1
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Sha T, Li Z, Xu S, Su T, Shopan J, Jin X, Deng Y, Lyu X, Hu Z, Zhang M, Yang J. eIF2Bβ confers resistance to Turnip mosaic virus by recruiting ALKBH9B to modify viral RNA methylation. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39229972 DOI: 10.1111/pbi.14442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 06/12/2024] [Accepted: 07/14/2024] [Indexed: 09/05/2024]
Abstract
Eukaryotic translation initiation factors (eIFs) are the primary targets for overcoming RNA virus resistance in plants. In a previous study, we mapped a BjeIF2Bβ from Brassica juncea representing a new class of plant virus resistance genes associated with resistance to Turnip mosaic virus (TuMV). However, the mechanism underlying eIF2Bβ-mediated virus resistance remains unclear. In this study, we discovered that the natural variation of BjeIF2Bβ in the allopolyploid B. juncea was inherited from one of its ancestors, B. rapa. By editing of eIF2Bβ, we were able to confer resistance to TuMV in B. juncea and in its sister species of B. napus. Additionally, we identified an N6-methyladenosine (m6A) demethylation factor, BjALKBH9B, for interaction with BjeIF2Bβ, where BjALKBH9B co-localized with both BjeIF2Bβ and TuMV. Furthermore, BjeIF2Bβ recruits BjALKBH9B to modify the m6A status of TuMV viral coat protein RNA, which lacks the ALKB homologue in its genomic RNA, thereby affecting viral infection. Our findings have applications for improving virus resistance in the Brassicaceae family through natural variation or genome editing of the eIF2Bβ. Moreover, we uncovered a non-canonical translational control of viral mRNA in the host plant.
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Affiliation(s)
- Tongyun Sha
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
| | - Shirui Xu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Tongbing Su
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jannat Shopan
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xingming Jin
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yueying Deng
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Xiaolong Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou, China
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2
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Thomas WJW, Amas JC, Dolatabadian A, Huang S, Zhang F, Zandberg JD, Neik TX, Edwards D, Batley J. Recent advances in the improvement of genetic resistance against disease in vegetable crops. PLANT PHYSIOLOGY 2024; 196:32-46. [PMID: 38796840 PMCID: PMC11376385 DOI: 10.1093/plphys/kiae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Affiliation(s)
- William J W Thomas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Junrey C Amas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Aria Dolatabadian
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Shuanglong Huang
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jaco D Zandberg
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Ting Xiang Neik
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
- NUS Agritech Centre, National University of Singapore, Singapore, 118258, Republic of Singapore
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
- Centre for Applied Bioinformatics, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
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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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Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [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: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
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5
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Chovatiya A, Rajyaguru R, Tomar RS, Joshi P. Revolutionizing Agriculture: Harnessing CRISPR/Cas9 for Crop Enhancement. Indian J Microbiol 2024; 64:59-69. [PMID: 38468733 PMCID: PMC10924811 DOI: 10.1007/s12088-023-01154-w] [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: 05/06/2023] [Accepted: 11/16/2023] [Indexed: 03/13/2024] Open
Abstract
Plant crops serve as essential sources of nutritional sustenance, supplying vital nutrients to human diets. However, their productivity and quality are severely jeopardized by factors such as pests, diseases, and adverse abiotic conditions. Addressing these challenges using innovative biotechnological approaches is imperative for advancing sustainable agriculture. In recent years, genome editing technologies have emerged as pivotal genetic tools, revolutionizing plant molecular biology. Among these, the CRISPR-Cas9 system has gained prominence due to its unparalleled precision, streamlined design, and heightened success rates. This review article highlights the profound impact of CRISPR/Cas9 technology on crop improvement. The article critically examines the breakthroughs, ongoing enhancements, and future prospects associated with this cutting-edge technology. In conclusion, the utilization of CRISPR/Cas9 presents a transformative shift in agricultural biotechnology, holding the potential to mitigate longstanding agricultural challenges.
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Affiliation(s)
- Ashish Chovatiya
- Department of Biotechnology, Atmiya University, Rajkot, Gujarat 360005 India
| | - Riddhi Rajyaguru
- Department of Biotechnology, Junagadh Agriculture University, Junagadh, Gujarat 362001 India
| | - Rukam Singh Tomar
- Department of Biotechnology, Junagadh Agriculture University, Junagadh, Gujarat 362001 India
| | - Preetam Joshi
- Department of Biotechnology, Atmiya University, Rajkot, Gujarat 360005 India
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6
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Saikia B, S R, Debbarma J, Maharana J, Sastry GN, Chikkaputtaiah C. CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicum L. in imparting genetic tolerance to multiple stress factors. FRONTIERS IN PLANT SCIENCE 2024; 15:1304381. [PMID: 38371406 PMCID: PMC10869523 DOI: 10.3389/fpls.2024.1304381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
CRISPR/Cas is a breakthrough genome editing system because of its precision, target specificity, and efficiency. As a speed breeding system, it is more robust than the conventional breeding and biotechnological approaches for qualitative and quantitative trait improvement. Tomato (Solanum lycopersicum L.) is an economically important crop, but its yield and productivity have been severely impacted due to different abiotic and biotic stresses. The recently identified SlHyPRP1 and SlDEA1 are two potential negative regulatory genes in response to different abiotic (drought and salinity) and biotic stress (bacterial leaf spot and bacterial wilt) conditions in S. lycopersicum L. The present study aimed to evaluate the drought, salinity, bacterial leaf spot, and bacterial wilt tolerance response in S. lycopersicum L. crop through CRISPR/Cas9 genome editing of SlHyPRP1 and SlDEA1 and their functional analysis. The transient single- and dual-gene SlHyPRP1 and SlDEA1 CRISPR-edited plants were phenotypically better responsive to multiple stress factors taken under the study. The CRISPR-edited SlHyPRP1 and SlDEA1 plants showed a higher level of chlorophyll and proline content compared to wild-type (WT) plants under abiotic stress conditions. Reactive oxygen species accumulation and the cell death count per total area of leaves and roots under biotic stress were less in CRISPR-edited SlHyPRP1 and SlDEA1 plants compared to WT plants. The study reveals that the combined loss-of-function of SlHyPRP1 along with SlDEA1 is essential for imparting significant multi-stress tolerance (drought, salinity, bacterial leaf spot, and bacterial wilt) in S. lycopersicum L. The main feature of the study is the detailed genetic characterization of SlDEA1, a poorly studied 8CM family gene in multi-stress tolerance, through the CRISPR/Cas9 gene editing system. The study revealed the key negative regulatory role of SlDEA1 that function together as an anchor gene with SlHyPRP1 in imparting multi-stress tolerance in S. lycopersicum L. It was interesting that the present study also showed that transient CRISPR/Cas9 editing events of SlHyPRP1 and SlDEA1 genes were successfully replicated in stably generated parent-genome-edited line (GEd0) and genome-edited first-generation lines (GEd1) of S. lycopersicum L. With these upshots, the study's key findings demonstrate outstanding value in developing sustainable multi-stress tolerance in S. lycopersicum L. and other crops to cope with climate change.
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Affiliation(s)
- Banashree Saikia
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Remya S
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Johni Debbarma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
| | - G. Narahari Sastry
- Advanced Computational and Data Science Division, CSIR-NEIST, Jorhat, Assam, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Lee SY, Kang B, Venkatesh J, Lee JH, Lee S, Kim JM, Back S, Kwon JK, Kang BC. Development of virus-induced genome editing methods in Solanaceous crops. HORTICULTURE RESEARCH 2024; 11:uhad233. [PMID: 38222822 PMCID: PMC10782499 DOI: 10.1093/hr/uhad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/01/2023] [Indexed: 01/16/2024]
Abstract
Genome editing (GE) using CRISPR/Cas systems has revolutionized plant mutagenesis. However, conventional transgene-mediated GE methods have limitations due to the time-consuming generation of stable transgenic lines expressing the Cas9/single guide RNA (sgRNA) module through tissue cultures. Virus-induced genome editing (VIGE) systems have been successfully employed in model plants, such as Arabidopsis thaliana and Nicotiana spp. In this study, we developed two VIGE methods for Solanaceous plants. First, we used the tobacco rattle virus (TRV) vector to deliver sgRNAs into a transgenic tomato (Solanum lycopersicum) line of cultivar Micro-Tom expressing Cas9. Second, we devised a transgene-free GE method based on a potato virus X (PVX) vector to deliver Cas9 and sgRNAs. We designed and cloned sgRNAs targeting Phytoene desaturase in the VIGE vectors and determined optimal conditions for VIGE. We evaluated VIGE efficiency through deep sequencing of the target gene after viral vector inoculation, detecting 40.3% and 36.5% mutation rates for TRV- and PVX-mediated GE, respectively. To improve editing efficiency, we applied a 37°C heat treatment, which increased the editing efficiency by 33% to 46% and 56% to 76% for TRV- and PVX-mediated VIGE, respectively. To obtain edited plants, we subjected inoculated cotyledons to tissue culture, yielding successful editing events. We also demonstrated that PVX-mediated GE can be applied to other Solanaceous crops, such as potato (Solanum tuberosum) and eggplant (Solanum melongena). These simple and highly efficient VIGE methods have great potential for generating genome-edited plants in Solanaceous crops.
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Affiliation(s)
- Seo-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bomi Kang
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jelli Venkatesh
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seyoung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungki Back
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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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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9
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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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10
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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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Lee YR, Siddique MI, Kim DS, Lee ES, Han K, Kim SG, Lee HE. CRISPR/Cas9-mediated gene editing to confer turnip mosaic virus (TuMV) resistance in Chinese cabbage ( Brassica rapa). HORTICULTURE RESEARCH 2023; 10:uhad078. [PMID: 37323233 PMCID: PMC10261878 DOI: 10.1093/hr/uhad078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Genome editing approaches, particularly the CRISPR/Cas9 technology, are becoming state-of-the-art for trait development in numerous breeding programs. Significant advances in improving plant traits are enabled by this influential tool, especially for disease resistance, compared to traditional breeding. One of the potyviruses, the turnip mosaic virus (TuMV), is the most widespread and damaging virus that infects Brassica spp. worldwide. We generated the targeted mutation at the eIF(iso)4E gene in the TuMV-susceptible cultivar "Seoul" using CRISPR/Cas9 to develop TuMV-resistant Chinese cabbage. We detected several heritable indel mutations in the edited T0 plants and developed T1 through generational progression. It was indicated in the sequence analysis of the eIF(iso)4E-edited T1 plants that the mutations were transferred to succeeding generations. These edited T1 plants conferred resistance to TuMV. It was shown with ELISA analysis the lack of accumulation of viral particles. Furthermore, we found a strong negative correlation (r = -0.938) between TuMV resistance and the genome editing frequency of eIF(iso)4E. Consequently, it was revealed in this study that CRISPR/Cas9 technique can expedite the breeding process to improve traits in Chinese cabbage plants.
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Affiliation(s)
- Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Muhammad Irfan Siddique
- Department of Horticultural Sciences, North Carolina State University Mountain Horticultural Crops Research, Extension Center 455 Research Drive, Mills River, NC 28759, USA
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, 34141, Republic of Korea
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12
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Kuroiwa K, Danilo B, Perrot L, Thenault C, Veillet F, Delacote F, Duchateau P, Nogué F, Mazier M, Gallois J. An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:918-930. [PMID: 36715107 PMCID: PMC10106848 DOI: 10.1111/pbi.14003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 05/04/2023]
Abstract
Resistance to potyviruses in plants has been largely provided by the selection of natural variant alleles of eukaryotic translation initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus isolates continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting the functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.
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Affiliation(s)
| | | | - Laura Perrot
- Toulouse Biotechnology Institute, Université de ToulouseToulouseFrance
| | | | - Florian Veillet
- INRAE, Agrocampus OuestUniversité de Rennes, IGEPPPloudanielFrance
| | | | | | - Fabien Nogué
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin (IJPB)VersaillesFrance
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13
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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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14
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Adeyinka OS, Tabassum B, Koloko BL, Ogungbe IV. Enhancing the quality of staple food crops through CRISPR/Cas-mediated site-directed mutagenesis. PLANTA 2023; 257:78. [PMID: 36913066 DOI: 10.1007/s00425-023-04110-6] [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: 11/20/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
The enhancement of CRISPR-Cas gene editing with robust nuclease activity promotes genetic modification of desirable agronomic traits, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits in crops. The genetic diversity of food crops has reduced tremendously over the past twelve millennia due to plant domestication. This reduction presents significant challenges for the future especially considering the risks posed by global climate change to food production. While crops with improved phenotypes have been generated through crossbreeding, mutation breeding, and transgenic breeding over the years, improving phenotypic traits through precise genetic diversification has been challenging. The challenges are broadly associated with the randomness of genetic recombination and conventional mutagenesis. This review highlights how emerging gene-editing technologies reduce the burden and time necessary for developing desired traits in plants. Our focus is to provide readers with an overview of the advances in CRISPR-Cas-based genome editing for crop improvement. The use of CRISPR-Cas systems in generating genetic diversity to enhance the quality and nutritional value of staple food crops is discussed. We also outlined recent applications of CRISPR-Cas in developing pest-resistant crops and removing unwanted traits, such as allergenicity from crops. Genome editing tools continue to evolve and present unprecedented opportunities to enhance crop germplasm via precise mutations at the desired loci of the plant genome.
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Affiliation(s)
- Olawale Samuel Adeyinka
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA.
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | | | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences Jackson State University, Jackson, MS, 39217, USA
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15
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Robertson G, Burger J, Campa M. CRISPR/Cas-based tools for the targeted control of plant viruses. MOLECULAR PLANT PATHOLOGY 2022; 23:1701-1718. [PMID: 35920132 PMCID: PMC9562834 DOI: 10.1111/mpp.13252] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/09/2022] [Accepted: 07/01/2022] [Indexed: 05/15/2023]
Abstract
Plant viruses are known to infect most economically important crops and pose a major threat to global food security. Currently, few resistant host phenotypes have been delineated, and while chemicals are used for crop protection against insect pests and bacterial or fungal diseases, these are inefficient against viral diseases. Genetic engineering emerged as a way of modifying the plant genome by introducing functional genes in plants to improve crop productivity under adverse environmental conditions. Recently, new breeding technologies, and in particular the exciting CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins) technology, was shown to be a powerful alternative to engineer resistance against plant viruses, thus has great potential for reducing crop losses and improving plant productivity to directly contribute to food security. Indeed, it could circumvent the "Genetic modification" issues because it allows for genome editing without the integration of foreign DNA or RNA into the genome of the host plant, and it is simpler and more versatile than other new breeding technologies. In this review, we describe the predominant features of the major CRISPR/Cas systems and outline strategies for the delivery of CRISPR/Cas reagents to plant cells. We also provide an overview of recent advances that have engineered CRISPR/Cas-based resistance against DNA and RNA viruses in plants through the targeted manipulation of either the viral genome or susceptibility factors of the host plant genome. Finally, we provide insight into the limitations and challenges that CRISPR/Cas technology currently faces and discuss a few alternative applications of the technology in virus research.
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Affiliation(s)
- Gaëlle Robertson
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
- Department of Experimental and Health SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Johan Burger
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
| | - Manuela Campa
- Department of GeneticsStellenbosch UniversityMatielandSouth Africa
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16
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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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17
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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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18
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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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19
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Lucioli A, Tavazza R, Baima S, Fatyol K, Burgyan J, Tavazza M. CRISPR-Cas9 Targeting of the eIF4E1 Gene Extends the Potato Virus Y Resistance Spectrum of the Solanum tuberosum L. cv. Desirée. Front Microbiol 2022; 13:873930. [PMID: 35722301 PMCID: PMC9198583 DOI: 10.3389/fmicb.2022.873930] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Abstract
Translation initiation factors and, in particular, the eIF4E family are the primary source of recessive resistance to potyviruses in many plant species. However, no eIF4E-mediated resistance to this virus genus has been identified in potato (Solanum tuberosum L.) germplasm. As in tomato, the potato eIF4E gene family consists of eIF4E1, its paralog eIF4E2, eIF(iso)4E, and nCBP. In tomato, eIF4E1 knockout (KO) confers resistance to a subset of potyviruses, while the eIF4E1/2 double KO, although conferring a broader spectrum of resistance, leads to plant developmental defects. Here, the tetraploid potato cv. Desirée owning the dominant Ny gene conferring resistance to potato virus Y (PVY) strain O but not NTN was used to evaluate the possibility to expand its PVY resistance spectrum by CRISPR-Cas9-mediated KO of the eIF4E1 susceptibility gene. After a double process of plant protoplast transfection-regeneration, eIF4E1 KO potatoes were obtained. The knockout was specific for the eIF4E1, and no mutations were identified in its eIF4E2 paralog. Expression analysis of the eIF4E family shows that the disruption of the eIF4E1 does not alter the RNA steady-state level of the other family members. The eIF4E1 KO lines challenged with a PVYNTN isolate showed a reduced viral accumulation and amelioration of virus-induced symptoms suggesting that the eIF4E1 gene was required but not essential for its multiplication. Our data show that eIF4E1 editing can be usefully exploited to broaden the PVY resistance spectrum of elite potato cultivars, such as Desirée, by pyramiding eIF4E-mediated recessive resistance.
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Affiliation(s)
- Alessandra Lucioli
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Raffaela Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Simona Baima
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome, Italy
| | - Karoly Fatyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Jozsef Burgyan
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Mario Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
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20
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Barka GD, Lee J. Advances in S gene targeted genome-editing and its applicability to disease resistance breeding in selected Solanaceae crop plants. Bioengineered 2022; 13:14646-14666. [PMID: 35891620 PMCID: PMC9342254 DOI: 10.1080/21655979.2022.2099599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Genome-editing tools for the development of traits to tolerate abiotic and biotic adversaries are the recently devised breeding techniques revolutionizing molecular breeding by addressing the issues of rapidness and precision. To that end, disease resistance development by disrupting disease susceptibility genes (S genes) to intervene in the biological mechanism of pathogenicity has significantly improved the techniques of molecular breeding. Despite the achievements in genome-editing aimed at the intervention of the function of susceptibility determinants or gene regulatory elements, off-target effects associated with yield-related traits are still the main setbacks. The challenges are attributed to the complexity of the inheritance of traits controlled by pleiotropic genes. Therefore, a more rigorous genome-editing tool with ultra-precision and efficiency for the development of broad-spectrum and durable disease resistance applied to staple crop plants is of critical importance in molecular breeding programs. The main objective of this article is to review the most impressive progresses achieved in resistance breeding against the main diseases of three Solanaceae crops (potato, Solanum tuberosum; tomato, Solanum lycopersicum and pepper, Capsicum annuum) using genome-editing by disrupting the sequences of S genes, their promoters, or pathogen genes. In this paper, we discussed the complexity and applicability of genome-editing tools, summarized the main disease of Solanaceae crops, and compiled the recent reports on disease resistance developed by S-gene silencing and their off-target effects. Moreover, GO count and gene annotation were made for pooled S-genes from biological databases. Achievements and prospects of S-gene-based next-generation breeding technologies are also discussed. Most S genes are membrane –anchored and are involved in infection and pre-penetration process S gene-editing is less likely to cause an off-target effect Gene-editing has been considered a more acceptable engineering tool Editing S genes either from the pathogen or host ends has opened new possibilities
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Affiliation(s)
- Geleta Dugassa Barka
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju, South Korea.,Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju, South Korea
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21
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Kuroiwa K, Thenault C, Nogué F, Perrot L, Mazier M, Gallois JL. CRISPR-based knock-out of eIF4E2 in a cherry tomato background successfully recapitulates resistance to pepper veinal mottle virus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111160. [PMID: 35151441 DOI: 10.1016/j.plantsci.2021.111160] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/22/2021] [Accepted: 12/17/2021] [Indexed: 05/15/2023]
Abstract
The host susceptibility factors are important targets to develop genetic resistances in crops. Genome editing tools offer exciting prospects to develop resistances based on these susceptibility factors, directly in the cultivar of choice. Translation initiation factors 4E have long been known to be a susceptibility factor to the main genus of Potyviridae, potyviruses, but the inactivation of the eIF4E2 gene has only recently been shown to provide resistance to some isolates of pepper veinal mottle virus (PVMV) in big-fruit tomato plants. Here, using CRISPR-Cas9-NG, we show how eIF4E2 can be targeted and inactivated in cherry tomato plants. Three independent knockout alleles caused by indel in the first exon of eIF4E2, resulted in the complete absence of the eIF4E2 protein. All three lines displayed a narrow resistance spectrum to potyvirus, similar to the one described earlier for an eIF4E2 EMS mutant of M82, a big-fruit tomato cultivar; the plants were fully resistant to PVMV-Ca31, partially to PVMV-IC and were fully susceptible to two isolates of PVY assayed: N605 and LYE84. These results show how easily a resistance based on eIF4E2 can be transferred across tomato cultivar, but also confirm that gene redundancy can narrow the resistances based on eIF4E knockout.
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Affiliation(s)
| | | | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Laura Perrot
- Toulouse Biotechnology Institute, Université de Toulouse, 135 avenue de Rangueil, 31077 Toulouse CEDEX 04, France
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22
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González Guzmán M, Cellini F, Fotopoulos V, Balestrini R, Arbona V. New approaches to improve crop tolerance to biotic and abiotic stresses. PHYSIOLOGIA PLANTARUM 2022; 174:e13547. [PMID: 34480798 PMCID: PMC9290814 DOI: 10.1111/ppl.13547] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 05/24/2023]
Abstract
During the last years, a great effort has been dedicated at the development and employment of diverse approaches for achieving more stress-tolerant and climate-flexible crops and sustainable yield increases to meet the food and energy demands of the future. The ongoing climate change is in fact leading to more frequent extreme events with a negative impact on food production, such as increased temperatures, drought, and soil salinization as well as invasive arthropod pests and diseases. In this review, diverse "green strategies" (e.g., chemical priming, root-associated microorganisms), and advanced technologies (e.g., genome editing, high-throughput phenotyping) are described on the basis of the most recent research evidence. Particularly, attention has been focused on the potential use in a context of sustainable and climate-smart agriculture (the so called "next agriculture generation") to improve plant tolerance and resilience to abiotic and biotic stresses. In addition, the gap between the results obtained in controlled experiments and those from application of these technologies in real field conditions (lab to field step) is also discussed.
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Affiliation(s)
- Miguel González Guzmán
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
| | - Francesco Cellini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA)MetapontoItaly
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vasileios Fotopoulos
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Department of Agricultural Sciences, Biotechnology & Food ScienceCyprus University of TechnologyLemesosCyprus
| | - Raffaella Balestrini
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante (CNR, IPSP)TorinoItaly
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi NaturalUniversitat Jaume ICastelló de la PlanaSpain
- The OPTIMUS PRIME consortium, European Union Partnership for Research and Innovation in the Mediterranean Area (PRIMA) Program
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Joo KA, Muszynski MG, Kantar MB, Wang ML, He X, Del Valle Echevarria AR. Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species. Front Genet 2021; 12:786140. [PMID: 34868276 PMCID: PMC8633396 DOI: 10.3389/fgene.2021.786140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.
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Affiliation(s)
- Kathleen A Joo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael G Muszynski
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Xiaoling He
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Angel R Del Valle Echevarria
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.,Hawaii Agriculture Research Center, Waipahu, HI, United States
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24
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Mushtaq M, Dar AA, Basu U, Bhat BA, Mir RA, Vats S, Dar MS, Tyagi A, Ali S, Bansal M, Rai GK, Wani SH. Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology. Front Genet 2021; 12:735489. [PMID: 34759957 PMCID: PMC8572880 DOI: 10.3389/fgene.2021.735489] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/16/2021] [Indexed: 12/26/2022] Open
Abstract
Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.
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Affiliation(s)
- Muntazir Mushtaq
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | | | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Sanskriti Vats
- Department of Agricultural Biotechnology, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - M. S. Dar
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Anshika Tyagi
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Monika Bansal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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25
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Zhu H, Deng M, Yang Z, Mao L, Jiang S, Yue Y, Zhao K. Two Tomato (S olanum lycopersicum) Thaumatin-Like Protein Genes Confer Enhanced Resistance to Late Blight ( Phytophthora infestans). PHYTOPATHOLOGY 2021; 111:1790-1799. [PMID: 33616418 DOI: 10.1094/phyto-06-20-0237-r] [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: 06/12/2023]
Abstract
Late blight (caused by Phytophthora infestans) poses a serious threat to tomato production but the number of late blight resistance genes isolated from tomato is limited, making resistance gene mining a high research priority. In this study, highly resistant CLN2037E and susceptible No. 5 tomato inbred lines were used to identify late blight resistance genes. Using transcriptome sequencing, we discovered 36 differentially expressed genes (DEGs), including 21 nucleotide binding site-leucine-rich repeat and 15 pathogenesis-related (PR) disease resistance genes. Cluster analysis and real-time quantitative PCR showed that these 36 genes possessed similar expression patterns in different inbred lines after inoculation with P. infestans. Moreover, two PR genes with unique responses were chosen to verify their functions when exposed to P. infestans: Solyc08g080660 and Solyc08g080670, both of which were thaumatin-like protein genes and were clustered in the tomato genome. Functions of these two genes were identified by gene overexpression and gene editing technology. Overexpression and knockout of single Solyc08g080660 and Solyc08g080670 corresponded to an increase and decrease in resistance to late blight, respectively, and Solyc08g080660 led to a greater change in disease resistance compared with Solyc08g080670. Cotransformation of dual genes resulted in a much greater effect than any single gene. This study provides novel candidate resistance genes for tomato breeding against late blight and insights into the interaction mechanisms between tomato and P. infestans.
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Affiliation(s)
- Haishan Zhu
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Minghua Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Zhengan Yang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Lianzhen Mao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Shurui Jiang
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Yanling Yue
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
| | - Kai Zhao
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming 650201, China
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26
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Pepper Mottle Virus and Its Host Interactions: Current State of Knowledge. Viruses 2021; 13:v13101930. [PMID: 34696360 PMCID: PMC8539092 DOI: 10.3390/v13101930] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
Pepper mottle virus (PepMoV) is a destructive pathogen that infects various solanaceous plants, including pepper, bell pepper, potato, and tomato. In this review, we summarize what is known about the molecular characteristics of PepMoV and its interactions with host plants. Comparisons of symptom variations caused by PepMoV isolates in plant hosts indicates a possible relationship between symptom development and genetic variation. Researchers have investigated the PepMoV–plant pathosystem to identify effective and durable genes that confer resistance to the pathogen. As a result, several recessive pvr or dominant Pvr resistance genes that confer resistance to PepMoV in pepper have been characterized. On the other hand, the molecular mechanisms underlying the interaction between these resistance genes and PepMoV-encoded genes remain largely unknown. Our understanding of the molecular interactions between PepMoV and host plants should be increased by reverse genetic approaches and comprehensive transcriptomic analyses of both the virus and the host genes.
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Xia X, Cheng X, Li R, Yao J, Li Z, Cheng Y. Advances in application of genome editing in tomato and recent development of genome editing technology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2727-2747. [PMID: 34076729 PMCID: PMC8170064 DOI: 10.1007/s00122-021-03874-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/25/2021] [Indexed: 05/07/2023]
Abstract
Genome editing, a revolutionary technology in molecular biology and represented by the CRISPR/Cas9 system, has become widely used in plants for characterizing gene function and crop improvement. Tomato, serving as an excellent model plant for fruit biology research and making a substantial nutritional contribution to the human diet, is one of the most important applied plants for genome editing. Using CRISPR/Cas9-mediated targeted mutagenesis, the re-evaluation of tomato genes essential for fruit ripening highlights that several aspects of fruit ripening should be reconsidered. Genome editing has also been applied in tomato breeding for improving fruit yield and quality, increasing stress resistance, accelerating the domestication of wild tomato, and recently customizing tomato cultivars for urban agriculture. In addition, genome editing is continuously innovating, and several new genome editing systems such as the recent prime editing, a breakthrough in precise genome editing, have recently been applied in plants. In this review, these advances in application of genome editing in tomato and recent development of genome editing technology are summarized, and their leaving important enlightenment to plant research and precision plant breeding is also discussed.
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Affiliation(s)
- Xuehan Xia
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xinhua Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Rui Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Juanni Yao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yulin Cheng
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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28
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Changes in Subcellular Localization of Host Proteins Induced by Plant Viruses. Viruses 2021; 13:v13040677. [PMID: 33920930 PMCID: PMC8071230 DOI: 10.3390/v13040677] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 12/24/2022] Open
Abstract
Viruses are dependent on host factors at all parts of the infection cycle, such as translation, genome replication, encapsidation, and cell-to-cell and systemic movement. RNA viruses replicate their genome in compartments associated with the endoplasmic reticulum, chloroplasts, and mitochondria or peroxisome membranes. In contrast, DNA viruses replicate in the nucleus. Viral infection causes changes in plant gene expression and in the subcellular localization of some host proteins. These changes may support or inhibit virus accumulation and spread. Here, we review host proteins that change their subcellular localization in the presence of a plant virus. The most frequent change is the movement of host cytoplasmic proteins into the sites of virus replication through interactions with viral proteins, and the protein contributes to essential viral processes. In contrast, only a small number of studies document changes in the subcellular localization of proteins with antiviral activity. Understanding the changes in the subcellular localization of host proteins during plant virus infection provides novel insights into the mechanisms of plant–virus interactions and may help the identification of targets for designing genetic resistance to plant viruses.
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29
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Selective Interaction of Sugarcane eIF4E with VPgs from Sugarcane Mosaic Pathogens. Viruses 2021; 13:v13030518. [PMID: 33809985 PMCID: PMC8005120 DOI: 10.3390/v13030518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) plays a key role in the infection of potyviruses in susceptible plants by interacting with viral genome-linked protein (VPg). Sugarcane (Saccharum spp.) production is threatened by mosaic disease caused by Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and Sugarcane streak mosaic virus (SCSMV). In this study, two eIF4Es and their isoform eIF(iso)4E and 4E-binding protein coding genes were cloned from sugarcane cultivar ROC22 and designated SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP, respectively. Real-time quantitative PCR analysis showed different expression profiles of these four genes upon SCMV challenge. A subcellular localization assay showed that SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP were distributed in the nucleus and cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that SceIF4Ea/b and SceIF(iso)4E were selectively employed by different sugarcane mosaic pathogens, i.e., SCMV-VPg interacted with SceIF4Ea/b and SceIF(iso)4E, SrMV-VPg interacted with both SceIF4Eb and SceIF(iso)4E, and SCSMV-VPg interacted only with SceIF(iso)4E. Intriguingly, the BiFC assays, but not the Y2H assays, showed that ScnCBP interacted with the VPgs of SCMV, SrMV, and SCSMV. Competitive interaction assays showed that SCMV-VPg, SrMV-VPg, and SCMV-VPg did not compete with each other to interact with SceIF(iso)4E, and SceIF(iso)4E competed with SceIF4Eb to interact with SrMV-VPg but not SCMV-VPg. This study sheds light on the molecular mechanism of sugarcane mosaic pathogen infection of sugarcane plants and benefits sugarcane breeding against the sugarcane mosaic disease.
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