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Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
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Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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Guo Y, Cheng L, Long W, Gao J, Zhang J, Chen S, Pu H, Hu M. Synergistic mutations of two rapeseed AHAS genes confer high resistance to sulfonylurea herbicides for weed control. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2811-2824. [PMID: 32556395 DOI: 10.1007/s00122-020-03633-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
A double mutant 5N of rapeseed was obtained with a synergistic effect of high resistance to sulfonylurea herbicide. Excellent weed control was observed in Ning R201 created by 5N resources. Sulfonylurea herbicides, which inhibit acetohydroxyacid synthase (AHAS), have become the most widely used herbicides worldwide. However, weed control in rapeseed crop production remains challenging in China due to the shortage of available herbicide-resistant cultivars. In this study, we developed a rapeseed line (PN19) with sulfonylurea herbicide resistance through seed mutagenesis. Molecular analysis revealed a Trp-574-Leu mutation in BnAHAS1-2R of PN19 according to the sequence of Arabidopsis thaliana, and an allele-specific cleaved amplified polymorphic sequence marker was developed to target the point mutation. A double mutant (5N) with very high sulfonylurea resistance was then created through pyramiding two mutant genes of PN19 and M342 by molecular marker-assisted selection. Herbicide resistance identification, toxicology testing, and an in vitro enzyme activity assay of AHAS in 5N indicated that each mutant was four and eight times more resistant to sulfonylurea than M342 and PN19, respectively. Protein structure analysis of AHAS1 demonstrated that the leucine of mutant Trp-574-Leu destroyed the original π-plane stacking effect of the local region for tribenuron-methyl binding, leading to herbicide tolerance. Isobole graph analysis showed a significant synergistic effect of the combination of two mutant genes in 5N for improved tolerance to sulfonylurea herbicides. Finally, we bred rapeseed variety Ning R201 using 5N herbicide resistance resources, and observed excellent weed control performance. Together, these results demonstrate the practical value of 5N application for optimizing and simplifying rapeseed cultivation in China.
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Affiliation(s)
- Yue Guo
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Li Cheng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
| | - Weihua Long
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianqin Gao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Song Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Huiming Pu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China.
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Maolong Hu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China.
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
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Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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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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Zaidi SSEA, Mukhtar MS, Mansoor S. Genome Editing: Targeting Susceptibility Genes for Plant Disease Resistance. Trends Biotechnol 2018; 36:898-906. [PMID: 29752192 DOI: 10.1016/j.tibtech.2018.04.005] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/08/2018] [Accepted: 04/17/2018] [Indexed: 10/17/2022]
Abstract
Plant pathogens pose a major threat to crop productivity. Typically, phytopathogens exploit plants' susceptibility (S) genes to facilitate their proliferation. Disrupting these S genes may interfere with the compatibility between the host and the pathogens and consequently provide broad-spectrum and durable disease resistance. In the past, genetic manipulation of such S genes has been shown to confer disease resistance in various economically important crops. Recent studies have accomplished this task in a transgene-free system using new genome editing tools, including clustered regularly interspaced palindromic repeats (CRISPR). In this Opinion article, we focus on the use of genome editing to target S genes for the development of transgene-free and durable disease-resistant crop varieties.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium; National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan. http://twitter.com/@SyedShanZaidi
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA. http://twitter.com/@SMukhtarlab
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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7
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Wheat genome editing expedited by efficient transformation techniques: Progress and perspectives. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.cj.2017.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Metje-Sprink J, Menz J, Modrzejewski D, Sprink T. DNA-Free Genome Editing: Past, Present and Future. FRONTIERS IN PLANT SCIENCE 2018; 9:1957. [PMID: 30693009 PMCID: PMC6339908 DOI: 10.3389/fpls.2018.01957] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
Genome Editing using engineered endonuclease (GEEN) systems rapidly took over the field of plant science and plant breeding. So far, Genome Editing techniques have been applied in more than fifty different plants; including model species like Arabidopsis; main crops like rice, maize or wheat as well as economically less important crops like strawberry, peanut and cucumber. These techniques have been used for basic research as proof-of-concept or to investigate gene functions in most of its applications. However, several market-oriented traits have been addressed including enhanced agronomic characteristics, improved food and feed quality, increased tolerance to abiotic and biotic stress and herbicide tolerance. These technologies are evolving at a tearing pace and especially the field of CRISPR based Genome Editing is advancing incredibly fast. CRISPR-Systems derived from a multitude of bacterial species are being used for targeted Gene Editing and many modifications have already been applied to the existing CRISPR-Systems such as (i) alter their protospacer adjacent motif (ii) increase their specificity (iii) alter their ability to cut DNA and (iv) fuse them with additional proteins. Besides, the classical transformation system using Agrobacteria tumefaciens or Rhizobium rhizogenes, other transformation technologies have become available and additional methods are on its way to the plant sector. Some of them are utilizing solely proteins or protein-RNA complexes for transformation, making it possible to alter the genome without the use of recombinant DNA. Due to this, it is impossible that foreign DNA is being incorporated into the host genome. In this review we will present the recent developments and techniques in the field of DNA-free Genome Editing, its advantages and pitfalls and give a perspective on technologies which might be available in the future for targeted Genome Editing in plants. Furthermore, we will discuss these techniques in the light of existing- and potential future regulations.
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Baltes NJ, Gil-Humanes J, Voytas DF. Genome Engineering and Agriculture: Opportunities and Challenges. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:1-26. [PMID: 28712492 PMCID: PMC8409219 DOI: 10.1016/bs.pmbts.2017.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, plant biotechnology has witnessed unprecedented technological change. Advances in high-throughput sequencing technologies have provided insight into the location and structure of functional elements within plant DNA. At the same time, improvements in genome engineering tools have enabled unprecedented control over genetic material. These technologies, combined with a growing understanding of plant systems biology, will irrevocably alter the way we create new crop varieties. As the first wave of genome-edited products emerge, we are just getting a glimpse of the immense opportunities the technology provides. We are also seeing its challenges and limitations. It is clear that genome editing will play an increased role in crop improvement and will help us to achieve food security in the coming decades; however, certain challenges and limitations must be overcome to realize the technology's full potential.
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Ran Y, Liang Z, Gao C. Current and future editing reagent delivery systems for plant genome editing. SCIENCE CHINA-LIFE SCIENCES 2017; 60:490-505. [PMID: 28527114 DOI: 10.1007/s11427-017-9022-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/22/2017] [Indexed: 01/01/2023]
Abstract
Many genome editing tools have been developed and new ones are anticipated; some have been extensively applied in plant genetics, biotechnology and breeding, especially the CRISPR/Cas9 system. These technologies have opened up a new era for crop improvement due to their precise editing of user-specified sequences related to agronomic traits. In this review, we will focus on an update of recent developments in the methodologies of editing reagent delivery, and consider the pros and cons of current delivery systems. Finally, we will reflect on possible future directions.
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Affiliation(s)
- Yidong Ran
- Genovo Biotechnology Co., Ltd., Tianjin, 301700, China.
| | - Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Pacher M, Puchta H. From classical mutagenesis to nuclease-based breeding - directing natural DNA repair for a natural end-product. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:819-833. [PMID: 28027431 DOI: 10.1111/tpj.13469] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 05/18/2023]
Abstract
Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants.
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Affiliation(s)
- Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
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Puchta H. Applying CRISPR/Cas for genome engineering in plants: the best is yet to come. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:1-8. [PMID: 27914284 DOI: 10.1016/j.pbi.2016.11.011] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/13/2016] [Indexed: 05/18/2023]
Abstract
Less than 5 years ago the CRISPR/Cas nuclease was first introduced into eukaryotes, shortly becoming the most efficient and widely used tool for genome engineering. For plants, efforts were centred on obtaining heritable changes in most transformable crop species by inducing mutations into open reading frames of interest, via non-homologous end joining. Now it is important to take the next steps and further develop the technology to reach its full potential. For breeding, besides using DNA-free editing and avoiding off target effects, it will be desirable to apply the system for the mutation of regulatory elements and for more complex genome rearrangements. Targeting enzymatic activities, like transcriptional regulators or DNA modifying enzymes, will be important for plant biology in the future.
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Affiliation(s)
- Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany.
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14
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Hilscher J, Bürstmayr H, Stoger E. Targeted modification of plant genomes for precision crop breeding. Biotechnol J 2017; 12. [PMID: 27726285 DOI: 10.1002/biot.201600173] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/22/2016] [Accepted: 09/09/2016] [Indexed: 02/03/2023]
Abstract
The development of gene targeting and gene editing techniques based on programmable site-directed nucleases (SDNs) has increased the precision of genome modification and made the outcomes more predictable and controllable. These approaches have achieved rapid advances in plant biotechnology, particularly the development of improved crop varieties. Here, we review the range of alterations which have already been implemented in plant genomes, and summarize the reported efficiencies of precise genome modification. Many crop varieties are being developed using SDN technologies and although their regulatory status in the USA is clear there is still a decision pending in the EU. DNA-free genome editing strategies are briefly discussed because they also present a unique regulatory challenge. The potential applications of genome editing in plant breeding and crop improvement are highlighted by drawing examples from the recent literature.
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Affiliation(s)
- Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Hermann Bürstmayr
- Institute for Biotechnology in Plant Production (IFA Tulln), University of Natural Resources and Life Sciences, Tulln, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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15
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Lowder L, Malzahn A, Qi Y. Rapid Evolution of Manifold CRISPR Systems for Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2016; 7:1683. [PMID: 27895652 PMCID: PMC5107562 DOI: 10.3389/fpls.2016.01683] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/25/2016] [Indexed: 05/19/2023]
Abstract
Advanced CRISPR-Cas9 based technologies first validated in mammalian cell systems are quickly being adapted for use in plants. These new technologies increase CRISPR-Cas9's utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. Here, we review the current state of advanced CRISPR-Cas9 and Cpf1 capabilities in plants and cover the rapid evolution of these tools from first generation inducers of double strand breaks for basic genetic manipulations to second and third generation multiplexed systems with myriad functionalities, capabilities, and specialized applications. We offer perspective on how to utilize these tools for currently untested research endeavors and analyze strengths and weaknesses of novel CRISPR systems in plants. Advanced CRISPR functionalities and delivery options demonstrated in plants are primarily reviewed but new technologies just coming to the forefront of CRISPR development, or those on the horizon, are briefly discussed. Topics covered are focused on the expansion of expression and delivery capabilities for CRISPR-Cas9 components and broadening targeting range through orthogonal Cas9 and Cpf1 proteins.
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