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Zaman QU, Raza A, Lozano-Juste J, Chao L, Jones MGK, Wang HF, Varshney RK. Engineering plants using diverse CRISPR-associated proteins and deregulation of genome-edited crops. Trends Biotechnol 2024; 42:560-574. [PMID: 37993299 DOI: 10.1016/j.tibtech.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson-Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changing climate, but need alignment of international regulations to operate in existing supply chains.
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Affiliation(s)
- Qamar U Zaman
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China; Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Valencia 46022, Spain
| | - Li Chao
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Xudong 2nd Road, Wuhan 430062, China
| | - Michael G K Jones
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia
| | - Hua-Feng Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Yazhou-Bay Seed Laboratory, Hainan University, Sanya, 572025, China; Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture, School of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, WA 6150, Australia.
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Ashraf S, Ahmad A, Khan SH, Jamil A, Sadia B, Brown JK. LbCas12a mediated suppression of Cotton leaf curl Multan virus. FRONTIERS IN PLANT SCIENCE 2023; 14:1233295. [PMID: 37636103 PMCID: PMC10456881 DOI: 10.3389/fpls.2023.1233295] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023]
Abstract
Begomoviruses are contagious and severely affect commercially important fiber and food crops. Cotton leaf curl Multan virus (CLCuMuV) is one of the most dominant specie of Begomovirus and a major constraint on cotton yield in Pakistan. Currently, the field of plant genome editing is being revolutionized by the CRISPR/Cas system applications such as base editing, prime editing and CRISPR based gene drives. CRISPR/Cas9 system has successfully been used against biotic and abiotic plant stresses with proof-of-concept studies in both model and crop plants. CRISPR/Cas12 and CRISPR/Cas13 have recently been applied in plant sciences for basic and applied research. In this study, we used a novel approach, multiplexed crRNA-based Cas12a toolbox to target the different ORFs of the CLCuMuV genome at multiple sites simultaneously. This method successfully eliminated the symptoms of CLCuMuV in Nicotiana benthamiana and Nicotiana tabacum. Three individual crRNAs were designed from the CLCuMuV genome, targeting the specific sites of four different ORFs (C1, V1 and overlapping region of C2 and C3). The Cas12a-based construct Cas12a-MV was designed through Golden Gate three-way cloning for precise editing of CLCuMuV genome. Cas12a-MV construct was confirmed through whole genome sequencing using the primers Ubi-intron-F1 and M13-R1. Transient assays were performed in 4 weeks old Nicotiana benthamiana plants, through the agroinfiltration method. Sanger sequencing indicated that the Cas12a-MV constructs made a considerable mutations at the target sites of the viral genome. In addition, TIDE analysis of Sanger sequencing results showed the editing efficiency of crRNA1 (21.7%), crRNA2 (24.9%) and crRNA3 (55.6%). Furthermore, the Cas12a-MV construct was stably transformed into Nicotiana tabacum through the leaf disc method to evaluate the potential of transgenic plants against CLCuMuV. For transgene analysis, the DNA of transgenic plants of Nicotiana tabacum was subjected to PCR to amplify Cas12a genes with specific primers. Infectious clones were agro-inoculated in transgenic and non-transgenic plants (control) for the infectivity assay. The transgenic plants containing Cas12a-MV showed rare symptoms and remained healthy compared to control plants with severe symptoms. The transgenic plants containing Cas12a-MV showed a significant reduction in virus accumulation (0.05) as compared to control plants (1.0). The results demonstrated the potential use of the multiplex LbCas12a system to develop virus resistance in model and crop plants against begomoviruses.
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Affiliation(s)
- Sidra Ashraf
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Cotton Biotechnology Lab, Center for Advanced Studies in Agriculture and Food Security (CASAFS), University of Agriculture, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Bushra Sadia
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
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Srivastava A, Pandey V, Al-Sadi AM, Shahid MS, Gaur R. An Insight into Emerging Begomoviruses and their Satellite Complex causing Papaya Leaf Curl Disease. Curr Genomics 2023; 24:2-17. [PMID: 37920727 PMCID: PMC10334704 DOI: 10.2174/1389202924666230207111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/02/2023] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Papaya leaf curl disease (PaLCD) was primarily detected in India and causes major economic damage to agriculture crops grown globally, seriously threatening food security. Begomoviruses are communicated by the vector Bemisia tabaci, and their transmission efficiency and persistence in the vector are the highest, exhibiting the widest host range due to adaptation and evolution. Symptoms induced during PaLCD include leaf curl, leaf yellowing, interveinal chlorosis, and reduced fruit quality and yield. Consequently, plants have evolved several multi-layered defense mechanisms to resist Begomovirus infection and distribution. Subsequently, Begomovirus genomes organise circular ssDNA of size ~2.5-2.7 kb of overlapping viral transcripts and carry six-seven ORFs encoding multifunctional proteins, which are precisely evolved by the viruses to maintain the genome-constraint and develop complex but integrated interactions with a variety of host components to expand and facilitate successful infection cycles, i.e., suppression of host defense strategies. Geographical distribution is continuing to increase due to the advent and evolution of new Begomoviruses, and sweep to new regions is a future scenario. This review summarizes the current information on the biological functions of papaya-infecting Begomoviruses and their encoded proteins in transmission through vectors and modulating host-mediated responses, which may improve our understanding of how to challenge these significant plant viruses by revealing new information on the development of antiviral approaches against Begomoviruses associated with PaLCD.
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Affiliation(s)
- Aarshi Srivastava
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Vineeta Pandey
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
| | - Abdullah. M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
| | - Muhammad S. Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod, Oman
| | - R.K. Gaur
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, India
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Yıldırım K, Kavas M, Küçük İS, Seçgin Z, Saraç ÇG. Development of Highly Efficient Resistance to Beet Curly Top Iran Virus (Becurtovirus) in Sugar Beet (B. vulgaris) via CRISPR/Cas9 System. Int J Mol Sci 2023; 24:ijms24076515. [PMID: 37047489 PMCID: PMC10095410 DOI: 10.3390/ijms24076515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Beet Curly Top Iran Virus (BCTIV, Becurtovirus) is a dominant and widespread pathogen responsible for great damage and yield reduction in sugar beet production in the Mediterranean and Middle East. CRISPR-based gene editing is a versatile tool that has been successfully used in plants to improve resistance against many viral pathogens. In this study, the efficiency of gRNA/Cas9 constructs targeting the expressed genes of BCTIV was assessed in sugar beet leaves by their transient expression. Almost all positive control sugar beets revealed systemic infection and severe disease symptoms (90%), with a great biomass reduction (68%) after BCTIV agroinoculation. On the other hand, sugar beets co-agronioculated with BCTIV and gRNA/Cas9 indicated much lower systemic infection (10–55%), disease symptoms and biomass reduction (13–45%). Viral inactivation was also verified by RCA and qPCR assays for gRNA/Cas9 treated sugar beets. PCR-RE digestion and sequencing assays confirmed the gRNA/Cas9-mediated INDEL mutations at the target sites of the BCTIV genome and represented high efficiencies (53–88%), especially for those targeting BCTIV’s movement gene and its overlapping region between capsid and ssDNA regulator genes. A multiplex CRISPR approach was also tested. The most effective four gRNAs targeting all the genes of BCTIV were cloned into a Cas9-containing vector and agroinoculated into virus-infected sugar beet leaves. The results of this multiplex CRISPR system revealed almost complete viral resistance with inhibition of systemic infection and mutant escape. This is the first report of CRSIPR-mediated broad-spectrum resistance against Becurtovirus in sugar beet.
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Xu J, Zhang N, Wang K, Xian Q, Dong J, Chen X. Exploring new strategies in diseases resistance of horticultural crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1021350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Horticultural crops are susceptible to various biotic stressors including fungi, oomycetes, bacteria, viruses, and root-knot nematodes. These pathogens limit the growth, development, yield, and quality of horticultural crops, and also limit their adaptability and geographic distribution. The continuous cropping model in horticultural facilities exacerbates soil-borne diseases, and severely restricts yield, quality, and productivity. Recent progress in the understanding of mechanisms that confer tolerance to different diseases through innovative strategies including host-induced gene silencing (HIGS), targeting susceptibility genes, and rootstocks grafting applications are reviewed to systematically explore the resistance mechanisms against horticultural plant diseases. Future work should successfully breed resistant varieties using these strategies combined with molecular biologic methods.
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CRISPR-Cas12c: a noncleaving DNA binder with minimal PAM requirement. Trends Biotechnol 2022; 40:1141-1143. [PMID: 35914977 DOI: 10.1016/j.tibtech.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022]
Abstract
The CRISPR-Cas toolbox is expanding swiftly. Every discovery of a novel and unique variant opens new frontiers in the field of synthetic and applied biology. Recently, Huang et al. revealed the CRISPR-Cas12c system that requires a single-nucleotide protospacer adjacent motif (PAM) to perform RNA-guided DNA targeting without DNA cleavage.
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Genome-based identification of beet curly top Iran virus infecting sugar beet in Turkey and investigation of its pathogenicity by agroinfection. J Virol Methods 2021; 300:114380. [PMID: 34838538 DOI: 10.1016/j.jviromet.2021.114380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/20/2021] [Accepted: 11/23/2021] [Indexed: 11/21/2022]
Abstract
Beet curly top disease (BCTD) is a yield-limiting viral infection of sugar beet (Beta vulgaris) throughout the arid and semi-arid regions of the world. Two virus species, belonging to two different genera of the family Geminiviridae (Curtovirus and Becurtovirus) had been described as the disease's causative agents on sugar beet. Despite the detection of the BCTD in some sugar beet fields of Turkey sixty years ago, the genome based characterization of BCTD-associated viruses have not been studied previously. In this study, 628 sugar beet plants exhibiting BCTD symptoms were collected from fourteen cities in central Anatolia, the major sugar beet production areas in Turkey. PCR assays of these samples using the respective Curtovirus and Becurtovirus genus-specific primers indicated that the Turkish sugar beet samples' viral sequences belong only to the genus Becurtovirus. The results of sequencing and phylogenetic analysis of the partial genome of the virus obtained from fourteen cities confirmed that BCTD-associated virus in Turkish sugar beet fields is beet curly top Iran virus (BCTIV-Becurtovirus) species. The whole genome of the collected viruses from fourteen cities were amplified by the rolling circle amplification (RCA) and the five most phylogenetically diverse viruses obtained from Afyon, Ankara, Adapazarı, Yozgat and Aksaray were sequenced. The results of whole genome sequence analysis indicated >98 % sequence identities with that of a BCTIV variants reported from Urmia province (bordering Turkey) of Iran. A virus genome from Yozgat city had a genomic sequence identity of >97 % with those of BCTIV isolated from cowpea, tomato, pepper and sugar beet in the northern part of Iran. These results suggested that the spread of BCTIV through the region could create a significant threat to the production of sugar beet as well as other agricultural crops. A tandem dimer of a BCTIV-Turkish variant isolated from Ankara city was cloned into Agrobacterium plasmid to be used for agro-infection studies. Agroinoculation of this construct on sugar beet leaves generated severe BCTD symptoms (84 %) which were also confirmed by RCA and qPCR analysis. These results constituted the first genome based characterization of BCTIV Turkish variants and the first report of BCTIV spreading out of Iran.
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Wheatley MS, Yang Y. Versatile Applications of the CRISPR/Cas Toolkit in Plant Pathology and Disease Management. PHYTOPATHOLOGY 2021; 111:1080-1090. [PMID: 33356427 DOI: 10.1094/phyto-08-20-0322-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
New tools and advanced technologies have played key roles in facilitating basic research in plant pathology and practical approaches for disease management and crop health. Recently, the CRISPR/Cas (clustered regularly interspersed short palindromic repeats/CRISPR-associated) system has emerged as a powerful and versatile tool for genome editing and other molecular applications. This review aims to introduce and highlight the CRISPR/Cas toolkit and its current and future impact on plant pathology and disease management. We will cover the rapidly expanding horizon of various CRISPR/Cas applications in the basic study of plant-pathogen interactions, genome engineering of plant disease resistance, and molecular diagnosis of diverse pathogens. Using the citrus greening disease as an example, various CRISPR/Cas-enabled strategies are presented to precisely edit the host genome for disease resistance, to rapidly detect the pathogen for disease management, and to potentially use gene drive for insect population control. At the cutting edge of nucleic acid manipulation and detection, the CRISPR/Cas toolkit will accelerate plant breeding and reshape crop production and disease management as we face the challenges of 21st century agriculture.
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Affiliation(s)
- Matthew S Wheatley
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology, and the Huck Institute of the Life Sciences, the Pennsylvania State University, University Park, PA 16802
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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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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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Bhat MA, Bhat MA, Kumar V, Wani IA, Bashir H, Shah AA, Rahman S, Jan AT. The era of editing plant genomes using CRISPR/Cas: A critical appraisal. J Biotechnol 2020; 324:34-60. [DOI: 10.1016/j.jbiotec.2020.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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Zaidi SSEA, Mahas A, Vanderschuren H, Mahfouz MM. Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants. Genome Biol 2020; 21:289. [PMID: 33256828 PMCID: PMC7702697 DOI: 10.1186/s13059-020-02204-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/13/2020] [Indexed: 12/19/2022] Open
Abstract
To meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of climate change. CRISPR genome-editing technology opens new opportunities to engineer disease resistance traits. With precise genome engineering and transgene-free applications, CRISPR is expected to resolve the major challenges to crop improvement. Here, we discuss the latest developments in CRISPR technologies for engineering resistance to viruses, bacteria, fungi, and pests. We conclude by highlighting current concerns and gaps in technology, as well as outstanding questions for future research.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hervé Vanderschuren
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, KU Leuven, Leuven, Belgium
| | - 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.
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Badar U, Venkataraman S, AbouHaidar M, Hefferon K. Molecular interactions of plant viral satellites. Virus Genes 2020; 57:1-22. [PMID: 33226576 DOI: 10.1007/s11262-020-01806-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/24/2020] [Indexed: 12/18/2022]
Abstract
Plant viral satellites fall under the category of subviral agents. Their genomes are composed of small RNA or DNA molecules a few hundred nucleotides in length and contain an assortment of highly complex and overlapping functions. Each lacks the ability to either replicate or undergo encapsidation or both in the absence of a helper virus (HV). As the number of known satellites increases steadily, our knowledge regarding their sequence conservation strategies, means of replication and specific interactions with host and helper viruses is improving. This review demonstrates that the molecular interactions of these satellites are unique and highly complex, largely influenced by the highly specific host plants and helper viruses that they associate with. Circularized forms of single-stranded RNA are of particular interest, as they have recently been found to play a variety of novel cellular functions. Linear forms of satRNA are also of great significance as they may complement the helper virus genome in exacerbating symptoms, or in certain instances, actively compete against it, thus reducing symptom severity. This review serves to describe the current literature with respect to these molecular mechanisms in detail as well as to discuss recent insights into this emerging field in terms of evolution, classification and symptom development. The review concludes with a discussion of future steps in plant viral satellite research and development.
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Affiliation(s)
- Uzma Badar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Mounir AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Kathleen Hefferon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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15
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Beam K, Ascencio-Ibáñez JT. Geminivirus Resistance: A Minireview. FRONTIERS IN PLANT SCIENCE 2020; 11:1131. [PMID: 32849693 PMCID: PMC7396689 DOI: 10.3389/fpls.2020.01131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/10/2020] [Indexed: 05/04/2023]
Abstract
A continuing challenge to crop production worldwide is the spectrum of diseases caused by geminiviruses, a large family of small circular single-stranded DNA viruses. These viruses are quite diverse, some containing mono- or bi-partite genomes, and infecting a multitude of monocot and dicot plants. There are currently many efforts directed at controlling these diseases. While some of the methods include controlling the insect vector using pesticides or genetic insect resistance (Rodríguez-López et al., 2011), this review will focus on the generation of plants that are resistant to geminiviruses themselves. Genetic resistance was traditionally found by surveying the wild relatives of modern crops for resistance loci; this method is still widely used and successful. However, the quick rate of virus evolution demands a rapid turnover of resistance genes. With better information about virus-host interactions, scientists are now able to target early stages of geminivirus infection in the host, preventing symptom development and viral DNA accumulation.
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16
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Mishra GP, Dikshit HK, S. V. R, Tripathi K, Kumar RR, Aski M, Singh A, Roy A, Priti, Kumari N, Dasgupta U, Kumar A, Praveen S, Nair RM. Yellow Mosaic Disease (YMD) of Mungbean ( Vigna radiata (L.) Wilczek): Current Status and Management Opportunities. FRONTIERS IN PLANT SCIENCE 2020; 11:918. [PMID: 32670329 PMCID: PMC7327115 DOI: 10.3389/fpls.2020.00918] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/04/2020] [Indexed: 03/30/2024]
Abstract
Globally, yellow mosaic disease (YMD) remains a major constraint of mungbean production, and management of this deadly disease is still the biggest challenge. Thus, finding ways to manage YMD including development of varieties possessing resistance against mungbean yellow mosaic virus (MYMV) and mungbean yellow mosaic India virus (MYMIV) is a research priority for mungbean crop. Characterization of YMD resistance using various advanced molecular and biochemical approaches during plant-virus interactions has unfolded a comprehensive network of pathogen survival, disease severity, and the response of plants to pathogen attack, including mechanisms of YMD resistance in mungbean. The biggest challenge in YMD management is the effective utilization of an array of information gained so far, in an integrated manner for the development of genotypes having durable resistance against yellow mosaic virus (YMV) infection. In this backdrop, this review summarizes the role of various begomoviruses, its genomic components, and vector whiteflies, including cryptic species in the YMD expression. Also, information about the genetics of YMD in both mungbean and blackgram crops is comprehensively presented, as both the species are crossable, and same viral strains are also found affecting these crops. Also, implications of various management strategies including the use of resistance sources, the primary source of inoculums and vector management, wide-hybridization, mutation breeding, marker-assisted selection (MAS), and pathogen-derived resistance (PDR) are thoroughly discussed. Finally, the prospects of employing various powerful emerging tools like translational genomics, and gene editing using CRISPR/Cas9 are also highlighted to complete the YMD management perspective in mungbean.
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Affiliation(s)
- Gyan P. Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh K. Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramesh S. V.
- Division of Physiology, Biochemistry and PHT, ICAR-Central Plantation, Kasaragod, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet R. Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anirban Roy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Nikki Kumari
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uttarayan Dasgupta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shelly Praveen
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ramakrishnan M. Nair
- World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad, India
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17
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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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18
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Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock R, Nie B, Zhang J. Generation of virus-resistant potato plants by RNA genome targeting. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1814-1822. [PMID: 30803101 PMCID: PMC6686122 DOI: 10.1111/pbi.13102] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas systems provide bacteria and archaea with molecular immunity against invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13a is an RNA-targeting CRISPR effector that provides protection against RNA phages. Here we report the repurposing of CRISPR/Cas13a to protect potato plants from a eukaryotic virus, Potato virus Y (PVY). Transgenic potato lines expressing Cas13a/sgRNA (small guide RNA) constructs showed suppressed PVY accumulation and disease symptoms. The levels of viral resistance correlated with the expression levels of the Cas13a/sgRNA construct in the plants. Our data further demonstrate that appropriately designed sgRNAs can specifically interfere with multiple PVY strains, while having no effect on unrelated viruses such as PVA or Potato virus S. Our findings provide a novel and highly efficient strategy for engineering crops with resistances to viral diseases.
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Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ziyang Zhong
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Ruhao Chen
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Yong Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ralph Bock
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Bihua Nie
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
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19
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Hameed A, Shan-E-Ali Zaidi S, Sattar MN, Iqbal Z, Tahir MN. CRISPR technology to combat plant RNA viruses: A theoretical model for Potato virus Y (PVY) resistance. Microb Pathog 2019; 133:103551. [PMID: 31125685 DOI: 10.1016/j.micpath.2019.103551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/17/2019] [Indexed: 12/26/2022]
Abstract
RNA viruses are the most diverse phytopathogens which cause severe epidemics in important agricultural crops and threaten the global food security. Being obligatory intracellular pathogens, these viruses have developed fine-tuned evading mechanisms and are non-responsive to most of the prophylactic treatments. Additionally, their sprint ability to overcome host defense demands a broad-spectrum and durable mechanism of resistance. In context of CRISPR-Cas discoveries, some variants of Cas effectors have been characterized as programmable RNA-guided RNases in the microbial genomes and could be reprogramed in mammalian and plant cells with guided RNase activity. Recently, the RNA variants of CRISPR-Cas systems have been successfully employed in plants to engineer resistance against RNA viruses. Some variants of CRISPR-Cas9 have been tamed either for directly targeting plant RNA viruses' genome or through targeting the host genes/factors assisting in viral proliferation. The new frontiers in CRISPR-Cas discoveries, and more importantly shifting towards RNA targeting will pyramid the opportunities in plant virus research. The current review highlights the probable implications of CRISPR-Cas system to confer the pathogen-derived or host-mediated resistance against phytopathogenic RNA viruses. Furthermore, a multiplexed CRISPR-Cas13a methodology is proposed here to combat Potato virus Y (PVY); a globally diverse phytopathogen infecting multiple crops.
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Affiliation(s)
- Amir Hameed
- Akhuwat Faisalabad Institute of Research Science and Technology, Faisalabad, Pakistan; Department of Bioinformatics & Biotechnology, Government College University, Allama Iqbal Road, Faisalabad, Pakistan.
| | | | - Muhammad Naeem Sattar
- Department of Biotechnology, College of Agriculture and Food Science, King Faisal University, Box 400, Al-Ahsa, 3192, Saudi Arabia
| | - Zafar Iqbal
- Department of Plant Pathology, University of Florida, Gainesville, 32611, FL, USA
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20
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Makarova SS, Khromov AV, Spechenkova NA, Taliansky ME, Kalinina NO. Application of the CRISPR/Cas System for Generation of Pathogen-Resistant Plants. BIOCHEMISTRY (MOSCOW) 2019; 83:1552-1562. [PMID: 30878030 DOI: 10.1134/s0006297918120131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of the CRISPR/Cas9 prokaryotic adaptive immune system has led to a breakthrough in targeted genome editing in eukaryotes. The CRISPR/Cas technology allows to generate organisms with desirable characteristics by introducing deletions/insertions into selected genome loci resulting in the knockout or modification of target genes. This review focuses on the current state of the CRISPR/Cas use for the generation of plants resistant to viruses, bacteria, and parasitic fungi. Resistance to DNA- and RNA-containing viruses is usually provided by expression in transgenic plants of the Cas endonuclease gene and short guide RNAs (sgRNAs) targeting certain sites in the viral or the host plant genomes to ensure either direct cleavage of the viral genome or modification of the plant host genome in order to decrease the efficiency of virus replication. Editing of plant genes involved in the defense response to pathogens increases plants resistance to bacteria and pathogenic fungi. The review explores strategies and prospects of the development of pathogen-resistant plants with a focus on the generation of non-transgenic (non-genetically modified) organisms, in particular, by using plasmid (DNA)-free systems for delivery of the Cas/sgRNA editing complex into plant cells.
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Affiliation(s)
- S S Makarova
- Doka-Gene Technology Ltd., 141880 Rogachevo, Moscow Region, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - A V Khromov
- Doka-Gene Technology Ltd., 141880 Rogachevo, Moscow Region, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - N A Spechenkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - M E Taliansky
- Doka-Gene Technology Ltd., 141880 Rogachevo, Moscow Region, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - N O Kalinina
- Doka-Gene Technology Ltd., 141880 Rogachevo, Moscow Region, Russia. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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21
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Mahas A, Ali Z, Tashkandi M, Mahfouz MM. Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Methods Mol Biol 2019; 1917:311-326. [PMID: 30610646 DOI: 10.1007/978-1-4939-8991-1_23] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Targeted modification of plant genomes is a powerful strategy for investigating and engineering cellular systems, paving the way for the discovery and development of important, novel agricultural traits. Cas9, an RNA-guided DNA endonuclease from the type II adaptive immune CRISPR system of the prokaryote Streptococcus pyogenes, has gained widespread popularity as a genome-editing tool for use in a wide array of cells and organisms, including model and crop plants. Effective genome engineering requires the delivery of the Cas9 protein and guide RNAs into target cells. However, in planta genome modification faces many hurdles, including the difficulty in efficiently delivering genome engineering reagents to the desired tissues. We recently developed a Tobacco rattle virus (TRV)-mediated genome engineering system for Nicotiana benthamiana. Using this platform, genome engineering reagents can be delivered into all plant parts in a simple, efficient manner, facilitating the recovery of progeny plants with the desired genomic modifications, thus bypassing the need for transformation and tissue culture. This platform expands the utility of the CRISPR/Cas9 system for in planta, targeted genome modification. Here, we provide a detailed protocol explaining the methodologies used to develop and implement TRV-mediated genome engineering in N. benthamiana. The protocol described here can be extended to any other plant species susceptible to systemic infection by TRV. However, this approach is not limited to vectors derived from TRV, as other RNA viruses could be used to develop similar delivery platforms.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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22
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Ali Z, Zaidi SSEA, Tashkandi M, Mahfouz MM. A Simplified Method to Engineer CRISPR/Cas9-Mediated Geminivirus Resistance in Plants. Methods Mol Biol 2019; 2028:167-183. [PMID: 31228115 DOI: 10.1007/978-1-4939-9635-3_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Throughout the world, geminiviruses cause devastating losses in economically important crops, including tomato, cotton, cassava, potato, chili, and cucumber; however, control mechanisms such as genetic resistance remain expensive and ineffective. CRISPR/Cas9 is an adaptive immunity mechanism used by prokaryotes to defend against invading nucleic acids of phages and plasmids. The CRISPR/Cas9 system has been harnessed for targeted genome editing in a variety of eukaryotic species, and in plants, CRISPR/Cas9 has been used to modify or introduce many traits, including virus resistance. Recently, we demonstrated that the CRISPR/Cas9 system could be used to engineer plant immunity against geminiviruses by directly targeting the viral genome for degradation. In this chapter, we describe a detailed method for engineering CRISPR/Cas9-mediated resistance against geminiviruses. This method may provide broad, durable viral resistance, as it can target conserved regions of the viral genome and can also be customized to emerging viral variants. Moreover, this method can be used in many crop species, as it requires little or no knowledge of the host plant's genome.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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23
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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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24
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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: 144] [Impact Index Per Article: 24.0] [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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25
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Ali Z, Eid A, Ali S, Mahfouz MM. Pea early-browning virus-mediated genome editing via the CRISPR/Cas9 system in Nicotiana benthamiana and Arabidopsis. Virus Res 2018; 244:333-337. [PMID: 29051052 DOI: 10.1016/j.virusres.2017.10.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/19/2017] [Accepted: 10/13/2017] [Indexed: 01/17/2023]
Abstract
The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system has enabled efficient genome engineering in diverse plant species. However, delivery of genome engineering reagents, such as the single guide RNA (sgRNA), into plant cells remains challenging. Here, we report the engineering of Tobacco rattle virus (TRV) and Pea early browning virus (PEBV) to deliver one or multiple sgRNAs into Nicotiana benthamiana and Arabidopsis thaliana (Col-0) plants that overexpress a nuclear localization signal containing Cas9. Our data showed that TRV and PEBV can deliver sgRNAs into inoculated and systemic leaves, and this resulted in mutagenesis of the targeted genomic loci. Moreover, in N. benthamiana, PEBV-based sgRNA delivery resulted in more targeted mutations than TRV-based delivery. Our data indicate that TRV and PEBV can facilitate plant genome engineering and can be used to produce targeted mutations for functional analysis and other biotechnological applications across diverse plant species. Key message: Delivery of genome engineering reagents into plant cells is challenging and inefficient and this limit the applications of this technology in many plant species. RNA viruses such as TRV and PEBV provide an efficient tool to systemically deliver sgRNAs for targeted genome modification.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shakila Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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26
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Naqvi RZ, Zaidi SSEA, Akhtar KP, Strickler S, Woldemariam M, Mishra B, Mukhtar MS, Scheffler BE, Scheffler JA, Jander G, Mueller LA, Asif M, Mansoor S. Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum. Sci Rep 2017; 7:15880. [PMID: 29162860 PMCID: PMC5698292 DOI: 10.1038/s41598-017-15963-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD.
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Affiliation(s)
- Rubab Zahra Naqvi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Syed Shan-E-Ali Zaidi
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture & Biology (NIAB), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Susan Strickler
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Melkamu Woldemariam
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Bharat Mishra
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - M Shahid Mukhtar
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit (USDA-ARS), Stoneville, MS, USA
| | - Jodi A Scheffler
- Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Cornell University, Ithaca, NY, USA
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Punjab, Pakistan.
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Varun P, Ranade SA, Saxena S. A molecular insight into papaya leaf curl-a severe viral disease. PROTOPLASMA 2017; 254:2055-2070. [PMID: 28540512 DOI: 10.1007/s00709-017-1126-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/12/2017] [Indexed: 06/07/2023]
Abstract
Papaya leaf curl disease (PaLCuD) caused by papaya leaf curl virus (PaLCuV) not only affects yield but also plant growth and fruit size and quality of papaya and is one of the most damaging and economically important disease. Management of PaLCuV is a challenging task due to diversity of viral strains, the alternate hosts, and the genomic complexities of the viruses. Several management strategies currently used by plant virologists to broadly control or eliminate the viruses have been discussed. In the absence of such strategies in the case of PaLCuV at present, the few available options to control the disease include methods like removal of affected plants from the field, insecticide treatments against the insect vector (Bemisia tabaci), and gene-specific control through transgenic constructs. This review presents the current understanding of papaya leaf curl disease, genomic components including satellite DNA associated with the virus, wide host and vector range, and management of the disease and suggests possible generic resistance strategies.
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Affiliation(s)
- Priyanka Varun
- Department of Biotechnology, School of Bioscience and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, U.P. State, India
| | - S A Ranade
- Genetics and Molecular Biology Department, CSIR-National Botanical Research Institute, Lucknow, U.P. State, India
| | - Sangeeta Saxena
- Department of Biotechnology, School of Bioscience and Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, U.P. State, India.
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Zubair M, Zaidi SSEA, Shakir S, Amin I, Mansoor S. An Insight into Cotton Leaf Curl Multan Betasatellite, the Most Important Component of Cotton Leaf Curl Disease Complex. Viruses 2017; 9:E280. [PMID: 28961220 PMCID: PMC5691632 DOI: 10.3390/v9100280] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 01/18/2023] Open
Abstract
Cotton leaf curl disease (CLCuD) is one of the most economically important diseases and is a constraint to cotton production in major producers, Pakistan and India. CLCuD is caused by monopartite plant viruses belonging to the family Geminiviridae (genus Begomovirus), in association with an essential, disease-specific satellite, Cotton leaf curl Multan betasatellite (CLCuMuB) belonging to a newly-established family Tolecusatellitidae (genus Betasatellite). CLCuMuB has a small genome (ca. 1350 nt) with a satellite conserved region, an adenine-rich region and a single gene that encodes for a multifunctional βC1 protein. CLCuMuB βC1 protein has a major role in pathogenicity and symptom determination, and alters several host cellular functions like autophagy, ubiquitination, and suppression of gene silencing, to assist CLCuD infectivity. Efficient trans-replication ability of CLCuMuB with several monopartite and bipartite begomoviruses, is also associated with the rapid evolution and spread of CLCuMuB. In this article we comprehensively reviewed the role of CLCuMuB in CLCuD, focusing on the βC1 functions and its interactions with host proteins.
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Affiliation(s)
- Muhammad Zubair
- National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences, Nilore, 45650 Islamabad, Pakistan.
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences, Nilore, 45650 Islamabad, Pakistan.
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium.
| | - Sara Shakir
- National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan.
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA.
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan.
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, 38000 Faisalabad, Pakistan.
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Zaidi SS, Martin DP, Amin I, Farooq M, Mansoor S. Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomoviruses. MOLECULAR PLANT PATHOLOGY 2017; 18:901-911. [PMID: 27553982 PMCID: PMC6638225 DOI: 10.1111/mpp.12481] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/08/2016] [Accepted: 08/21/2016] [Indexed: 05/26/2023]
Abstract
UNLABELLED Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite-associated begomoviruses with mostly narrow geographical ranges predominate, it is widespread, with a geographical range also including the Far East, Middle East, North Africa and Europe. The success of ToLCNDV probably derives from its broad host range and highly flexible genomic configuration: its DNA-A component is capable of productively interacting with, and trans-replicating, diverse DNA-B components and betasatellites. An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions. Towards this end, we used available ToLCNDV sequences to reconstruct the history of ToLCNDV spread. TAXONOMY Family Geminiviridae, Genus Begomovirus. ToLCNDV is a bipartite begomovirus. Following the revised begomovirus taxonomic criteria of 91% and 94% nucleotide identity for species and strain demarcation, respectively, ToLCNDV is a distinct species with two strains: ToLCNDV and ToLCNDV-Spain. HOST RANGE The primary cultivated host of ToLCNDV is tomato (Solanum lycopersicum), but the virus is also known to infect 43 other plant species from a range of families, including Cucurbitaceae, Euphorbiaceae, Solanaceae, Malvaceae and Fabaceae. DISEASE SYMPTOMS Typical symptoms of ToLCNDV infection in its various hosts include leaf curling, vein thickening, puckering, purpling/darkening of leaf margins, leaf area reduction, internode shortening and severe stunting.
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Affiliation(s)
- Syed Shan‐E‐Ali Zaidi
- National Institute for Biotechnology and Genetic EngineeringJhang RoadFaisalabad. PO Box 577, Pakistan
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Division of Computational BiologyUniversity of Cape TownAnzio RdObservatoryCape Town, 7925, South Africa
| | - Imran Amin
- National Institute for Biotechnology and Genetic EngineeringJhang RoadFaisalabad. PO Box 577, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic EngineeringJhang RoadFaisalabad. PO Box 577, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringJhang RoadFaisalabad. PO Box 577, Pakistan
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Strausbaugh CA, Eujayl IA, Wintermantel WM. Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection. PLANT DISEASE 2017; 101:1373-1382. [PMID: 30678603 DOI: 10.1094/pdis-03-17-0381-re] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Curly top of sugar beet is a serious, yield-limiting disease in semiarid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2006-to-2007 collection but changes in disease severity suggested a need for reevaluation. Therefore, 406 leaf samples symptomatic for curly top were collected from sugar beet plants in commercial sugar beet fields in Idaho and Oregon from 2012 to 2015. DNA was isolated and BCTV strain composition was investigated based on polymerase chain reaction assays with strain-specific primers for the Severe (Svr) and California/Logan (CA/Logan) strains and primers that amplified a group of Worland (Wor)-like strains. The BCTV strain distribution averaged 2% Svr, 30% CA/Logan, and 87% Wor-like (16% had mixed infections), which differed from the previously published 2006-to-2007 collection (87% Svr, 7% CA/Logan, and 60% Wor-like; 59% mixed infections) based on a contingency test (P < 0.0001). Whole-genome sequencing (GenBank accessions KT276895 to KT276920 and KX867015 to KX867057) with overlapping primers found that the Wor-like strains included Wor, Colorado and a previously undescribed strain designated Kimberly1. Results confirm a shift from Svr being one of the dominant BCTV strains in commercial sugar beet fields in 2006 to 2007 to becoming undetectable at times during recent years.
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Affiliation(s)
- Carl A Strausbaugh
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Northwest Irrigation and Soils Research Laboratory, Kimberly, ID 83341
| | - Imad A Eujayl
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Northwest Irrigation and Soils Research Laboratory, Kimberly, ID 83341
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Rahman MU, Khan AQ, Rahmat Z, Iqbal MA, Zafar Y. Genetics and Genomics of Cotton Leaf Curl Disease, Its Viral Causal Agents and Whitefly Vector: A Way Forward to Sustain Cotton Fiber Security. FRONTIERS IN PLANT SCIENCE 2017; 8:1157. [PMID: 28725230 PMCID: PMC5495822 DOI: 10.3389/fpls.2017.01157] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
Cotton leaf curl disease (CLCuD) after its first epidemic in 1912 in Nigeria, has spread to different cotton growing countries including United States, Pakistan, India, and China. The disease is of viral origin-transmitted by the whitefly Bemisia tabaci, which is difficult to control because of the prevalence of multiple virulent viral strains or related species. The problem is further complicated as the CLCuD causing virus complex has a higher recombination rate. The availability of alternate host crops like tomato, okra, etc., and practicing mixed type farming system have further exaggerated the situation by adding synergy to the evolution of new viral strains and vectors. Efforts to control this disease using host plant resistance remained successful using two gene based-resistance that was broken by the evolution of new resistance breaking strain called Burewala virus. Development of transgenic cotton using both pathogen and non-pathogenic derived approaches are in progress. In future, screening for new forms of host resistance, use of DNA markers for the rapid incorporation of resistance into adapted cultivars overlaid with transgenics and using genome editing by CRISPR/Cas system would be instrumental in adding multiple layers of defense to control the disease-thus cotton fiber production will be sustained.
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Affiliation(s)
- Mehboob-ur- Rahman
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Ali Q. Khan
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Zainab Rahmat
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad A. Iqbal
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Yusuf Zafar
- Pakistan Agricultural Research CouncilIslamabad, Pakistan
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Khatodia S, Bhatotia K, Tuteja N. Development of CRISPR/Cas9 mediated virus resistance in agriculturally important crops. Bioengineered 2017; 8:274-279. [PMID: 28581909 PMCID: PMC5470520 DOI: 10.1080/21655979.2017.1297347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023] Open
Abstract
Clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9) system of targeted genome editing has already revolutionized the plant science research. This is a RNA guided programmable endonuclease based system composed of 2 components, the Cas9 nuclease and an engineered guide RNA targeting any DNA sequence of the form N20-NGG for novel genome editing applications. The CRISPR/Cas9 technology of targeted genome editing has been recently applied for imparting virus resistance in plants. The robustness, wide adaptability, and easy engineering of this system has proved its potential as an antiviral tool for plants. Novel DNA free genome editing by using the preassembled Cas9/gRNA ribonucleoprotein complex for development of virus resistance in any plant species have been prospected for the future. Also, in this review we have discussed the reports of CRISPR/Cas9 mediated virus resistance strategy against geminiviruses by targeting the viral genome and transgene free strategy against RNA viruses by targeting the host plant factors. In conclusion, CRISPR/Cas9 technology will provide a more durable and broad spectrum viral resistance in agriculturally important crops which will eventually lead to public acceptance and commercialization in the near future.
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Affiliation(s)
- Surender Khatodia
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, India
| | - Kirti Bhatotia
- Amity Institute of Biotechnology, Amity University Haryana, Gurgaon, India
| | - Narendra Tuteja
- Amity Institute of Microbial Technology, Amity University, Noida, India
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Zaidi SSEA, Tashkandi M, Mahfouz MM. Engineering Molecular Immunity Against Plant Viruses. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:167-186. [PMID: 28712496 DOI: 10.1016/bs.pmbts.2017.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomic engineering has been used to precisely alter eukaryotic genomes at the single-base level for targeted gene editing, replacement, fusion, and mutagenesis, and plant viruses such as Tobacco rattle virus have been developed into efficient vectors for delivering genome-engineering reagents. In addition to altering the host genome, these methods can target pathogens to engineer molecular immunity. Indeed, recent studies have shown that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems that target the genomes of DNA viruses can interfere with viral activity and limit viral symptoms in planta, demonstrating the utility of this system for engineering molecular immunity in plants. CRISPR/Cas9 can efficiently target single and multiple viral infections and confer plant immunity. Here, we discuss the use of site-specific nucleases to engineer molecular immunity against DNA and RNA viruses in plants. We also explore how to address the potential challenges encountered when producing plants with engineered resistance to single and mixed viral infections.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Zaidi SSEA, Mansoor S. Viral Vectors for Plant Genome Engineering. FRONTIERS IN PLANT SCIENCE 2017; 8:539. [PMID: 28443125 PMCID: PMC5386974 DOI: 10.3389/fpls.2017.00539] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/27/2017] [Indexed: 05/19/2023]
Abstract
Recent advances in genome engineering (GE) has made it possible to precisely alter DNA sequences in plant cells, providing specifically engineered plants with traits of interest. Gene targeting efficiency depends on the delivery-method of both sequence-specific nucleases and repair templates, to plant cells. Typically, this is achieved using Agrobacterium mediated transformation or particle bombardment, both of which transform only a subset of cells in treated tissues. The alternate in planta approaches, stably integrating nuclease-encoding cassettes and repair templates into the plant genome, are time consuming, expensive and require extra regulations. More efficient GE reagents delivery methods are clearly needed if GE is to become routine, especially in economically important crops that are difficult to transform. Recently, autonomously replicating virus-based vectors have been demonstrated as efficient means of delivering GE reagents in plants. Both DNA viruses (Bean yellow dwarf virus, Wheat dwarf virus and Cabbage leaf curl virus) and RNA virus (Tobacco rattle virus) have demonstrated efficient gene targeting frequencies in model plants (Nicotiana benthamiana) and crops (potato, tomato, rice, and wheat). Here we discuss the recent advances using viral vectors for plant genome engineering, the current limitations and future directions.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Shahid Mansoor
- Molecular Virology and Gene Silencing Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
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35
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Zubair M, Zaidi SSEA, Shakir S, Farooq M, Amin I, Scheffler JA, Scheffler BE, Mansoor S. Multiple begomoviruses found associated with cotton leaf curl disease in Pakistan in early 1990 are back in cultivated cotton. Sci Rep 2017; 7:680. [PMID: 28386113 PMCID: PMC5429635 DOI: 10.1038/s41598-017-00727-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/10/2017] [Indexed: 11/09/2022] Open
Abstract
The first epidemic of cotton leaf curl disease (CLCuD) in early 1990's in the Indian subcontinent was associated with several distinct begomoviruses along with a disease-specific betasatellite. Resistant cotton varieties were introduced in late 1990's but soon resistance was broken and was associated with a single recombinant begomovirus named Burewala strain of Cotton leaf curl Kokhran virus that lacks a full complement of a gene encoding a transcription activator protein (TrAP). In order to understand the ongoing changes in CLCuD complex in Pakistan, CLCuD affected plants from cotton fields at Vehari were collected. Illumina sequencing was used to assess the diversity of CLCuD complex. At least three distinct begomoviruses characterized from the first epidemic; Cotton leaf curl Multan virus, Cotton leaf curl Kokhran virus and Cotton leaf curl Alabad virus, several distinct species of alphasatellites and cotton leaf curl Multan betasatellite were found associated with CLCuD. These viruses were also cloned and sequenced through Sanger sequencing to confirm the identity of the begomoviruses and that all clones possessed a full complement of the TrAP gene. A new strain of betasatellite was identified here and named CLCuMuBVeh. The implications of these findings in efforts to control CLCuD are discussed.
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Affiliation(s)
- Muhammad Zubair
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Sara Shakir
- Centre for Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jodi A Scheffler
- USDA-ARS, Crop Genetics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, 141 Experiment Station Rd, Stoneville, MS, 38776, USA
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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36
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Saeed ST, Samad A. Emerging threats of begomoviruses to the cultivation of medicinal and aromatic crops and their management strategies. Virusdisease 2017; 28:1-17. [PMID: 28466050 PMCID: PMC5377872 DOI: 10.1007/s13337-016-0358-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/30/2016] [Indexed: 12/01/2022] Open
Abstract
Begomoviruses (family Geminiviridae) are responsible for extreme yield reduction in a number of economically important crops including medicinal and aromatic plants (MAPs). Emergence of new variants of viruses due to recombination and mutations in the genomes, modern cropping systems, introduction of susceptible plant varieties, global trade in agricultural products, and changes in climatic conditions are responsible for aggravating the begomovirus problems during the last two decades. This review summaries the current research work on begomoviruses affecting MAPs and provides various traditional and advanced strategies for the management of begomoviruses and vector in MAPs.
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Affiliation(s)
- Sana Tabanda Saeed
- Department of Plant Pathology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015 India
| | - Abdul Samad
- Department of Plant Pathology, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015 India
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37
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Butt H, Eid A, Ali Z, Atia MAM, Mokhtar MM, Hassan N, Lee CM, Bao G, Mahfouz MM. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule. FRONTIERS IN PLANT SCIENCE 2017; 8:1441. [PMID: 28883826 PMCID: PMC5573723 DOI: 10.3389/fpls.2017.01441] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/03/2017] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.
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Affiliation(s)
- Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Mohamed A. M. Atia
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Morad M. Mokhtar
- Molecular Genetics and Genome Mapping Laboratory, Agricultural Genetic Engineering Research Institute, Agricultural Research CenterGiza, Egypt
| | - Norhan Hassan
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, HoustonTX, United States
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- *Correspondence: Magdy M. Mahfouz,
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Zaidi SSEA, Briddon RW, Mansoor S. Engineering Dual Begomovirus-Bemisia tabaci Resistance in Plants. TRENDS IN PLANT SCIENCE 2017; 22:6-8. [PMID: 27890609 DOI: 10.1016/j.tplants.2016.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 06/06/2023]
Abstract
The whitefly Bemisia tabaci is an important pest of many economically important crops and the vector of begomoviruses (family Geminiviridae). Recently, the expression of insecticidal proteins and/or toxins or double-stranded (ds)RNA homologous to B. tabaci genes has been demonstrated to provide the plant with protection against B. tabaci and the viruses that it transmits.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Rob W Briddon
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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39
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Hsing HX, Lin YJ, Tong CG, Li MJ, Chen YJ, Ko SS. Efficient and heritable transformation of Phalaenopsis orchids. BOTANICAL STUDIES 2016; 57:30. [PMID: 28597440 PMCID: PMC5430590 DOI: 10.1186/s40529-016-0146-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/13/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Phalaenopsis orchid (Phal. orchid) is visually attractive and it is important economic floriculture species. Phal. orchids have many unique biological features. However, investigation of these features and validation on their biological functions are limited due to the lack of an efficient transformation method. RESULTS We developed a heritable and efficient Agrobacterium- mediated transformation using protocorms derived from tetraploid or diploid Phal. orchids. A T-DNA vector construct containing eGFP driven by ubiquitin promoter was subjected to transformation. An approximate 1.2-5.2 % transformation rate was achieved. Genomic PCR confirmed that hygromycin selection marker, HptII gene and target gene eGFP were integrated into the orchid genome. Southern blotting indicated a low T-DNA insertion number in the orchid genome of the transformants. Western blot confirmed the expression of eGFP protein in the transgenic orchids. Furthermore, the GFP signal was detected in the transgenic orchids under microscopy. After backcrossing the pollinia of the transgenic plants to four different Phal. orchid varieties, the BC1 progenies showed hygromycin resistance and all surviving BC1 seedlings were HptII positive in PCR and expressed GFP protein as shown by western blot. CONCLUSIONS This study demonstrated a stable transformation system was generated for Phal. orchids. This useful transformation protocol enables functional genomics studies and molecular breeding.
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Affiliation(s)
- Hong-Xian Hsing
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Yi-Jyun Lin
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Chii-Gong Tong
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Min-Jeng Li
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Yun-Jin Chen
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
| | - Swee-Suak Ko
- Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, 741 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115 Taiwan
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Zaidi SSEA, Tashkandi M, Mansoor S, Mahfouz MM. Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1673. [PMID: 27877187 PMCID: PMC5099147 DOI: 10.3389/fpls.2016.01673] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/24/2016] [Indexed: 05/19/2023]
Abstract
Plant viruses infect many economically important crops, including wheat, cotton, maize, cassava, and other vegetables. These viruses pose a serious threat to agriculture worldwide, as decreases in cropland area per capita may cause production to fall short of that required to feed the increasing world population. Under these circumstances, conventional strategies can fail to control rapidly evolving and emerging plant viruses. Genome-engineering strategies have recently emerged as promising tools to introduce desirable traits in many eukaryotic species, including plants. Among these genome engineering technologies, the CRISPR (clustered regularly interspaced palindromic repeats)/CRISPR-associated 9 (CRISPR/Cas9) system has received special interest because of its simplicity, efficiency, and reproducibility. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. Here, we briefly describe the biology of the CRISPR/Cas9 system and plant viruses, and how different genome engineering technologies have been used to target these viruses. We further describe the main findings from recent studies of CRISPR/Cas9-mediated viral interference and discuss how these findings can be applied to improve global agriculture. We conclude by pinpointing the gaps in our knowledge and the outstanding questions regarding CRISPR/Cas9-mediated viral immunity.
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Affiliation(s)
- Syed Shan-e-Ali Zaidi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia
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Fondong VN, Nagalakshmi U, Dinesh-Kumar SP. Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses. PHYTOPATHOLOGY 2016; 106:1231-1239. [PMID: 27392181 DOI: 10.1094/phyto-03-16-0145-fi] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advances in functional genomics and genome editing approaches have provided new opportunities and potential to accelerate plant virus control efforts through modification of host and viral genomes in a precise and predictable manner. Here, we discuss application of RNA-based technologies, including artificial micro RNA, transacting small interfering RNA, and Cas9 (clustered regularly interspaced short palindromic repeat-associated protein 9), which are currently being successfully deployed in generating virus-resistant plants. We further discuss the reverse genetics approach, targeting induced local lesions in genomes (TILLING) and its variant, known as EcoTILLING, that are used in the identification of plant virus recessive resistance gene alleles. In addition to describing specific applications of these technologies in plant virus control, this review discusses their advantages and limitations.
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Affiliation(s)
- Vincent N Fondong
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Ugrappa Nagalakshmi
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Savithramma P Dinesh-Kumar
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
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Schaeffer SM, Nakata PA. The expanding footprint of CRISPR/Cas9 in the plant sciences. PLANT CELL REPORTS 2016; 35:1451-68. [PMID: 27137209 DOI: 10.1007/s00299-016-1987-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 04/19/2016] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 has evolved and transformed the field of biology at an unprecedented pace. From the initial purpose of introducing a site specific mutation within a genome of choice, this technology has morphed into enabling a wide array of molecular applications, including site-specific transgene insertion and multiplexing for the simultaneous induction of multiple cleavage events. Efficiency, specificity, and flexibility are key attributes that have solidified CRISPR/Cas9 as the genome-editing tool of choice by scientists from all areas of biology. Within the field of plant biology, several CRISPR/Cas9 technologies, developed in other biological systems, have been successfully implemented to probe plant gene function and to modify specific crop traits. It is anticipated that this trend will persist and lead to the development of new applications and modifications of the CRISPR technology, adding to an ever-expanding collection of genome-editing tools. We envision that these tools will bestow plant researchers with new utilities to alter genome complexity, engineer site-specific integration events, control gene expression, generate transgene-free edited crops, and prevent or cure plant viral disease. The successful implementation of such utilities will represent a new frontier in plant biotechnology.
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Affiliation(s)
- Scott M Schaeffer
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Houston, TX, 77030-2600, USA
| | - Paul A Nakata
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, 1100 Bates St., Houston, TX, 77030-2600, USA.
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Ali Z, Ali S, Tashkandi M, Zaidi SSEA, Mahfouz MM. CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion. Sci Rep 2016; 6:26912. [PMID: 27225592 PMCID: PMC4881029 DOI: 10.1038/srep26912] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/11/2016] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system has recently been used to confer molecular immunity against several eukaryotic viruses, including plant DNA geminiviruses. Here, we provide a detailed analysis of the efficiencies of targeting different coding and non-coding sequences in the genomes of multiple geminiviruses. Moreover, we analyze the ability of geminiviruses to evade the CRISPR/Cas9 machinery. Our results demonstrate that the CRISPR/Cas9 machinery can efficiently target coding and non-coding sequences and interfere with various geminiviruses. Furthermore, targeting the coding sequences of different geminiviruses resulted in the generation of viral variants capable of replication and systemic movement. By contrast, targeting the noncoding intergenic region sequences of geminiviruses resulted in interference, but with inefficient recovery of mutated viral variants, which thus limited the generation of variants capable of replication and movement. Taken together, our results indicate that targeting noncoding, intergenic sequences provides viral interference activity and significantly limits the generation of viral variants capable of replication and systemic infection, which is essential for developing durable resistance strategies for long-term virus control.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shakila Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Syed Shan-e-Ali Zaidi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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