H, Toki S, Ishibashi K. Potato Virus X Vector-Mediated DNA-Free Genome Editing in Plants. PLANT & CELL PHYSIOLOGY 2020; 61:1946-1953. [PMID: 32991731 PMCID: PMC7758033 DOI: 10.1093/pcp/pcaa123] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/14/2020] [Indexed: 05/04/2023]
Abstract
Genome editing technology is important for plant science and crop breeding. Genome-edited plants prepared using general CRISPR-Cas9 methods usually contain foreign DNA, which is problematic for the production of genome-edited transgene-free plants for vegetative propagation or highly heterozygous hybrid cultivars. Here, we describe a method for highly efficient targeted mutagenesis in Nicotiana benthamiana through the expression of Cas9 and single-guide (sg)RNA using a potato virus X (PVX) vector. Following Agrobacterium-mediated introduction of virus vector cDNA, >60% of shoots regenerated without antibiotic selection carried targeted mutations, while ≤18% of shoots contained T-DNA. The PVX vector was also used to express a base editor consisting of modified Cas9 fused with cytidine deaminase to introduce targeted nucleotide substitution in regenerated shoots. We also report exogenous DNA-free genome editing by mechanical inoculation of virions comprising the PVX vector expressing Cas9. This simple and efficient virus vector-mediated delivery of CRISPR-Cas9 could facilitate transgene-free gene editing in plants.
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Affiliation(s)
- Hirotaka Ariga
- Plant and Microbial Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602 Japan
- Plant Diversity Research Team, Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba 305-8602, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602 Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027 Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 236-0027 Japan
| | - Kazuhiro Ishibashi
- Plant and Microbial Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, 305-8602 Japan
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Yanagawa Y, Takeuchi K, Endo M, Furutani A, Ochiai H, Toki S, Mitsuhara I. I- SceI Endonuclease-Mediated Plant Genome Editing by Protein Transport through a Bacterial Type III Secretion System. PLANTS 2020; 9:plants9091070. [PMID: 32825459 PMCID: PMC7570400 DOI: 10.3390/plants9091070] [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: 07/30/2020] [Revised: 08/13/2020] [Accepted: 08/18/2020] [Indexed: 12/24/2022]
Abstract
Xanthomonas campestris is one of bacteria carrying a type III secretion system which transports their effector proteins into host plant cells to disturb host defense system for their infection. To establish a genome editing system without introducing any foreign gene, we attempted to introduce genome editing enzymes through the type III secretion system. In a test of protein transfer, X. campestris pv. campestris (Xcc) transported a considerable amount of a reporter protein sGFP-CyaA into tobacco plant cells under the control of the type III secretion system while maintaining cell viability. For proof of concept for genome editing, we used a reporter tobacco plant containing a luciferase (LUC) gene interrupted by a meganuclease I-SceI recognition sequence; this plant exhibits chemiluminescence of LUC only when a frameshift mutation is introduced at the I-SceI recognition site. Luciferase signal was observed in tobacco leaves infected by Xcc carrying an I-SceI gene which secretes I-SceI protein through the type III system, but not leaves infected by Xcc carrying a vector control. Genome-edited tobacco plant could be regenerated from a piece of infected leaf piece by repeated selection of LUC positive calli. Sequence analysis revealed that the regenerated tobacco plant possessed a base deletion in the I-SceI recognition sequence that activated the LUC gene, indicating genome editing by I-SceI protein transferred through the type III secretion system of Xcc.
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Affiliation(s)
- Yuki Yanagawa
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
| | - Kasumi Takeuchi
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
| | - Masaki Endo
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
| | - Ayako Furutani
- Gene Research Center, Ibaraki University, 3-21-1 Ami, Inashiki, Ibaraki 300-0393, Japan;
| | - Hirokazu Ochiai
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
| | - Seiichi Toki
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
| | - Ichiro Mitsuhara
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; (Y.Y.); (K.T.); (M.E.); (H.O.); (S.T.)
- Correspondence: ; Tel.: +81-29-838-7440
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Jansing J, Schiermeyer A, Schillberg S, Fischer R, Bortesi L. Genome Editing in Agriculture: Technical and Practical Considerations. Int J Mol Sci 2019; 20:E2888. [PMID: 31200517 PMCID: PMC6627516 DOI: 10.3390/ijms20122888] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.
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Affiliation(s)
- Julia Jansing
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Rainer Fischer
- Indiana Biosciences Research Institute (IBRI), 1345 W. 16th St. Suite 300, Indianapolis, IN 46202, USA.
| | - Luisa Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
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Pasin F, Menzel W, Daròs J. Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1010-1026. [PMID: 30677208 PMCID: PMC6523588 DOI: 10.1111/pbi.13084] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/09/2018] [Accepted: 01/15/2019] [Indexed: 05/12/2023]
Abstract
Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T-DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus-based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next-generation virus-based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.
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Affiliation(s)
- Fabio Pasin
- Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
| | - Wulf Menzel
- Leibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweigGermany
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)ValenciaSpain
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Development of the VIGS System in the Dioecious Plant Silene latifolia. Int J Mol Sci 2019; 20:ijms20051031. [PMID: 30818769 PMCID: PMC6429067 DOI: 10.3390/ijms20051031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/08/2023] Open
Abstract
(1) Background: Silene latifolia is a dioecious plant, whose sex is determined by XY-type sex chromosomes. Microbotryum lychnidis-dioicae is a smut fungus that infects S. latifolia plants and causes masculinization in female flowers, as if Microbotryum were acting as a sex-determining gene. Recent large-scale sequencing efforts have promised to provide candidate genes that are involved in the sex determination machinery in plants. These candidate genes are to be analyzed for functional characterization. A virus vector can be a tool for functional gene analyses; (2) Methods: To develop a viral vector system in S. latifolia plants, we selected Apple latent spherical virus (ALSV) as an appropriate virus vector that has a wide host range; (3) Results: Following the optimization of the ALSV inoculation method, S. latifolia plants were infected with ALSV at high rates in the upper leaves. In situ hybridization analysis revealed that ALSV can migrate into the flower meristems in S. latifolia plants. Successful VIGS (virus-induced gene silencing) in S. latifolia plants was demonstrated with knockdown of the phytoene desaturase gene. Finally, the developed method was applied to floral organ genes to evaluate its usability in flowers; (4) Conclusion: The developed system enables functional gene analyses in S. latifolia plants, which can unveil gene functions and networks of S. latifolia plants, such as the mechanisms of sex determination and fungal-induced masculinization.
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Yamamoto T, Kashojiya S, Kamimura S, Kameyama T, Ariizumi T, Ezura H, Miura K. Application and development of genome editing technologies to the Solanaceae plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:37-46. [PMID: 29523384 DOI: 10.1016/j.plaphy.2018.02.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 05/22/2023]
Abstract
Genome editing technology using artificial nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas9, can mutagenize the target sites of genes of interest. This technology has been successfully applied in several crops, including the Solanaceae plants, such as tomato, potato, tobacco, and petunia. Among the three nucleases, CRISPR-Cas9 is the best for breeding, crop improvement, and the functional analysis of genes of interest, because of its simplicity and high efficiency. Although the technology is useful for reverse genetics, its use in plants is limited due to a lack of regeneration protocols and sequence information. In this review, the present status of genome editing technology in Solanaceae plants is described, and techniques that may improve genome editing technologies are discussed.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Sachiko Kashojiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Saori Kamimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Takato Kameyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
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Gal-On A, Fuchs M, Gray S. Generation of novel resistance genes using mutation and targeted gene editing. Curr Opin Virol 2017; 26:98-103. [DOI: 10.1016/j.coviro.2017.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023]
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