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Shawky A, Hatawsh A, Al-Saadi N, Farzan R, Eltawy N, Francis M, Abousamra S, Ismail YY, Attia K, Fakhouri AS, Abdelrahman M. Revolutionizing Tomato Cultivation: CRISPR/Cas9 Mediated Biotic Stress Resistance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2269. [PMID: 39204705 PMCID: PMC11360581 DOI: 10.3390/plants13162269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Tomato (Solanum lycopersicon L.) is one of the most widely consumed and produced vegetable crops worldwide. It offers numerous health benefits due to its rich content of many therapeutic elements such as vitamins, carotenoids, and phenolic compounds. Biotic stressors such as bacteria, viruses, fungi, nematodes, and insects cause severe yield losses as well as decreasing fruit quality. Conventional breeding strategies have succeeded in developing resistant genotypes, but these approaches require significant time and effort. The advent of state-of-the-art genome editing technologies, particularly CRISPR/Cas9, provides a rapid and straightforward method for developing high-quality biotic stress-resistant tomato lines. The advantage of genome editing over other approaches is the ability to make precise, minute adjustments without leaving foreign DNA inside the transformed plant. The tomato genome has been precisely modified via CRISPR/Cas9 to induce resistance genes or knock out susceptibility genes, resulting in lines resistant to common bacterial, fungal, and viral diseases. This review provides the recent advances and application of CRISPR/Cas9 in developing tomato lines with resistance to biotic stress.
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Affiliation(s)
- Abdelrahman Shawky
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Abdulrahman Hatawsh
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Nabil Al-Saadi
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Raed Farzan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11433, Saudi Arabia
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh 11451, Saudi Arabia; (K.A.); (A.S.F.)
| | - Nour Eltawy
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Mariz Francis
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Sara Abousamra
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Yomna Y. Ismail
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
| | - Kotb Attia
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh 11451, Saudi Arabia; (K.A.); (A.S.F.)
| | - Abdulaziz S. Fakhouri
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh 11451, Saudi Arabia; (K.A.); (A.S.F.)
- Department of Biomedical Technology, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Mohamed Abdelrahman
- Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City 12588, Giza, Egypt; (A.S.); (A.H.); (N.A.-S.); (N.E.); (M.F.); (S.A.); (Y.Y.I.)
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Cao X, Huang M, Wang S, Li T, Huang Y. Tomato yellow leaf curl virus: Characteristics, influence, and regulation mechanism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108812. [PMID: 38875781 DOI: 10.1016/j.plaphy.2024.108812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/05/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024]
Abstract
Tomato yellow leaf curl virus (TYLCV), a DNA virus belonging to the genus Begomovirus, significantly impedes the growth and development of numerous host plants, including tomatoes and peppers. Due to its rapid mutation rate and frequent recombination events, achieving complete control of TYLCV proves exceptionally challenging. Consequently, identifying resistance mechanisms become crucial for safeguarding host plants from TYLCV-induced damage. This review article delves into the global distribution, dispersal patterns, and defining characteristics of TYLCV. Moreover, the intricate interplay between TYLCV and various influencing factors, such as insect vectors, susceptible host plants, and abiotic stresses, plays a pivotal role in plant-TYLCV interactions. The review offers an updated perspective on recent investigations focused on plant response mechanisms to TYLCV infection, including the intricate relationship between TYLCV, whiteflies, and regulatory factors. This comprehensive analysis aims to establish a foundation for future research endeavors exploring the molecular mechanisms underlying TYLCV infection and the development of plant resistance through breeding programs.
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Affiliation(s)
- Xue Cao
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong Province, 276000, China
| | - Mengna Huang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong Province, 276000, China
| | - Shimei Wang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Tong Li
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China.
| | - Ying Huang
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong Province, 276000, China.
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Ramulifho E, Rey C. A Coiled-Coil Nucleotide-Binding Domain Leucine-Rich Repeat Receptor Gene MeRPPL1 Plays a Role in the Replication of a Geminivirus in Cassava. Viruses 2024; 16:941. [PMID: 38932233 PMCID: PMC11209366 DOI: 10.3390/v16060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Disease resistance gene (R gene)-encoded nucleotide-binding leucine-rich repeat proteins (NLRs) are critical players in plant host defence mechanisms because of their role as receptors that recognise pathogen effectors and trigger plant effector-triggered immunity (ETI). This study aimed to determine the putative role of a cassava coiled-coil (CC)-NLR (CNL) gene MeRPPL1 (Manes.12G091600) (single allele) located on chromosome 12 in the tolerance or susceptibility to South African cassava mosaic virus (SACMV), one of the causal agents of cassava mosaic disease (CMD). A transient protoplast system was used to knock down the expression of MeRPPL1 by clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9 (CRISPR-Cas9). The MeRPPL1-targeting CRISPR vectors and/or SACMV DNA A and DNA B infectious clones were used to transfect protoplasts isolated from leaf mesophyll cells from the SACMV-tolerant cassava (Manihot esculenta) cultivar TME3. The CRISPR/Cas9 silencing vector significantly reduced MeRPPL1 expression in protoplasts whether with or without SACMV co-infection. Notably, SACMV DNA A replication was higher in protoplasts with lower MeRPPL1 expression levels than in non-silenced protoplasts. Mutagenesis studies revealed that protoplast co-transfection with CRISPR-MeRPPL1 silencing vector + SACMV and transfection with only SACMV induced nucleotide substitution mutations that led to altered amino acids in the highly conserved MHD motif of the MeRPPL1-translated polypeptide. This may abolish or alter the regulatory role of the MHD motif in controlling R protein activity and could contribute to the increase in SACMV-DNA A accumulation observed in MeRPPL1-silenced protoplasts. The results herein demonstrate for the first time a role for a CNL gene in tolerance to a geminivirus in TME3.
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Affiliation(s)
- Elelwani Ramulifho
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
- Germplasm Development, Agricultural Research Council, Small Grain Institute, Bethlehem 9700, South Africa
| | - Chrissie Rey
- Plant Biotechnology Laboratory, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2001, South Africa;
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Wang H, Chen Q, Feng W. The Emerging Role of 2OGDs as Candidate Targets for Engineering Crops with Broad-Spectrum Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2024; 13:1129. [PMID: 38674537 PMCID: PMC11054871 DOI: 10.3390/plants13081129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Plant diseases caused by pathogens result in a marked decrease in crop yield and quality annually, greatly threatening food production and security worldwide. The creation and cultivation of disease-resistant cultivars is one of the most effective strategies to control plant diseases. Broad-spectrum resistance (BSR) is highly preferred by breeders because it confers plant resistance to diverse pathogen species or to multiple races or strains of one species. Recently, accumulating evidence has revealed the roles of 2-oxoglutarate (2OG)-dependent oxygenases (2OGDs) as essential regulators of plant disease resistance. Indeed, 2OGDs catalyze a large number of oxidative reactions, participating in the plant-specialized metabolism or biosynthesis of the major phytohormones and various secondary metabolites. Moreover, several 2OGD genes are characterized as negative regulators of plant defense responses, and the disruption of these genes via genome editing tools leads to enhanced BSR against pathogens in crops. Here, the recent advances in the isolation and identification of defense-related 2OGD genes in plants and their exploitation in crop improvement are comprehensively reviewed. Also, the strategies for the utilization of 2OGD genes as targets for engineering BSR crops are discussed.
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Affiliation(s)
- Han Wang
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China;
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Hwarari D, Radani Y, Ke Y, Chen J, Yang L. CRISPR/Cas genome editing in plants: mechanisms, applications, and overcoming bottlenecks. Funct Integr Genomics 2024; 24:50. [PMID: 38441816 DOI: 10.1007/s10142-024-01314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
The CRISPR/Cas systems have emerged as transformative tools for precisely manipulating plant genomes and enhancement. It has provided unparalleled applications from modifying the plant genomes to resistant enhancement. This review manuscript summarises the mechanism, application, and current challenges in the CRISPR/Cas genome editing technology. It addresses the molecular mechanisms of different Cas genes, elucidating their applications in various plants through crop improvement, disease resistance, and trait improvement. The advent of the CRISPR/Cas systems has enabled researchers to precisely modify plant genomes through gene knockouts, knock-ins, and gene expression modulation. Despite these successes, the CRISPR/Cas technology faces challenges, including off-target effects, Cas toxicity, and efficiency. In this manuscript, we also discuss these challenges and outline ongoing strategies employed to overcome these challenges, including the development of novel CRISPR/Cas variants with improved specificity and specific delivery methods for different plant species. The manuscript will conclude by addressing the future perspectives of the CRISPR/Cas technology in plants. Although this review manuscript is not conclusive, it aims to provide immense insights into the current state and future potential of CRISPR/Cas in sustainable and secure plant production.
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Affiliation(s)
- Delight Hwarari
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Yongchao Ke
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China.
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Larriba E, Yaroshko O, Pérez-Pérez JM. Recent Advances in Tomato Gene Editing. Int J Mol Sci 2024; 25:2606. [PMID: 38473859 DOI: 10.3390/ijms25052606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.
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Affiliation(s)
- Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Olha Yaroshko
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
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Park SJ, Park JS, Yang JH, Moon KB, Shin SY, Jeon JH, Kim HS, Lee HJ. MicroRNA396 negatively regulates shoot regeneration in tomato. HORTICULTURE RESEARCH 2024; 11:uhad291. [PMID: 38371631 PMCID: PMC10873581 DOI: 10.1093/hr/uhad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.
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Affiliation(s)
- Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Jin Ho Yang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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Bui TP, Le H, Ta DT, Nguyen CX, Le NT, Tran TT, Van Nguyen P, Stacey G, Stacey MG, Pham NB, Chu HH, Do PT. Enhancing powdery mildew resistance in soybean by targeted mutation of MLO genes using the CRISPR/Cas9 system. BMC PLANT BIOLOGY 2023; 23:533. [PMID: 37919649 PMCID: PMC10623788 DOI: 10.1186/s12870-023-04549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 10/19/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND Powdery mildew is a major disease that causes great losses in soybean yield and seed quality. Disease-resistant varieties, which are generated by reducing the impact of susceptibility genes through mutation in host plants, would be an effective approach to protect crops from this disease. The Mildew Locus O (MLO) genes are well-known susceptibility genes for powdery mildew in plant. In this study, we utilized the CRISPR/Cas9 system to induce targeted mutations in the soybean GmMLO genes to improve powdery mildew resistance. RESULTS A dual-sgRNA CRISPR/Cas9 construct was designed and successfully transferred into the Vietnamese soybean cultivar DT26 through Agrobacterium tumefaciens-mediated transformation. Various mutant forms of the GmMLO genes including biallelic, chimeric and homozygous were found at the T0 generation. The inheritance and segregation of CRISPR/Cas9-induced mutations were confirmed and validated at the T1 and T2 generations. Out of six GmMLO genes in the soybean genome, we obtained the Gmmlo02/Gmmlo19/Gmmlo23 triple and Gmmlo02/Gmmlo19/Gmmlo20/Gmmlo23 quadruple knockout mutants at the T2 generation. When challenged with Erysiphe diffusa, a fungus that causes soybean powdery mildew, all mutant plants showed enhanced resistance to the pathogen, especially the quadruple mutant. The powdery mildew severity in the mutant soybeans was reduced by up to 36.4% compared to wild-type plants. In addition, no pleiotropic effect on soybean growth and development under net-house conditions was observed in the CRISPR/Cas9 mutants. CONCLUSIONS Our results indicate the involvement of GmMLO02, GmMLO19, GmMLO20 and GmMLO23 genes in powdery mildew susceptibility in soybean. Further research should be conducted to investigate the roles of individual tested genes and the involvement of other GmMLO genes in this disease infection mechanism. Importantly, utilizing the CRISPR/Cas9 system successfully created the Gmmlo transgene-free homozygous mutant lines with enhanced resistance to powdery mildew, which could be potential materials for soybean breeding programs.
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Affiliation(s)
- Thao Phuong Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huy Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Present address: Department of Biology, Washington University in St. Louis, St. Louis, USA
| | - Dong Thi Ta
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Cuong Xuan Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Ngoc Thu Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Truong Thi Tran
- Legumes Research and Development Center, Vietnam Academy of Agriculture Science, Hanoi, Vietnam
| | - Phuong Van Nguyen
- University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Gary Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Minviluz G Stacey
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Ngoc Bich Pham
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang Chu
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phat Tien Do
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
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Shahriari Z, Su X, Zheng K, Zhang Z. Advances and Prospects of Virus-Resistant Breeding in Tomatoes. Int J Mol Sci 2023; 24:15448. [PMID: 37895127 PMCID: PMC10607384 DOI: 10.3390/ijms242015448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.
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Affiliation(s)
- Zolfaghar Shahriari
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
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11
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Sardar A. Genetic amelioration of fruit and vegetable crops to increase biotic and abiotic stress resistance through CRISPR Genome Editing. FRONTIERS IN PLANT SCIENCE 2023; 14:1260102. [PMID: 37841604 PMCID: PMC10570431 DOI: 10.3389/fpls.2023.1260102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Environmental changes and increasing population are major concerns for crop production and food security as a whole. To address this, researchers had focussed on the improvement of cereals and pulses and have made considerable progress till the beginning of this decade. However, cereals and pulses together, without vegetables and fruits, are inadequate to meet the dietary and nutritional demands of human life. Production of good quality vegetables and fruits is highly challenging owing to their perishable nature and short shelf life as well as abiotic and biotic stresses encountered during pre- and post-harvest. Genetic engineering approaches to produce good quality, to increase shelf life and stress-resistance, and to change the time of flowering and fruit ripening by introducing foreign genes to produce genetically modified crops were quite successful. However, several biosafety concerns, such as the risk of transgene-outcrossing, limited their production, marketing, and consumption. Modern genome editing techniques, like the CRISPR/Cas9 system, provide a perfect solution in this scenario, as it can produce transgene-free genetically edited plants. Hence, these genetically edited plants can easily satisfy the biosafety norms for crop production and consumption. This review highlights the potential of the CRISPR/Cas9 system for the successful generation of abiotic and biotic stress resistance and thereby improving the quality, yield, and overall productivity of vegetables and fruits.
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Affiliation(s)
- Atish Sardar
- Department of Botany, Jogesh Chandra Chaudhuri College, West Bengal, Kolkata, India
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12
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Kasi Viswanath K, Hamid A, Ateka E, Pappu HR. CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management. PHYTOPATHOLOGY 2023; 113:1661-1676. [PMID: 37486077 DOI: 10.1094/phyto-01-23-0002-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.
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Affiliation(s)
| | - Aflaq Hamid
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
| | - Elijah Ateka
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A
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13
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Shahwar D, Ahn N, Kim D, Ahn W, Park Y. Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108473. [PMID: 37716439 DOI: 10.1016/j.mrrev.2023.108473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.
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Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Namju Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Donghyun Kim
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Wooseong Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea.
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14
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Ijaz M, Khan F, Zaki HEM, Khan MM, Radwan KSA, Jiang Y, Qian J, Ahmed T, Shahid MS, Luo J, Li B. Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091911. [PMID: 37176969 PMCID: PMC10180734 DOI: 10.3390/plants12091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.
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Affiliation(s)
- Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fahad Khan
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250, Australia
| | - Haitham E M Zaki
- Horticulture Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
- Applied Biotechnology Department, University of Technology and Applied Sciences-Sur, Sur 411, Oman
| | - Muhammad Munem Khan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khlode S A Radwan
- Plant Pathology Department, Faculty of Agriculture, Minia University, El-Minia 61517, Egypt
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou 311400, China
| | - Jiahui Qian
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khod 123, Oman
| | - Jinyan Luo
- Department of Plant Quarantine, Shanghai Extension and Service Center of Agriculture Technology, Shanghai 201103, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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15
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Jogam P, Sandhya D, Alok A, Peddaboina V, Singh SP, Abbagani S, Zhang B, Allini VR. Editing of TOM1 gene in tobacco using CRISPR/Cas9 confers resistance to Tobacco mosaic virus. Mol Biol Rep 2023; 50:5165-5176. [PMID: 37119416 DOI: 10.1007/s11033-023-08440-2] [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: 10/13/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND Genome editing technology has become one of the excellent tools for precise plant breeding to develop novel plant germplasm. The Tobacco mosaic virus (TMV) is the most prominent pathogen that infects several Solanaceae plants, such as tobacco, tomato, and capsicum, which requires critical host factors for infection and replication of its genomic RNA in the host. The Tobamovirus multiplication (TOM) genes, such as TOM1, TOM2A, TOM2B, and TOM3, are involved in the multiplication of Tobamoviruses. TOM1 is a transmembrane protein necessary for efficient TMV multiplication in several plant species. The TOM genes are crucial recessive resistance genes that act against the tobamoviruses in various plant species. METHODS AND RESULTS The single guided RNA (sgRNA) was designed to target the first exon of the NtTOM1 gene and cloned into the pHSE401 vector. The pHSE401-NtTOM1 vector was introduced into Agrobacterium tumefaciens strain LBA4404 and then transformed into tobacco plants. The analysis on T0 transgenic plants showed the presence of the hptII and Cas9 transgenes. The sequence analysis of the NtTOM1 from T0 plants showed the indels. Genotypic evaluation of the NtTOM1 mutant lines displayed the stable inheritance of the mutations in the subsequent generations of tobacco plants. The NtTOM1 mutant lines successfully conferred resistance to TMV. CONCLUSIONS CRISPR/Cas genome editing is a reliable tool for investigating gene function and precision breeding across different plant species, especially the species in the Solanaceae family.
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Affiliation(s)
- Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Anshu Alok
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, 55108, USA
| | | | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Mohali, 140306, Punjab, India
| | - Sadanandam Abbagani
- Department of Biotechnology, Kakatiya University, Warangal, 506009, Telangana, India
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Antony Ceasar S, Ignacimuthu S. CRISPR/Cas genome editing in plants: Dawn of Agrobacterium transformation for recalcitrant and transgene-free plants for future crop breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:724-730. [PMID: 36812799 DOI: 10.1016/j.plaphy.2023.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Genome editing tools based on CRISPR/Cas system have been posed to solve many issues in agriculture and improve food production. Genetic engineering by Agrobacterium-mediated transformation has helped to impart specific traits straightaway in many crops. Many GM crops have also reached the field for commercial cultivation. Genetic engineering requires mostly a transformation protocol often mediated by Agrobacterium to insert a specific gene at a random locus. Genome editing with CRISPR/Cas system is a more precise technique for the targeted modification of genes/bases in the host plant genome. Unlike the conventional transformation system, wherein elimination of marker/foreign gene was possible only post-transformation, CRISPR/Cas system could generate transgene-free plants by delivering CRISPR/Cas reagents such as the Cas protein and guide RNAs gRNA(s) preassembled to form ribonucleoproteins (RNPs) into plant cells. CRISPR reagent delivery might be helpful to overcome issues with plants that are recalcitrant to Agrobacterium transformation and the legal hurdles due to the presence of the foreign gene. More recently, the grafting of wild-type shoots to transgenic donor rootstocks developed by the CRISPR/Cas system has reported transgene-free genome editing. CRISPR/Cas system also requires only a small piece of gRNA besides Cas9 or other effectors to target a specific region in the genome. So this system has been projected to be a key contributor to future crop breeding. In this article, we recap the main events of plant transformation, compare the difference between genetic transformation and CRISPR/Cas-mediated genome editing, and draw insights into the future application of the CRISPR/Cas system.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Molecular Biology & Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, 683 104, Kerala, India.
| | - S Ignacimuthu
- Xavier Research Foundation, St. Xavier's College, Affiliated to the Manonmaniam Sundaranar University, Palayamkottai, 627 002, Tamil Nadu, India
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Tiwari JK, Singh AK, Behera TK. CRISPR/Cas genome editing in tomato improvement: Advances and applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1121209. [PMID: 36909403 PMCID: PMC9995852 DOI: 10.3389/fpls.2023.1121209] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 06/12/2023]
Abstract
The narrow genetic base of tomato poses serious challenges in breeding. Hence, with the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, fast and efficient breeding has become possible in tomato breeding. Many traits have been edited and functionally characterized using CRISPR/Cas9 in tomato such as plant architecture and flower characters (e.g. leaf, stem, flower, male sterility, fruit, parthenocarpy), fruit ripening, quality and nutrition (e.g., lycopene, carotenoid, GABA, TSS, anthocyanin, shelf-life), disease resistance (e.g. TYLCV, powdery mildew, late blight), abiotic stress tolerance (e.g. heat, drought, salinity), C-N metabolism, and herbicide resistance. CRISPR/Cas9 has been proven in introgression of de novo domestication of elite traits from wild relatives to the cultivated tomato and vice versa. Innovations in CRISPR/Cas allow the use of online tools for single guide RNA design and multiplexing, cloning (e.g. Golden Gate cloning, GoldenBraid, and BioBrick technology), robust CRISPR/Cas constructs, efficient transformation protocols such as Agrobacterium, and DNA-free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex, Cas9 variants like PAM-free Cas12a, and Cas9-NG/XNG-Cas9, homologous recombination (HR)-based gene knock-in (HKI) by geminivirus replicon, and base/prime editing (Target-AID technology). This mini-review highlights the current research advances in CRISPR/Cas for fast and efficient breeding of tomato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anand Kumar Singh
- Division of Horticulture, Indian Council of Agricultural Research, Krishi Anusandhan Bhawan - II, Pusa, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Debbarma J, Saikia B, Singha DL, Das D, Keot AK, Maharana J, Velmurugan N, Arunkumar KP, Reddy PS, Chikkaputtaiah C. CRISPR/Cas9-Mediated Mutation in XSP10 and SlSAMT Genes Impart Genetic Tolerance to Fusarium Wilt Disease of Tomato ( Solanum lycopersicum L.). Genes (Basel) 2023; 14:488. [PMID: 36833415 PMCID: PMC9956927 DOI: 10.3390/genes14020488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
Fusarium wilt is a major devastating fungal disease of tomato (Solanum lycopersicum L.) caused by Fusarium oxysporum f. sp. lycopersici (Fol) which reduces the yield and production. Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) are two putative negative regulatory genes associated with Fusarium wilt of tomato. Fusarium wilt tolerance in tomato can be developed by targeting these susceptible (S) genes. Due to its efficiency, high target specificity, and versatility, CRISPR/Cas9 has emerged as one of the most promising techniques for knocking out disease susceptibility genes in a variety of model and agricultural plants to increase tolerance/resistance to various plant diseases in recent years. Though alternative methods, like RNAi, have been attempted to knock down these two S genes in order to confer resistance in tomato against Fusarium wilt, there has been no report of employing the CRISPR/Cas9 system for this specific intent. In this study, we provide a comprehensive downstream analysis of the two S genes via CRISPR/Cas9-mediated editing of single (XSP10 and SlSAMT individually) and dual-gene (XSP10 and SlSAMT simultaneously). Prior to directly advancing on to the generation of stable lines, the editing efficacy of the sgRNA-Cas9 complex was first validated using single cell (protoplast) transformation. In the transient leaf disc assay, the dual-gene editing showed strong phenotypic tolerance to Fusarium wilt disease with INDEL mutations than single-gene editing. In stable genetic transformation of tomato at the GE1 generation, dual-gene CRISPR transformants of XSP10 and SlSAMT primarily exhibited INDEL mutations than single-gene-edited lines. The dual-gene CRISPR-edited lines (CRELs) of XSP10 and SlSAMT at GE1 generation conferred a strong phenotypic tolerance to Fusarium wilt disease compared to single-gene-edited lines. Taken together, the reverse genetic studies in transient and stable lines of tomato revealed that, XSP10 and SlSAMT function together as negative regulators in conferring genetic tolerance to Fusarium wilt disease.
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Affiliation(s)
- Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Dhanawantari L. Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Jitendra Maharana
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat 785013, Assam, India
| | - Natarajan Velmurugan
- Branch Laboratory-Itanagar, Biological Sciences Division, CSIR-NEIST, Naharlagun 791110, Arunachal Pradesh, India
| | - Kallare P. Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat 785700, Assam, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Hyderabad 502324, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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20
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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21
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Lim JA, Yaacob JS, Mohd Rasli SRA, Eyahmalay JE, El Enshasy HA, Zakaria MRS. Mitigating the repercussions of climate change on diseases affecting important crop commodities in Southeast Asia, for food security and environmental sustainability—A review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1030540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Southeast Asia is a fertile land with a warm and humid climate which tends to accommodate various food crops. The development and advancement of the agricultural sector not only allows the countries in the region to feed the increasing population, but are also able to boost the nation's economy through exportation of the crops. Some of the well-known and economically-significant plant commodities found in the region include rice, oil palm, rubber, coconut, banana, sugarcane, pineapple, black pepper, maize, cocoa, durian, and jackfruit. Due to the high production of crops, Southeast Asia is able to stand among the top world producers of these commodities. Nevertheless, the widespread of pathogenic microorganisms has posed a serious threat to the industry over the years; with hundreds of millions of money wasted and total yield being lost due to the devastating diseases associated with each type of the plants. A lot of attention and effort have been continuously devoted to find effective plant management strategies to combat plant diseases, starting from traditional physical and chemical methods to the increasing discoveries on biological approaches made in recent decades. Due to the challenges and limitations faced by conventional approaches and the rising awareness toward the environment, more work has been focused on establishing the application of beneficial microorganisms to tackle plant diseases through direct mechanisms. Thus, by bringing the common plant commodities in Southeast Asia, their associated diseases and various physical, chemical and biological control measures together, this review aims to provide clearer insights and practical information to those who seek to limit the damages caused by plant diseases.
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Vuong UT, Iswanto ABB, Nguyen Q, Kang H, Lee J, Moon J, Kim SH. Engineering plant immune circuit: walking to the bright future with a novel toolbox. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:17-45. [PMID: 36036862 PMCID: PMC9829404 DOI: 10.1111/pbi.13916] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Plant pathogens destroy crops and cause severe yield losses, leading to an insufficient food supply to sustain the human population. Apart from relying on natural plant immune systems to combat biological agents or waiting for the appropriate evolutionary steps to occur over time, researchers are currently seeking new breakthrough methods to boost disease resistance in plants through genetic engineering. Here, we summarize the past two decades of research in disease resistance engineering against an assortment of pathogens through modifying the plant immune components (internal and external) with several biotechnological techniques. We also discuss potential strategies and provide perspectives on engineering plant immune systems for enhanced pathogen resistance and plant fitness.
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Affiliation(s)
- Uyen Thi Vuong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Arya Bagus Boedi Iswanto
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Quang‐Minh Nguyen
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Hobin Kang
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jihyun Lee
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Jiyun Moon
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinjuRepublic of Korea
- Division of Life ScienceGyeongsang National UniversityJinjuRepublic of Korea
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H. El-Sappah A, Qi S, A. Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus. FRONTIERS IN PLANT SCIENCE 2022; 13:1081549. [PMID: 36600922 PMCID: PMC9807178 DOI: 10.3389/fpls.2022.1081549] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.
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Affiliation(s)
- Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Shiming Qi
- College of Agriculture and Ecological Engineering, Hexi University, Zhangye, China
| | - Salma A. Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Alaa M. Saleh
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Lingyun Wan
- Key Laboratory of Guangxi for High-quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guo-ting Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Muhammad Ihtisham
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Zarqa Noor
- School of Chemical Engineering Beijing Institute of Technology, Beijing, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST–Kashmir, Sopore, India
| | - Xin Zhao
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Kuan Yan
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Jia Li
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
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CRISPR/Cas Genome Editing Technologies for Plant Improvement against Biotic and Abiotic Stresses: Advances, Limitations, and Future Perspectives. Cells 2022; 11:cells11233928. [PMID: 36497186 PMCID: PMC9736268 DOI: 10.3390/cells11233928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Crossbreeding, mutation breeding, and traditional transgenic breeding take much time to improve desirable characters/traits. CRISPR/Cas-mediated genome editing (GE) is a game-changing tool that can create variation in desired traits, such as biotic and abiotic resistance, increase quality and yield in less time with easy applications, high efficiency, and low cost in producing the targeted edits for rapid improvement of crop plants. Plant pathogens and the severe environment cause considerable crop losses worldwide. GE approaches have emerged and opened new doors for breeding multiple-resistance crop varieties. Here, we have summarized recent advances in CRISPR/Cas-mediated GE for resistance against biotic and abiotic stresses in a crop molecular breeding program that includes the modification and improvement of genes response to biotic stresses induced by fungus, virus, and bacterial pathogens. We also discussed in depth the application of CRISPR/Cas for abiotic stresses (herbicide, drought, heat, and cold) in plants. In addition, we discussed the limitations and future challenges faced by breeders using GE tools for crop improvement and suggested directions for future improvements in GE for agricultural applications, providing novel ideas to create super cultivars with broad resistance to biotic and abiotic stress.
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25
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Devi R, Chauhan S, Dhillon TS. Genome editing for vegetable crop improvement: Challenges and future prospects. Front Genet 2022; 13:1037091. [DOI: 10.3389/fgene.2022.1037091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
Abstract
Vegetable crops are known as protective foods due to their potential role in a balanced human diet, especially for vegetarians as they are a rich source of vitamins and minerals along with dietary fibers. Many biotic and abiotic stresses threaten the crop growth, yield and quality of these crops. These crops are annual, biennial and perennial in breeding behavior. Traditional breeding strategies pose many challenges in improving economic crop traits. As in most of the cases the large number of backcrosses and stringent selection pressure is required for the introgression of the useful traits into the germplasm, which is time and labour-intensive process. Plant scientists have improved economic traits like yield, quality, biotic stress resistance, abiotic stress tolerance, and improved nutritional quality of crops more precisely and accurately through the use of the revolutionary breeding method known as clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein-9 (Cas9). The high mutation efficiency, less off-target consequences and simplicity of this technique has made it possible to attain novel germplasm resources through gene-directed mutation. It facilitates mutagenic response even in complicated genomes which are difficult to breed using traditional approaches. The revelation of functions of important genes with the advancement of whole-genome sequencing has facilitated the CRISPR-Cas9 editing to mutate the desired target genes. This technology speeds up the creation of new germplasm resources having better agro-economical traits. This review entails a detailed description of CRISPR-Cas9 gene editing technology along with its potential applications in olericulture, challenges faced and future prospects.
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Park J, Lee S, Choi Y, Park G, Park S, Je B, Park Y. Germplasm Screening Using DNA Markers and Genome-Wide Association Study for the Identification of Powdery Mildew Resistance Loci in Tomato. Int J Mol Sci 2022; 23:13610. [PMID: 36362397 PMCID: PMC9657208 DOI: 10.3390/ijms232113610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 08/17/2024] Open
Abstract
Powdery mildew (PM), caused by Oidium spp. in tomato, is a global concern that leads to diminished yield. We aimed to evaluate previously reported DNA markers linked to powdery mildew resistance (PMR) and identify novel quantitative trait loci (QTLs) for PMR through a genome-wide association study in tomato. Sequencing analysis of the internal transcribed spacer (ITS) of a PM strain (PNU_PM) isolated from Miryang, Gyeongnam, led to its identification as Oidium neolycopersici. Thereafter, a PM bioassay was conducted for a total of 295 tomato accessions, among which 24 accessions (4 S. lycopersicum accessions and 20 accessions of seven wild species) showed high levels of resistance to PNU_PM. Subsequently, we genotyped 11 markers previously linked to PMR in 56 accessions. PMR-specific banding patterns were detected in 15/22 PMR accessions, while no such bands were observed in the powdery mildew-susceptible accessions. The genome-wide association study was performed using TASSEL and GAPIT, based on the phenotypic data of 290 accessions and 11,912 single nucleotide polymorphisms (SNPs) obtained from the Axiom® Tomato SNP Chip Array. Nine significant SNPs in chromosomes 1, 4, 6, 8, and 12, were selected and five novel QTL regions distinct from previously known PMR-QTL regions were identified. Of these QTL regions, three putative candidate genes for PMR were selected from chromosomes 4 and 8, including two nucleotide binding site-leucine rich repeat class genes and a receptor-like kinase gene, all of which have been identified previously as causative genes for PMR in several crop species. The SNPs discovered in these genes provide useful information for understanding the molecular basis of PMR and developing DNA markers for marker-assisted selection of PMR in tomato.
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Affiliation(s)
- Jiyeon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Siyoung Lee
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Yunseo Choi
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Girim Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Seoyeon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Byoungil Je
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Korea
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Karmakar S, Das P, Panda D, Xie K, Baig MJ, Molla KA. A detailed landscape of CRISPR-Cas-mediated plant disease and pest management. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111376. [PMID: 35835393 DOI: 10.1016/j.plantsci.2022.111376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Genome editing technology has rapidly evolved to knock-out genes, create targeted genetic variation, install precise insertion/deletion and single nucleotide changes, and perform large-scale alteration. The flexible and multipurpose editing technologies have started playing a substantial role in the field of plant disease management. CRISPR-Cas has reduced many limitations of earlier technologies and emerged as a versatile toolbox for genome manipulation. This review summarizes the phenomenal progress of the use of the CRISPR toolkit in the field of plant pathology. CRISPR-Cas toolbox aids in the basic studies on host-pathogen interaction, in identifying virulence genes in pathogens, deciphering resistance and susceptibility factors in host plants, and engineering host genome for developing resistance. We extensively reviewed the successful genome editing applications for host plant resistance against a wide range of biotic factors, including viruses, fungi, oomycetes, bacteria, nematodes, insect pests, and parasitic plants. Recent use of CRISPR-Cas gene drive to suppress the population of pathogens and pests has also been discussed. Furthermore, we highlight exciting new uses of the CRISPR-Cas system as diagnostic tools, which rapidly detect pathogenic microorganism. This comprehensive yet concise review discusses innumerable strategies to reduce the burden of crop protection.
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Affiliation(s)
| | - Priya Das
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Debasmita Panda
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mirza J Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India.
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Simultaneously induced mutations in eIF4E genes by CRISPR/Cas9 enhance PVY resistance in tobacco. Sci Rep 2022; 12:14627. [PMID: 36028578 PMCID: PMC9418239 DOI: 10.1038/s41598-022-18923-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Tobacco is an important commercial crop and a rich source of alkaloids for pharmaceutical and agricultural applications. However, its yield can be reduced by up to 70% due to virus infections, especially by a potyvirus Potato virus Y (PVY). The replication of PVY relies on host factors, and eukaryotic translation initiation factor 4Es (eIF4Es) have already been identified as recessive resistance genes against potyviruses in many plant species. To investigate the molecular basis of PVY resistance in the widely cultivated allotetraploid tobacco variety K326, we developed a dual guide RNA CRISPR/Cas9 system for combinatorial gene editing of two clades, eIF4E1 (eIF4E1-S and eIF4E1-T) and eIF4E2 (eIF4E2-S and eIF4E2-T) in the eIF4E gene family comprising six members in tobacco. We screened for CRISPR/Cas9-induced mutations by heteroduplex analysis and Sanger sequencing, and monitored PVYO accumulation in virus challenged regenerated plants by DAS-ELISA both in T0 and T1 generations. We found that all T0 lines carrying targeted mutations in the eIF4E1-S gene displayed enhanced resistance to PVYO confirming previous reports. More importantly, our combinatorial approach revealed that eIF4E1-S is necessary but not sufficient for complete PVY resistance. Only the quadruple mutants harboring loss-of-function mutations in eIF4E1-S, eIF4E1-T, eIF4E2-S and eIF4E2-T showed heritable high-level resistance to PVYO in tobacco. Our work highlights the importance of understanding host factor redundancy in virus replication and provides a roadmap to generate virus resistance by combinatorial CRISPR/Cas9-mediated editing in non-model crop plants with complex genomes.
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29
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Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
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MLO Proteins from Tomato (Solanum lycopersicum L.) and Related Species in the Broad Phylogenetic Context. PLANTS 2022; 11:plants11121588. [PMID: 35736740 PMCID: PMC9229925 DOI: 10.3390/plants11121588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/06/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
MLO proteins are a family of transmembrane proteins in land plants that play an important role in plant immunity and host–pathogen interactions, as well as a wide range of development processes. Understanding the evolutionary history of MLO proteins is important for understanding plant physiology and health. In the present work, we conducted a phylogenetic analysis on a large set of MLO protein sequences from publicly available databases, specifically emphasising MLOs from the tomato plant and related species. As a result, 4886 protein sequences were identified and used to construct a phylogenetic tree. In comparison to previous findings, we identified nine phylogenetic clades, revealed the internal structure of clades I and II as additional clades and showed the presence of monocotyledon species in all MLO clades. We identified a set of 19 protein motifs that allowed for the identification of particular clades. Sixteen SlMLO proteins from tomato were located in the phylogenetic tree and identified in relation to homologous sequences from other Solanaceae species. The obtained results could be useful for further work on the use of MLO proteins in the study of mildew resistance in Solanaceae and other plant families.
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Viviani A, Spada M, Giordani T, Fambrini M, Pugliesi C. Origin of the genome editing systems: application for crop improvement. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ishikawa M, Yoshida T, Matsuyama M, Kouzai Y, Kano A, Ishibashi K. Tomato brown rugose fruit virus resistance generated by quadruple knockout of homologs of TOBAMOVIRUS MULTIPLICATION1 in tomato. PLANT PHYSIOLOGY 2022; 189:679-686. [PMID: 35262730 PMCID: PMC9157163 DOI: 10.1093/plphys/kiac103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/24/2022] [Indexed: 05/20/2023]
Abstract
Tomato brown rugose fruit virus (ToBRFV) is an emerging virus of the genus Tobamovirus. ToBRFV overcomes the tobamovirus resistance gene Tm-22 and is rapidly spreading worldwide. Genetic resources for ToBRFV resistance are urgently needed. Here, we show that clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9)-mediated targeted mutagenesis of four tomato (Solanum lycopersicum) homologs of TOBAMOVIRUS MULTIPLICATION1 (TOM1), an Arabidopsis (Arabidopsis thaliana) gene essential for tobamovirus multiplication, confers resistance to ToBRFV in tomato plants. Quadruple-mutant plants did not show detectable ToBRFV coat protein (CP) accumulation or obvious defects in growth or fruit production. When any three of the four TOM1 homologs were disrupted, ToBRFV CP accumulation was detectable but greatly reduced. In the triple mutant, in which ToBRFV CP accumulation was most strongly suppressed, mutant viruses capable of more efficient multiplication in the mutant plants emerged. However, these mutant viruses did not infect the quadruple-mutant plants, suggesting that the resistance of the quadruple-mutant plants is highly durable. The quadruple-mutant plants also showed resistance to three other tobamovirus species. Therefore, tomato plants with strong resistance to tobamoviruses, including ToBRFV, can be generated by CRISPR/Cas9-mediated multiplexed genome editing. The genome-edited plants could facilitate ToBRFV-resistant tomato breeding.
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Affiliation(s)
- Masayuki Ishikawa
- Crop Disease Research Group, Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Tetsuya Yoshida
- Crop Disease Research Group, Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Momoko Matsuyama
- Crop Disease Research Group, Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Yusuke Kouzai
- Crop Stress Management Group, Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Akihito Kano
- Plant Breeding and Experiment Station, Takii and Company Limited, Shiga 520-3231, Japan
| | - Kazuhiro Ishibashi
- Crop Disease Research Group, Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO, 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Silva FDA, Fontes EPB. Clustered Regularly Interspaced Short Palindromic Repeats-Associated Protein System for Resistance Against Plant Viruses: Applications and Perspectives. FRONTIERS IN PLANT SCIENCE 2022; 13:904829. [PMID: 35693174 PMCID: PMC9178237 DOI: 10.3389/fpls.2022.904829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Different genome editing approaches have been used to engineer resistance against plant viruses. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas; CRISPR/Cas) systems to create pinpoint genetic mutations have emerged as a powerful tool for molecular engineering of plant immunity and increasing resistance against plant viruses. This review presents (i) recent advances in engineering resistance against plant viruses by CRISPR/Cas and (ii) an overview of the potential host factors as targets for the CRISPR/Cas system-mediated broad-range resistance and immunity. Applications, challenges, and perspectives in enabling the CRISPR/Cas system for crop protection are also outlined.
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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Helderman TA, Deurhof L, Bertran A, Richard MMS, Kormelink R, Prins M, Joosten MHAJ, van den Burg HA. Members of the ribosomal protein S6 (RPS6) family act as pro-viral factor for tomato spotted wilt orthotospovirus infectivity in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2022; 23:431-446. [PMID: 34913556 PMCID: PMC8828452 DOI: 10.1111/mpp.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 05/07/2023]
Abstract
To identify host factors for tomato spotted wilt orthotospovirus (TSWV), a virus-induced gene silencing (VIGS) screen using tobacco rattle virus (TRV) was performed on Nicotiana benthamiana for TSWV susceptibility. To rule out any negative effect on the plants' performance due to a double viral infection, the method was optimized to allow screening of hundreds of clones in a standardized fashion. To normalize the results obtained in and between experiments, a set of controls was developed to evaluate in a consist manner both VIGS efficacy and the level of TSWV resistance. Using this method, 4532 random clones of an N. benthamiana cDNA library were tested, resulting in five TRV clones that provided nearly complete resistance against TSWV. Here we report on one of these clones, of which the insert targets a small gene family coding for the ribosomal protein S6 (RPS6) that is part of the 40S ribosomal subunit. This RPS6 family is represented by three gene clades in the genome of Solanaceae family members, which were jointly important for TSWV susceptibility. Interestingly, RPS6 is a known host factor implicated in the replication of different plant RNA viruses, including the negative-stranded TSWV and the positive-stranded potato virus X.
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Affiliation(s)
- Tieme A. Helderman
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Laurens Deurhof
- Laboratory of PhytopathologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - André Bertran
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Manon M. S. Richard
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Richard Kormelink
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Marcel Prins
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
- KeyGene N.V.WageningenNetherlands
| | | | - Harrold A. van den Burg
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
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Khan ZA, Kumar R, Dasgupta I. CRISPR/Cas-Mediated Resistance against Viruses in Plants. Int J Mol Sci 2022; 23:ijms23042303. [PMID: 35216418 PMCID: PMC8879314 DOI: 10.3390/ijms23042303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas9 provides a robust and widely adaptable system with enormous potential for genome editing directed towards generating useful products. It has been used extensively to generate resistance against viruses infecting plants with more effective and prolonged efficiency as compared with previous antiviral approaches, thus holding promise to alleviate crop losses. In this review, we have discussed the reports of CRISPR/Cas-based virus resistance strategies against plant viruses. These strategies include approaches targeting single or multiple genes (or non-coding region) in the viral genome and targeting host factors essential for virus propagation. In addition, the utilization of base editing has been discussed to generate transgene-free plants resistant to viruses. This review also compares the efficiencies of these approaches. Finally, we discuss combinatorial approaches, including multiplexing, to increase editing efficiency and bypass the generation of escape mutants.
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Shelake RM, Pramanik D, Kim JY. In Vivo Rapid Investigation of CRISPR-Based Base Editing Components in Escherichia coli (IRI-CCE): A Platform for Evaluating Base Editing Tools and Their Components. Int J Mol Sci 2022; 23:ijms23031145. [PMID: 35163069 PMCID: PMC8834901 DOI: 10.3390/ijms23031145] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid assessment of clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing (GE) tools and their components is a critical aspect for successful GE applications in different organisms. In many bacteria, double-strand breaks (DSBs) generated by CRISPR/Cas tool generally cause cell death due to the lack of an efficient nonhomologous end-joining pathway and restricts its use. CRISPR-based DSB-free base editors (BEs) have been applied for precise nucleotide (nt) editing in bacteria, which does not need to make DSBs. However, optimization of newer BE tools in bacteria is challenging owing to the toxic effects of BE reagents expressed using strong promoters. Improved variants of two main BEs, cytidine base editor (CBE) and adenine base editor (ABE), capable of converting C to T and A to G, respectively, have been recently developed but yet to be tested for editing characteristics in bacteria. Here, we report a platform for in vivo rapid investigation of CRISPR-BE components in Escherichia coli (IRI-CCE) comprising a combination of promoters and terminators enabling the expression of nCas9-based BE and sgRNA to nontoxic levels, eventually leading to successful base editing. We demonstrate the use of IRI-CCE to characterize different variants of CBEs (PmCDA1, evoCDA1, APOBEC3A) and ABEs (ABE8e, ABE9e) for bacteria, exhibiting that each independent BE has its specific editing pattern for a given target site depending on protospacer length. In summary, CRISPR-BE components expressed without lethal effects on cell survival in the IRI-CCE allow an analysis of various BE tools, including cloned biopart modules and sgRNAs.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Correspondence: (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea;
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea
- Correspondence: (R.M.S.); (J.-Y.K.)
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Rasheed A, Gill RA, Hassan MU, Mahmood A, Qari S, Zaman QU, Ilyas M, Aamer M, Batool M, Li H, Wu Z. A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises. Curr Issues Mol Biol 2021; 43:1950-1976. [PMID: 34889892 PMCID: PMC8929161 DOI: 10.3390/cimb43030135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Genome editing (GE) has revolutionized the biological sciences by creating a novel approach for manipulating the genomes of living organisms. Many tools have been developed in recent years to enable the editing of complex genomes. Therefore, a reliable and rapid approach for increasing yield and tolerance to various environmental stresses is necessary to sustain agricultural crop production for global food security. This critical review elaborates the GE tools used for crop improvement. These tools include mega-nucleases (MNs), such as zinc-finger nucleases (ZFNs), and transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Specifically, this review addresses the latest advancements in the role of CRISPR/Cas9 for genome manipulation for major crop improvement, including yield and quality development of biotic stress- and abiotic stress-tolerant crops. Implementation of this technique will lead to the production of non-transgene crops with preferred characteristics that can result in enhanced yield capacity under various environmental stresses. The CRISPR/Cas9 technique can be combined with current and potential breeding methods (e.g., speed breeding and omics-assisted breeding) to enhance agricultural productivity to ensure food security. We have also discussed the challenges and limitations of CRISPR/Cas9. This information will be useful to plant breeders and researchers in the thorough investigation of the use of CRISPR/Cas9 to boost crops by targeting the gene of interest.
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Affiliation(s)
- Adnan Rasheed
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Sameer Qari
- Biology Department, (Genetics and Molecular Biology Central Laboratory), Aljumum University College, Umm Al-Qura University, Makkah 24382, Saudi Arabia;
| | - Qamar U. Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China; (R.A.G.); (Q.U.Z.)
| | - Muhammad Ilyas
- University College of Dera Murad Jamali, Nasirabad 80700, Balochistan, Pakistan;
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.U.H.); (M.A.)
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Huijie Li
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
- College of Humanity and Public Administration, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziming Wu
- Key Laboratory of Crops Physiology, Ecology and Genetic Breeding, Ministry of Education/College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China; (A.R.); (H.L.)
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Chandrasekaran M, Boopathi T, Paramasivan M. A status-quo review on CRISPR-Cas9 gene editing applications in tomato. Int J Biol Macromol 2021; 190:120-129. [PMID: 34474054 DOI: 10.1016/j.ijbiomac.2021.08.169] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/09/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
Epigenetic changes are emancipated in horticultural crops including tomato due to a variety of environmental factors. These modifications rely on plant phenotypes mediated by genetic architecture consequently resulting in hereditary epigenetic memory. Genome editing strategies like CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)/CRISPR-associated protein 9 (Cas9) technologies have revolutionized plants biology foreseeing stable inheritance of epigenetic modifications. CRISPR/Cas9 strategy poses as explicit advancement in providing precise genome editing with minimal off-target mutations, ease of experimental design, higher efficiency, versatility, and cost-effectiveness. Dicot crops, especially tomato remain an ideal candidate for CRISPR/Cas9 based gene modulations thereby augmenting productivity and yields. In the present review, key questions on CRISPR/Cas9 applications aid in enhanced growth based on optimal gene discovery, de novo modification, trait improvement, and biotic/abiotic stress management are discussed. In addition, comparative scenario in tomato and similar horticultural crops are adequately summarized for the pros and cons. Further, limitations hampering potential benefits and success phenomena of the lab to field transition of gene editing alterations are discussed collaterally in addressing futuristic optimization for CRISPR/Cas9 research in tomato.
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Affiliation(s)
- Murugesan Chandrasekaran
- Department of Food Science and Biotechnology, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul 05006, Republic of Korea.
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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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42
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Genome editing for resistance against plant pests and pathogens. Transgenic Res 2021; 30:427-459. [PMID: 34143358 DOI: 10.1007/s11248-021-00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 05/27/2021] [Indexed: 12/12/2022]
Abstract
The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.
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Son GH, Moon J, Shelake RM, Vuong UT, Ingle RA, Gassmann W, Kim JY, Kim SH. Conserved Opposite Functions in Plant Resistance to Biotrophic and Necrotrophic Pathogens of the Immune Regulator SRFR1. Int J Mol Sci 2021; 22:6427. [PMID: 34204013 PMCID: PMC8233967 DOI: 10.3390/ijms22126427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
Plant immunity is mediated in large part by specific interactions between a host resistance protein and a pathogen effector protein, named effector-triggered immunity (ETI). ETI needs to be tightly controlled both positively and negatively to enable normal plant growth because constitutively activated defense responses are detrimental to the host. In previous work, we reported that mutations in SUPPRESSOR OF rps4-RLD1 (SRFR1), identified in a suppressor screen, reactivated EDS1-dependent ETI to Pseudomonas syringae pv. tomato (Pto) DC3000. Besides, mutations in SRFR1 boosted defense responses to the generalist chewing insect Spodoptera exigua and the sugar beet cyst nematode Heterodera schachtii. Here, we show that mutations in SRFR1 enhance susceptibility to the fungal necrotrophs Fusarium oxysporum f. sp. lycopersici (FOL) and Botrytis cinerea in Arabidopsis. To translate knowledge obtained in AtSRFR1 research to crops, we generated SlSRFR1 alleles in tomato using a CRISPR/Cas9 system. Interestingly, slsrfr1 mutants increased expression of SA-pathway defense genes and enhanced resistance to Pto DC3000. In contrast, slsrfr1 mutants elevated susceptibility to FOL. Together, these data suggest that SRFR1 is functionally conserved in both Arabidopsis and tomato and functions antagonistically as a negative regulator to (hemi-) biotrophic pathogens and a positive regulator to necrotrophic pathogens.
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Affiliation(s)
- Geon Hui Son
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
| | - Jiyun Moon
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
| | - Uyen Thi Vuong
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
| | - Robert A. Ingle
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7700, South Africa;
| | - Walter Gassmann
- Division of Plant Sciences, Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA;
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Sang Hee Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; (G.H.S.); (J.M.); (R.M.S.); (U.T.V.); (J.-Y.K.)
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
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44
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Chourasia KN, Lal MK, Tiwari RK, Dev D, Kardile HB, Patil VU, Kumar A, Vanishree G, Kumar D, Bhardwaj V, Meena JK, Mangal V, Shelake RM, Kim JY, Pramanik D. Salinity Stress in Potato: Understanding Physiological, Biochemical and Molecular Responses. Life (Basel) 2021; 11:life11060545. [PMID: 34200706 PMCID: PMC8228783 DOI: 10.3390/life11060545] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/20/2022] Open
Abstract
Among abiotic stresses, salinity is a major global threat to agriculture, causing severe damage to crop production and productivity. Potato (Solanum tuberosum) is regarded as a future food crop by FAO to ensure food security, which is severely affected by salinity. The growth of the potato plant is inhibited under salt stress due to osmotic stress-induced ion toxicity. Salinity-mediated osmotic stress leads to physiological changes in the plant, including nutrient imbalance, impairment in detoxifying reactive oxygen species (ROS), membrane damage, and reduced photosynthetic activities. Several physiological and biochemical phenomena, such as the maintenance of plant water status, transpiration, respiration, water use efficiency, hormonal balance, leaf area, germination, and antioxidants production are adversely affected. The ROS under salinity stress leads to the increased plasma membrane permeability and extravasations of substances, which causes water imbalance and plasmolysis. However, potato plants cope with salinity mediated oxidative stress conditions by enhancing both enzymatic and non-enzymatic antioxidant activities. The osmoprotectants, such as proline, polyols (sorbitol, mannitol, xylitol, lactitol, and maltitol), and quaternary ammonium compound (glycine betaine) are synthesized to overcome the adverse effect of salinity. The salinity response and tolerance include complex and multifaceted mechanisms that are controlled by multiple proteins and their interactions. This review aims to redraw the attention of researchers to explore the current physiological, biochemical and molecular responses and subsequently develop potential mitigation strategies against salt stress in potatoes.
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Affiliation(s)
- Kumar Nishant Chourasia
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
- Correspondence: (K.N.C.); (D.P.)
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Devanshu Dev
- School of Agricultural Sciences, G D Goenka University, Gurugram 122103, Haryana, India;
| | - Hemant Balasaheb Kardile
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Virupaksh U. Patil
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Amarjeet Kumar
- Department of Genetics and Plant Breeding, MTTC&VTC, Central Agriculture University, Imphal 795004, Manipur, India;
| | - Girimalla Vanishree
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Dharmendra Kumar
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Jitendra Kumar Meena
- ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata 700120, West Bengal, India;
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India; (M.K.L.); (R.K.T.); (H.B.K.); (V.U.P.); (G.V.); (D.K.); (V.B.); (V.M.)
| | - Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (R.M.S.); (J.-Y.K.)
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (R.M.S.); (J.-Y.K.)
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea; (R.M.S.); (J.-Y.K.)
- Correspondence: (K.N.C.); (D.P.)
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