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Jhu MY, Ellison EE, Sinha NR. CRISPR gene editing to improve crop resistance to parasitic plants. Front Genome Ed 2023; 5:1289416. [PMID: 37965302 PMCID: PMC10642197 DOI: 10.3389/fgeed.2023.1289416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Parasitic plants pose a significant threat to global agriculture, causing substantial crop losses and hampering food security. In recent years, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology has emerged as a promising tool for developing resistance against various plant pathogens. Its application in combating parasitic plants, however, remains largely unexplored. This review aims to summarise current knowledge and research gaps in utilising CRISPR to develop resistance against parasitic plants. First, we outline recent improvements in CRISPR gene editing tools, and what has been used to combat various plant pathogens. To realise the immense potential of CRISPR, a greater understanding of the genetic basis underlying parasitic plant-host interactions is critical to identify suitable target genes for modification. Therefore, we discuss the intricate interactions between parasitic plants and their hosts, highlighting essential genes and molecular mechanisms involved in defence response and multilayer resistance. These include host resistance responses directly repressing parasitic plant germination or growth and indirectly influencing parasitic plant development via manipulating environmental factors. Finally, we evaluate CRISPR-mediated effectiveness and long-term implications for host resistance and crop improvement, including inducible resistance response and tissue-specific activity. In conclusion, this review highlights the challenges and opportunities CRISPR technology provides to combat parasitic plants and provides insights for future research directions to safeguard global agricultural productivity.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Evan E. Ellison
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
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2
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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3
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The rising threat of geminiviruses: molecular insights into the disease mechanism and mitigation strategies. Mol Biol Rep 2023; 50:3835-3848. [PMID: 36701042 DOI: 10.1007/s11033-023-08266-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
BACKGROUND Geminiviruses are among the most threatening emerging plant viruses, accountable for a huge loss to agricultural production worldwide. These viruses have been responsible for some serious outbreaks during the last few decades across different parts of the world. Sincere efforts have been made to regulate the disease incidence by incorporating a multi-dimensional approach, and this process has been facilitated greatly by the advent of molecular techniques. But, the mixed infection due to the polyphagous nature of vectors results in viral recombination followed by the emergence of novel viral strains which thus renders the existing mitigation strategies ineffective. Hence, a multifaceted insight into the molecular mechanism of the disease is really needed to understand the regulatory points; much has been done in this direction during the last few years. The present review aims to explore all the latest developments made so far and to organize the information in a comprehensive manner so that some novel hypotheses for controlling the disease may be generated. METHODS AND RESULTS Starting with the background information, diverse genera of geminiviruses are listed along with their pathological and economic impacts. A comprehensive and detailed mechanism of infection is elaborated to study the interactions between vector, host, and virus at different stages in the life cycle of geminiviruses. Finally, an effort isalso made to analyze the progress made at the molecular level for the development of various mitigation strategies and suggest more effective and better approaches for controlling the disease. CONCLUSION The study has provided a thorough understanding of molecular mechanism of geminivirus infection.
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Yang Y, Chaffin TA, Ahkami AH, Blumwald E, Stewart CN. Plant synthetic biology innovations for biofuels and bioproducts. Trends Biotechnol 2022; 40:1454-1468. [PMID: 36241578 DOI: 10.1016/j.tibtech.2022.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/26/2022] [Accepted: 09/15/2022] [Indexed: 01/21/2023]
Abstract
Plant-based biosynthesis of fuels, chemicals, and materials promotes environmental sustainability, which includes decreases in greenhouse gas emissions, water pollution, and loss of biodiversity. Advances in plant synthetic biology (synbio) should improve precision and efficacy of genetic engineering for sustainability. Applicable synbio innovations include genome editing, gene circuit design, synthetic promoter development, gene stacking technologies, and the design of environmental sensors. Moreover, recent advancements in developing spatially resolved and single-cell omics contribute to the discovery and characterization of cell-type-specific mechanisms and spatiotemporal gene regulations in distinct plant tissues for the expression of cell- and tissue-specific genes, resulting in improved bioproduction. This review highlights recent plant synbio progress and new single-cell molecular profiling towards sustainable biofuel and biomaterial production.
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Affiliation(s)
- Yongil Yang
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Timothy Alexander Chaffin
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charles Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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5
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Li Y, Wu X, Zhang Y, Zhang Q. CRISPR/Cas genome editing improves abiotic and biotic stress tolerance of crops. Front Genome Ed 2022; 4:987817. [PMID: 36188128 PMCID: PMC9524261 DOI: 10.3389/fgeed.2022.987817] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Abiotic stress such as cold, drought, saline-alkali stress and biotic stress including disease and insect pest are the main factors that affect plant growth and limit agricultural productivity. In recent years, with the rapid development of molecular biology, genome editing techniques have been widely used in botany and agronomy due to their characteristics of high efficiency, controllable and directional editing. Genome editing techniques have great application potential in breeding resistant varieties. These techniques have achieved remarkable results in resistance breeding of important cereal crops (such as maize, rice, wheat, etc.), vegetable and fruit crops. Among them, CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) provides a guarantee for the stability of crop yield worldwide. In this paper, the development of CRISRR/Cas and its application in different resistance breeding of important crops are reviewed, the advantages and importance of CRISRR/Cas technology in breeding are emphasized, and the possible problems are pointed out.
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Affiliation(s)
- Yangyang Li
- Hunan Tobacco Research Institute, Changsha, China
| | - Xiuzhe Wu
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yan Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Qiang Zhang, ; Yan Zhang,
| | - Qiang Zhang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
- *Correspondence: Qiang Zhang, ; Yan Zhang,
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6
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Rahman F, Mishra A, Gupta A, Sharma R. Spatiotemporal Regulation of CRISPR/Cas9 Enables Efficient, Precise, and Heritable Edits in Plant Genomes. Front Genome Ed 2022; 4:870108. [PMID: 35558825 PMCID: PMC9087570 DOI: 10.3389/fgeed.2022.870108] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/24/2022] [Indexed: 12/04/2022] Open
Abstract
CRISPR/Cas-mediated editing has revolutionized crop engineering. Due to the broad scope and potential of this technology, many studies have been carried out in the past decade towards optimizing genome editing constructs. Clearly, the choice of the promoter used to drive gRNA and Cas9 expression is critical to achieving high editing efficiency, precision, and heritability. While some important considerations for choosing a promoter include the number and nature of targets, host organism, mode of transformation and goal of the experiment, spatiotemporal regulation of Cas9 expression using tissue-specific or inducible promoters enables higher heritability and efficiency of targeted mutagenesis with reduced off-target effects. In this review, we discuss specific studies that highlight the prospects and trade-offs associated with the choice of promoters on genome editing and emphasize the need for inductive exploration and discovery to further advance this area of research in crop plants.
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Affiliation(s)
- Farhanur Rahman
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Apurva Mishra
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
| | - Archit Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, India
- *Correspondence: Rita Sharma, ,
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Bhattacharjee B, Hallan V. Geminivirus-Derived Vectors as Tools for Functional Genomics. Front Microbiol 2022; 13:799345. [PMID: 35432267 PMCID: PMC9010885 DOI: 10.3389/fmicb.2022.799345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
A persistent issue in the agricultural sector worldwide is the intensive damage caused to crops by the geminivirus family of viruses. The diverse types of viruses, rapid virus evolution rate, and broad host range make this group of viruses one of the most devastating in nature, leading to millions of dollars' worth of crop damage. Geminiviruses have a small genome and can be either monopartite or bipartite, with or without satellites. Their ability to independently replicate within the plant without integration into the host genome and the relatively easy handling make them excellent candidates for plant bioengineering. This aspect is of great importance as geminiviruses can act as natural nanoparticles in plants which can be utilized for a plethora of functions ranging from vaccine development systems to geminivirus-induced gene silencing (GIGS), through deconstructed viral vectors. Thus, the investigation of these plant viruses is pertinent to understanding their crucial roles in nature and subsequently utilizing them as beneficial tools in functional genomics. This review, therefore, highlights some of the characteristics of these viruses that can be deemed significant and the subsequent successful case studies for exploitation of these potentially significant pathogens for role mining in functional biology.
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Affiliation(s)
- Bipasha Bhattacharjee
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Vipin Hallan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Plant Virology Laboratory, Division of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
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8
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Lai Z, Huang Z, Sun J, Jing X, Xiang L, Zhao H, Mo C, Hou X. CRISPR/Cas基因组编辑技术及其在农作物品种改良中的应用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Yu Y, Pan Z, Wang X, Bian X, Wang W, Liang Q, Kou M, Ji H, Li Y, Ma D, Li Z, Sun J. Targeting of SPCSV-RNase3 via CRISPR-Cas13 confers resistance against sweet potato virus disease. MOLECULAR PLANT PATHOLOGY 2022; 23:104-117. [PMID: 34633749 PMCID: PMC8659606 DOI: 10.1111/mpp.13146] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Sweet potato (Ipomoea batatas) is one of the most important crops in the world, and its production rate is mainly decreased by the sweet potato virus disease (SPVD) caused by the co-infection of sweet potato chlorotic stunt virus (SPCSV) and sweet potato feathery mottle virus. However, methods for improving SPVD resistance have not been established. Thus, this study aimed to enhance SPVD resistance by targeting one of its important pathogenesis-related factors (i.e., SPCSV-RNase3) by using the CRISPR-Cas13 technique. First, the RNA targeting activity of four CRISPR-Cas13 variants were compared using a transient expression system in Nicotiana benthamiana. LwaCas13a and RfxCas13d had more efficient RNA and RNA virus targeting activity than PspCas13b and LshCas13a. Driven by the pCmYLCV promoter for the expression of gRNAs, RfxCas13d exhibited higher RNA targeting activity than that driven by the pAtU6 promoter. Furthermore, the targeting of SPCSV-RNase3 using the LwaCas13a system inhibited its RNA silencing suppressor activity and recovered the RNA silencing activity in N. benthamiana leaf cells. Compared with the wild type, transgenic N. benthamiana plants carrying an RNase3-targeted LwaCas13a system exhibited enhanced resistance against turnip mosaic virus TuMV-GFP and cucumber mosaic virus CMV-RNase3 co-infection. Moreover, transgenic sweet potato plants carrying an RNase3-targeted RfxCas13d system exhibited substantially improved SPVD resistance. This method may contribute to the development of SPVD immune germplasm and the enhancement of sweet potato production in SPVD-prevalent regions.
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Affiliation(s)
- Yicheng Yu
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Zhiyuan Pan
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Xiao Wang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Xiaofeng Bian
- Institute of Food CropsProvincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjingChina
| | - Weichi Wang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Qiang Liang
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Meng Kou
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhou, Jiangsu ProvinceChina
| | - Hongtao Ji
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Yanjuan Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Daifu Ma
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai DistrictXuzhou, Jiangsu ProvinceChina
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jian Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative GenomicsSchool of Life SciencesJiangsu Normal UniversityXuzhouChina
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10
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Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z. A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises. Curr Issues Mol Biol 2021; 43:1950-1976. [PMID: 34889892 PMCID: PMC8929161 DOI: 10.3390/cimb43030135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Genome editing (GE) has revolutionized the biological sciences by creating a novel approach for manipulating the genomes of living organisms. Many tools have been developed in recent years to enable the editing of complex genomes. Therefore, a reliable and rapid approach for increasing yield and tolerance to various environmental stresses is necessary to sustain agricultural crop production for global food security. This critical review elaborates the GE tools used for crop improvement. These tools include mega-nucleases (MNs), such as zinc-finger nucleases (ZFNs), and transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Specifically, this review addresses the latest advancements in the role of CRISPR/Cas9 for genome manipulation for major crop improvement, including yield and quality development of biotic stress- and abiotic stress-tolerant crops. Implementation of this technique will lead to the production of non-transgene crops with preferred characteristics that can result in enhanced yield capacity under various environmental stresses. The CRISPR/Cas9 technique can be combined with current and potential breeding methods (e.g., speed breeding and omics-assisted breeding) to enhance agricultural productivity to ensure food security. We have also discussed the challenges and limitations of CRISPR/Cas9. This information will be useful to plant breeders and researchers in the thorough investigation of the use of CRISPR/Cas9 to boost crops by targeting the gene of interest.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Sameer Qari
- Biology Department, (Genetics and Molecular Biology Central Laboratory), Aljumum University College, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Qamar U. Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Ilyas
- University College of Dera Murad Jamali, Nasirabad 80700, Balochistan, Pakistan;
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Huijie Li
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziming Wu
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- Correspondence:
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11
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Samalova M, Moore I. The steroid-inducible pOp6/LhGR gene expression system is fast, sensitive and does not cause plant growth defects in rice (Oryza sativa). BMC PLANT BIOLOGY 2021; 21:461. [PMID: 34627147 PMCID: PMC8501728 DOI: 10.1186/s12870-021-03241-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Inducible systems for transgene expression activated by a chemical inducer or an inducer of non-plant origin are desirable tools for both basic plant research and biotechnology. Although, the technology has been widely exploited in dicotyledonous model plants such as Arabidopsis, it has not been optimised for use with the monocotyledonous model species, namely rice. We have adapted the dexamethasone-inducible pOp6/LhGR system for rice and the results indicated that it is fast, sensitive and tightly regulated, with high levels of induction that remain stable over several generations. Most importantly, we have shown that the system does not cause negative growth defects in vitro or in soil grown plants. Interestingly in the process of testing, we found that another steroid, triamcinolone acetonide, is a more potent inducer in rice than dexamethasone. We present serious considerations for the construct design to avoid undesirable effects caused by the system in plants, leakiness and possible silencing, as well as simple steps to maximize translation efficiency of a gene of interest. Finally, we compare the performance of the pOp6/LhGR system with other chemically inducible systems tested in rice in terms of the properties of an ideal inducible system.
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Affiliation(s)
- Marketa Samalova
- Department of Experimental Biology, Masaryk University, Brno, Czech Republic.
| | - Ian Moore
- Department of Plant Sciences, Oxford University, Oxford, UK
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12
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Ali Z, Mahfouz MM. CRISPR/Cas systems versus plant viruses: engineering plant immunity and beyond. PLANT PHYSIOLOGY 2021; 186:1770-1785. [PMID: 35237805 PMCID: PMC8331158 DOI: 10.1093/plphys/kiab220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 05/02/2023]
Abstract
Molecular engineering of plant immunity to confer resistance against plant viruses holds great promise for mitigating crop losses and improving plant productivity and yields, thereby enhancing food security. Several approaches have been employed to boost immunity in plants by interfering with the transmission or lifecycles of viruses. In this review, we discuss the successful application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) (CRISPR/Cas) systems to engineer plant immunity, increase plant resistance to viruses, and develop viral diagnostic tools. Furthermore, we examine the use of plant viruses as delivery systems to engineer virus resistance in plants and provide insight into the limitations of current CRISPR/Cas approaches and the potential of newly discovered CRISPR/Cas systems to engineer better immunity and develop better diagnostics tools for plant viruses. Finally, we outline potential solutions to key challenges in the field to enable the practical use of these systems for crop protection and viral diagnostics.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Author for communication:
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13
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Shahriar SA, Islam MN, Chun CNW, Rahim MA, Paul NC, Uddain J, Siddiquee S. Control of Plant Viral Diseases by CRISPR/Cas9: Resistance Mechanisms, Strategies and Challenges in Food Crops. PLANTS (BASEL, SWITZERLAND) 2021; 10:1264. [PMID: 34206201 PMCID: PMC8309070 DOI: 10.3390/plants10071264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/07/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022]
Abstract
Protecting food crops from viral pathogens is a significant challenge for agriculture. An integral approach to genome-editing, known as CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR associated protein 9), is used to produce virus-resistant cultivars. The CRISPR/Cas9 tool is an essential part of modern plant breeding due to its attractive features. Advances in plant breeding programs due to the incorporation of Cas9 have enabled the development of cultivars with heritable resistance to plant viruses. The resistance to viral DNA and RNA is generally provided using the Cas9 endonuclease and sgRNAs (single-guide RNAs) complex, targeting particular virus and host plant genomes by interrupting the viral cleavage or altering the plant host genome, thus reducing the replication ability of the virus. In this review, the CRISPR/Cas9 system and its application to staple food crops resistance against several destructive plant viruses are briefly described. We outline the key findings of recent Cas9 applications, including enhanced virus resistance, genetic mechanisms, research strategies, and challenges in economically important and globally cultivated food crop species. The research outcome of this emerging molecular technology can extend the development of agriculture and food security. We also describe the information gaps and address the unanswered concerns relating to plant viral resistance mediated by CRISPR/Cas9.
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Affiliation(s)
- Saleh Ahmed Shahriar
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia;
| | - M. Nazrul Islam
- Laboratory of Plant Pathology and Microbiology, Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada;
| | - Charles Ng Wai Chun
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang 11800, Malaysia;
| | - Md. Abdur Rahim
- Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh;
| | - Narayan Chandra Paul
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Korea;
| | - Jasim Uddain
- Department of Horticulture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh;
| | - Shafiquzzaman Siddiquee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jln UMS, Kota Kinabalu 88400, Malaysia
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14
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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15
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Yan Z, Wolters AMA, Navas-Castillo J, Bai Y. The Global Dimension of Tomato Yellow Leaf Curl Disease: Current Status and Breeding Perspectives. Microorganisms 2021; 9:740. [PMID: 33916319 PMCID: PMC8066563 DOI: 10.3390/microorganisms9040740] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of the vectors, whiteflies of the Bemisia tabaci complex, has been responsible for many TYLCD outbreaks. In this review, we summarize the current knowledge of TYLCV and TYLV-like begomoviruses and the driving forces of the increasing global significance through rapid evolution of begomovirus variants, mixed infection in the field, association with betasatellites and host range expansion. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in controlling TYLCD. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Currently, Ty-1 and Ty-3 are the primary resistance genes widely used in tomato breeding programs. Ty-2 is also exploited commercially either alone or in combination with other Ty-genes (i.e., Ty-1, Ty-3 or ty-5). Additionally, screening of a large collection of wild tomato species has resulted in the identification of novel TYLCD resistance sources. In this review, we focus on genetic resources used to date in breeding for TYLCVD resistance. For future breeding strategies, we discuss several leads in order to make full use of the naturally occurring and engineered resistance to mount a broad-spectrum and sustainable begomovirus resistance.
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Affiliation(s)
- Zhe Yan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Anne-Marie A. Wolters
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Weinberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
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16
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The evolution and history of gene editing technologies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:1-62. [PMID: 33685594 DOI: 10.1016/bs.pmbts.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scientific enquiry must be the driving force of research. This sentiment is manifested as the profound impact gene editing technologies are having in our current world. There exist three main gene editing technologies today: Zinc Finger Nucleases, TALENs and the CRISPR-Cas system. When these systems were being uncovered, none of the scientists set out to design tools to engineer genomes. They were simply trying to understand the mechanisms existing in nature. If it was not for this simple sense of wonder, we probably would not have these breakthrough technologies. In this chapter, we will discuss the history, applications and ethical issues surrounding these technologies, focusing on the now predominant CRISPR-Cas technology. Gene editing technologies, as we know them now, are poised to have an overwhelming impact on our world. However, it is impossible to predict the route they will take in the future or to comprehend the full impact of its repercussions.
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17
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Varanda CMR, Félix MDR, Campos MD, Patanita M, Materatski P. Plant Viruses: From Targets to Tools for CRISPR. Viruses 2021; 13:141. [PMID: 33478128 PMCID: PMC7835971 DOI: 10.3390/v13010141] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/17/2021] [Indexed: 12/26/2022] Open
Abstract
Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present, there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virus-resistant varieties, but which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for 'clustered regularly interspaced short palindromic repeats' and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology can been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection; or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different, beneficial perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry, and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology; namely, to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing some of the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects.
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Affiliation(s)
- Carla M. R. Varanda
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (M.D.C.); (M.P.)
| | - Maria do Rosário Félix
- MED—Mediterranean Institute for Agriculture, Environment and Development & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Maria Doroteia Campos
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (M.D.C.); (M.P.)
| | - Mariana Patanita
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (M.D.C.); (M.P.)
| | - Patrick Materatski
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (M.D.C.); (M.P.)
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18
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Shahid MS, Sattar MN, Iqbal Z, Raza A, Al-Sadi AM. Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective. Front Microbiol 2021; 11:609376. [PMID: 33584572 PMCID: PMC7874184 DOI: 10.3389/fmicb.2020.609376] [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: 09/23/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.
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Affiliation(s)
- Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Zafar Iqbal
- Central Laboratories, King Faisal University, Hofuf, Saudi Arabia
| | - Amir Raza
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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19
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Modrzejewski D, Hartung F, Lehnert H, Sprink T, Kohl C, Keilwagen J, Wilhelm R. Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:574959. [PMID: 33329634 PMCID: PMC7719684 DOI: 10.3389/fpls.2020.574959] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/30/2020] [Indexed: 05/03/2023]
Abstract
CRISPR/Cas enables a targeted modification of DNA sequences. Despite their ease and efficient use, one limitation is the potential occurrence of associated off-target effects. This systematic review aims to answer the following research question: Which factors affect the occurrence of off-target effects caused by the use of CRISPR/Cas in plants? Literature published until March 2019 was considered for this review. Articles were screened for relevance based on pre-defined inclusion criteria. Relevant studies were subject to critical appraisal. All studies included in the systematic review were synthesized in a narrative report, but studies rated as high and medium/high validity were reported separately from studies rated as low and medium/low or unclear validity. In addition, we ran a binary logistic regression analysis to verify five factors that may affect the occurrence of off-target effects: (1) Number of mismatches (2) Position of mismatches (3) GC-content of the targeting sequence (4) Altered nuclease variants (5) Delivery methods. In total, 180 relevant articles were included in this review containing 468 studies therein. Seventy nine percentage of these studies were rated as having high or medium/high validity. Within these studies, 6,416 potential off-target sequences were assessed for the occurrence of off-target effects. Results clearly indicate that an increased number of mismatches between the on-target and potential off-target sequence steeply decreases the likelihood of off-target effects. The observed rate of off-target effects decreased from 59% when there is one mismatch between the on-target and off-target sequences toward 0% when four or more mismatches exist. In addition, mismatch/es located within the first eight nucleotides proximal to the PAM significantly decreased the occurrence of off-target effects. There is no evidence that the GC-content significantly affects off-target effects. The database regarding the impact of the nuclease variant and the delivery method is very poor as the majority of studies applied the standard nuclease SpCas9 and the CRISPR/Cas system was stably delivered in the genome. Hence, a general significant impact of these two factors on the occurrence of off-target effects cannot be proved. This identified evidence gap needs to be filled by systematic studies exploring these individual factors in sufficient numbers.
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Affiliation(s)
- Dominik Modrzejewski
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
| | - Frank Hartung
- Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute, Quedlinburg, Germany
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20
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Cao Y, Zhou H, Zhou X, Li F. Control of Plant Viruses by CRISPR/Cas System-Mediated Adaptive Immunity. Front Microbiol 2020; 11:593700. [PMID: 33193268 PMCID: PMC7649272 DOI: 10.3389/fmicb.2020.593700] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by invading plant viruses pose serious threats to agricultural production in the world, and the antiviral engineering initiated by molecular biotechnology has been an effective strategy to prevent and control plant viruses. Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system-mediated DNA or RNA editing/interference in plants make them very attractive tools applicable to the plant protection field. Here, we review the development of CRISPR/Cas systems and summarize their applications in controlling different plant viruses by targeting viral sequences or host susceptibility genes. We list some potential recessive resistance genes that can be utilized in antiviral breeding and emphasize the importance and promise of recessive resistance gene-based antiviral breeding to generate transgene-free plants without developmental defects. Finally, we discuss the challenges and opportunities for the application of CRISPR/Cas techniques in the prevention and control of plant viruses in the field.
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Affiliation(s)
- Yongsen Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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21
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CRISPR-Cas9 system: A genome-editing tool with endless possibilities. J Biotechnol 2020; 319:36-53. [DOI: 10.1016/j.jbiotec.2020.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
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22
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Cana-Quijada P, Romero-Rodríguez B, Vallejo PG, Castillo AG, Bejarano ER. Cutting-edge technology to generate plant immunity against geminiviruses. Curr Opin Virol 2020; 42:58-64. [PMID: 32698102 DOI: 10.1016/j.coviro.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 11/28/2022]
Abstract
Geminiviruses (viruses with circular, single-stranded DNA genomes) are one of the major groups of plant viruses causing severe economic problems for agriculture worldwide. The control of these pathogens has become a priority to maintain the production of important crops, including cotton, maize, cassava, and other vegetables. Obtaining resistant plants is the most powerful strategy and a key factor to stablish an effective integrated pest management for a robust control. In the last few decades, numerous studies have successfully approached that goal using diverse strategies based on plant variability or on the engineered expression of proteins/RNAs. The increasing knowledge of the mechanisms involved in the geminivirus-plant-vector interactions, in combination with the development of gene editing technology and nanoparticles, draw new and promising strategies for a durable control of these emerging pathogens.
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Affiliation(s)
- Pepe Cana-Quijada
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Beatriz Romero-Rodríguez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Pablo G Vallejo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Araceli G Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Departamento de Genética, Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, E-29071 Málaga, Spain
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23
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Dort EN, Tanguay P, Hamelin RC. CRISPR/Cas9 Gene Editing: An Unexplored Frontier for Forest Pathology. FRONTIERS IN PLANT SCIENCE 2020; 11:1126. [PMID: 32793272 PMCID: PMC7387688 DOI: 10.3389/fpls.2020.01126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/08/2020] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas9 gene editing technology has taken the scientific community by storm since its development in 2012. First discovered in 1987, CRISPR/Cas systems act as an adaptive immune response in archaea and bacteria that defends against invading bacteriophages and plasmids. CRISPR/Cas9 gene editing technology modifies this immune response to function in eukaryotic cells as a highly specific, RNA-guided complex that can edit almost any genetic target. This technology has applications in all biological fields, including plant pathology. However, examples of its use in forest pathology are essentially nonexistent. The aim of this review is to give researchers a deeper understanding of the native CRISPR/Cas systems and how they were adapted into the CRISPR/Cas9 technology used today in plant pathology-this information is crucial for researchers aiming to use this technology in the pathosystems they study. We review the current applications of CRISPR/Cas9 in plant pathology and propose future directions for research in forest pathosystems where this technology is currently underutilized.
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Affiliation(s)
- Erika N. Dort
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département des Sciences du bois et de la Forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, QC, Canada
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24
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Pyott DE, Fei Y, Molnar A. Potential for gene editing in antiviral resistance. Curr Opin Virol 2020; 42:47-52. [PMID: 32512313 DOI: 10.1016/j.coviro.2020.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/17/2022]
Abstract
The discovery of CRISPR/Cas systems and their subsequent application in genome modifications and in gene expression control have fundamentally changed both basic and applied research. They have already been employed to generate novel virus resistance traits either by modifying host factors in the plant genome or by directly inducing targeted virus degradation. Here we summarise the latest developments in this field and discuss the potential applications and concerns around this technology.
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Affiliation(s)
- Douglas Euan Pyott
- The University of Edinburgh, Institute of Molecular Plant Sciences, Mayfield Road, Edinburgh, EH9 3BF, United Kingdom
| | - Yue Fei
- The University of Edinburgh, Institute of Molecular Plant Sciences, Mayfield Road, Edinburgh, EH9 3BF, United Kingdom
| | - Attila Molnar
- The University of Edinburgh, Institute of Molecular Plant Sciences, Mayfield Road, Edinburgh, EH9 3BF, United Kingdom.
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25
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Ghorbani Faal P, Farsi M, Seifi A, Mirshamsi Kakhki A. Virus-induced CRISPR-Cas9 system improved resistance against tomato yellow leaf curl virus. Mol Biol Rep 2020; 47:3369-3376. [PMID: 32297291 DOI: 10.1007/s11033-020-05409-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 03/26/2020] [Indexed: 12/26/2022]
Abstract
Plant viruses are the most significant factors associated with massive economical losses in agricultural industries worldwide. Accordingly, many studies are dedicated to making virus-resistant crop varieties each year due to the ever-changing nature of viruses. Recently genome engineering methods have been used to confer interference against eukaryotic viruses. Research results on genome editing technics, in particular, CRISPR-Cas9, promises a feasible solution to make virus-resistant crops. In this research, we explored the possibility of utilizing CRISPR-Cas9 to obtain TYLCV resistant tomato varieties. Moreover, to overcome any potential off-target effects of Cas9, we used an inducible promoter to initiate Cas9 activity in case of the virus attack. Cas9 vector was transformed by the rgsCaM promoter, known as an endogenous silencer of RNAi and overexpressed after a virus attack. The golden gate cloning method was applied to construct sgRNAs. Intergenic region and coat protein-coding sequences of TYLCV were used to design sgRNAs. Infiltrated sensitive Money Maker varieties analyzed by real-time PCR, showed a significant reduction or delayed accumulation of viral DNA compared to the control plants. This result demonstrates the efficiency of using an inducible promoter in CRISPR-Cas9 constructs.
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Affiliation(s)
- Parisa Ghorbani Faal
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Farsi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Alireza Seifi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Mirshamsi Kakhki
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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26
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Loriato VAP, Martins LGC, Euclydes NC, Reis PAB, Duarte CEM, Fontes EPB. Engineering resistance against geminiviruses: A review of suppressed natural defenses and the use of RNAi and the CRISPR/Cas system. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 292:110410. [PMID: 32005374 DOI: 10.1016/j.plantsci.2020.110410] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/22/2019] [Accepted: 01/07/2020] [Indexed: 05/21/2023]
Abstract
The Geminiviridae family is one of the most successful and largest families of plant viruses that infect a large variety of important dicotyledonous and monocotyledonous crops and cause significant yield losses worldwide. This broad spectrum of host range is only possible because geminiviruses have evolved sophisticated strategies to overcome the arsenal of antiviral defenses in such diverse plant species. In addition, geminiviruses evolve rapidly through recombination and pseudo-recombination to naturally create a great diversity of virus species with divergent genome sequences giving the virus an advantage over the host recognition system. Therefore, it is not surprising that efficient molecular strategies to combat geminivirus infection under open field conditions have not been fully addressed. In this review, we present the anti-geminiviral arsenal of plant defenses, the evolved virulence strategies of geminiviruses to overcome these plant defenses and the most recent strategies that have been engineered for transgenic resistance. Although, the in vitro reactivation of suppressed natural defenses as well as the use of RNAi and CRISPR/Cas systems hold the potential for achieving broad-range resistance and/or immunity, potential drawbacks have been associated with each case.
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Affiliation(s)
- Virgílio A P Loriato
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Laura G C Martins
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Nívea C Euclydes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Pedro A B Reis
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Christiane E M Duarte
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - Elizabeth P B Fontes
- National Institute of Science and Technology in Plant-Pest Interactions, Bioagro, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil; Departament of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
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27
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Zhao Y, Yang X, Zhou G, Zhang T. Engineering plant virus resistance: from RNA silencing to genome editing strategies. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:328-336. [PMID: 31618513 PMCID: PMC6953188 DOI: 10.1111/pbi.13278] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/06/2019] [Accepted: 10/14/2019] [Indexed: 05/09/2023]
Abstract
Viral diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant virus resistance is essential for sustainable agriculture. In the last decades, several modern technologies were applied in plant antiviral engineering. Here we summarized breakthroughs of the two major antiviral strategies, RNA silencing and genome editing. RNA silencing strategy has been used in antiviral breeding for more than thirty years, and many crops engineered to stably express small RNAs targeting various viruses have been approved for commercial release. Genome editing technology has emerged in the past decade, especially CRISPR/Cas, which provides new methods for genetic improvement of plant virus resistance and accelerates resistance breeding. Finally, we discuss the potential of these technologies for breeding crops, and the challenges and solutions they may face in the future.
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Affiliation(s)
- Yaling Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlCollege of AgricultureSouth China Agricultural UniversityGuangzhouChina
- Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina
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28
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Mushtaq M, Mukhtar S, Sakina A, Dar AA, Bhat R, Deshmukh R, Molla K, Kundoo AA, Dar MS. Tweaking genome-editing approaches for virus interference in crop plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:242-250. [PMID: 31881433 DOI: 10.1016/j.plaphy.2019.12.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 12/18/2019] [Accepted: 12/18/2019] [Indexed: 05/13/2023]
Abstract
Plant viruses infect various economically important crops and cause a serious threat to agriculture. As of now, conventional strategies employed are inadequate to circumvent the proliferation of rapidly evolving plant viruses. In this regard, recent advancement in genome-editing approach looks promising to produce plants resistant to DNA/RNA virus infections. Clustered regularly interspaced palindromic repeats (CRISPR) system has been emerged as a promising genome-editing tool that has received special interest because of its ease, competence and reproducibility. Recent studies have demonstrated that CRISPR/Cas9 system has great potential to confer plant immunity by either directly targeting or cleaving the viral genome in both RNA and DNA viruses. Similarly, the approach can be used for targeting the host susceptibility genes more particularly in case of RNA viruses. In the present review, different approaches and strategies being used to improve plant resistance against devastating viruses are discussed in view of recent advances in CRISPR systems. This review also describes the major pitfalls of CRISPR/Cas9 system that utilizes highly efficient and novel platforms to engineer interference to single and multiple plant RNA viruses.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India
| | - Shazia Mukhtar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India
| | - Aafreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, J&K, 180009, India.
| | - Rohini Bhat
- ICAR-Directorate of Onion and Garlic Research, Rajagurunagar, Pune, Maharashtra, 410505, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Sector 81, Sahibzada Ajit Singh Nagar, Punjab, 140308, India
| | - Kutubuddin Molla
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Ajaz Ahmad Kundoo
- Division of Entomology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Mohd Saleem Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
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29
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Yang X, Zhou H, Zhou X. Rock paper scissors: CRISPR/Cas9-mediated interference with geminiviruses in plants. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1389-1391. [DOI: 10.1007/s11427-019-9825-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 09/16/2019] [Indexed: 12/23/2022]
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30
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Razzaq A, Saleem F, Kanwal M, Mustafa G, Yousaf S, Imran Arshad HM, Hameed MK, Khan MS, Joyia FA. Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox. Int J Mol Sci 2019; 20:E4045. [PMID: 31430902 PMCID: PMC6720679 DOI: 10.3390/ijms20164045] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Mehak Kanwal
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | - Ghulam Mustafa
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Sumaira Yousaf
- Nuclear Institute for Agriculture and Biology (NIAB), P.O. Box 128, Faisalabad 38000, Pakistan
| | | | - Muhammad Khalid Hameed
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Sarwar Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz Ahmad Joyia
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.
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31
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CRISPR editing-mediated antiviral immunity: a versatile source of resistance to combat plant virus infections. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1246-1249. [PMID: 31418136 DOI: 10.1007/s11427-019-9722-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/02/2019] [Indexed: 12/24/2022]
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32
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 613] [Impact Index Per Article: 122.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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33
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Ji X, Si X, Zhang Y, Zhang H, Zhang F, Gao C. Conferring DNA virus resistance with high specificity in plants using virus-inducible genome-editing system. Genome Biol 2018; 19:197. [PMID: 30442181 PMCID: PMC6238286 DOI: 10.1186/s13059-018-1580-4] [Citation(s) in RCA: 41] [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: 08/21/2018] [Accepted: 11/03/2018] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 system has recently been engineered to confer resistance to geminiviruses in plants. However, we show here that the usefulness of this antiviral strategy is undermined by off-target effects identified by deep sequencing in Arabidopsis. We construct two virus-inducible CRISPR/Cas9 vectors that efficiently inhibit beet severe curly top virus (BSCTV) accumulation in both transient assays (Nicotiana benthamiana) and transgenic lines (Arabidopsis). Deep sequencing detects no off-target effect in candidate sites of the transgenic Arabidopsis. This kind of virus-inducible genome-editing system should be widely applicable for generating virus-resistant plants without off-target costs.
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Affiliation(s)
- Xiang Ji
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomin Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Zhang
- Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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