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Zarrabian M, Sherif SM. Silence is not always golden: A closer look at potential environmental and ecotoxicological impacts of large-scale dsRNA application. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175311. [PMID: 39122031 DOI: 10.1016/j.scitotenv.2024.175311] [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: 06/05/2024] [Revised: 08/02/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
RNA interference (RNAi) technology has emerged as a pivotal strategy in sustainable pest management, offering a targeted approach that significantly mitigates the environmental and health risks associated with traditional insecticides. Originally implemented through genetically modified organisms (GMOs) to produce specific RNAi constructs, the technology has evolved in response to public and regulatory concerns over GMOs. This evolution has spurred the development of non-transgenic RNAi applications such as spray-induced gene silencing (SIGS), which employs double-stranded RNA (dsRNA) to silence pest genes directly without altering the plant's genetic makeup. Despite its advantages in specificity and reduced ecological footprint, SIGS faces significant obstacles, particularly the instability of dsRNA in field conditions, which limits its practical efficacy. To overcome these limitations, innovative delivery mechanisms have been developed. These include nanotechnology-based systems, minicells, and nanovesicles, which are designed to protect dsRNA from degradation and enhance its delivery to target organisms. While these advancements have improved the stability and application efficiency of dsRNA, comprehensive assessments of their environmental safety and the potential for increased exposure risks to non-target organisms remain incomplete. This comprehensive review aims to elucidate the environmental fate of dsRNA and evaluate the potential risks associated with its widespread application on non-target organisms, encompassing soil microorganisms, beneficial insects, host plants, and mammals. The objective is to establish a more refined framework for RNAi risk assessment within environmental and ecotoxicological contexts, thereby fostering the development of safer, non-transgenic RNAi-based pest control strategies.
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Affiliation(s)
- Mohammad Zarrabian
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States
| | - Sherif M Sherif
- Virginia Tech, School of Plant and Environmental Sciences, Alson H. Smith Jr. Agricultural Research, and Extension Center, Winchester, VA 22602, United States.
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2
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Ali A, Shahbaz M, Ölmez F, Fatima N, Umar UUD, Ali MA, Akram M, Seelan JSS, Baloch FS. RNA interference: a promising biotechnological approach to combat plant pathogens, mechanism and future prospects. World J Microbiol Biotechnol 2024; 40:339. [PMID: 39358476 DOI: 10.1007/s11274-024-04143-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/13/2024] [Indexed: 10/04/2024]
Abstract
Plant pathogens and other biological pests represent significant obstacles to crop Protection worldwide. Even though there are many effective conventional methods for controlling plant diseases, new methods that are also effective, environmentally safe, and cost-effective are required. While plant breeding has traditionally been used to manipulate the plant genome to develop resistant cultivars for controlling plant diseases, the emergence of genetic engineering has introduced a completely new approach to render plants resistant to bacteria, nematodes, fungi, and viruses. The RNA interference (RNAi) approach has recently emerged as a potentially useful tool for mitigating the inherent risks associated with the development of conventional transgenics. These risks include the use of specific transgenes, gene control sequences, or marker genes. Utilizing RNAi to silence certain genes is a promising solution to this dilemma as disease-resistant transgenic plants can be generated within a legislative structure. Recent investigations have shown that using target double stranded RNAs via an effective vector system can produce significant silencing effects. Both dsRNA-containing crop sprays and transgenic plants carrying RNAi vectors have proven effective in controlling plant diseases that threaten commercially significant crop species. This article discusses the methods and applications of the most recent RNAi technology for reducing plant diseases to ensure sustainable agricultural yields.
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Affiliation(s)
- Amjad Ali
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Muhammad Shahbaz
- Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, Jalan UMS, 88400, Kota kinabalu, Malaysia
| | - Fatih Ölmez
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Turkey
| | - Noor Fatima
- Department of Botany, Lahore College for Women University, 54000, Lahore, Punjab, Pakistan
| | - Ummad Ud Din Umar
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Main Campus, Bosan Road, 60800, Multan, Pakistan
| | - Md Arshad Ali
- Biotechnology Program, Faculty of Science and Natural, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Muhammad Akram
- Department of Botany, The Islamia University of Bahawalpur, 63100, Bahawalpur, Punjab, Pakistan
| | - Jaya Seelan Sathiya Seelan
- Institute for Tropical Biology and Conservation (ITBC), Universiti Malaysia Sabah, Jalan UMS, 88400, Kota kinabalu, Malaysia.
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33343, Yenişehir Mersin, Turkey.
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Liu Y, Liu J, Sun M, Mao Y, Feng S, Shen S, Liu T, Cao Z, Li Z, Hao Z, Dong J. The genome sequencing and comparative genomics analysis of Rhizoctonia solani reveals a novel effector family owning a uinque domain in Basidiomycetes. Int J Biol Macromol 2024; 278:134328. [PMID: 39098663 DOI: 10.1016/j.ijbiomac.2024.134328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Rhizoctonia solani is a soil-borne pathogen with 14 anastomosis groups (AGs), and different subgroups are genetically diverse. However, the genetic factors contributing to the pathogenicity of the fungus have not been well characterized. In this study, the genome of R. solani AG1-ZJ was sequenced. As the result, a 41.57 Mb draft genome containing 12,197 putative coding genes was obtained. Comparative genomic analysis of 11 different AGs revealed conservation and unique characteristics between the AGs. Furthermore, a novel effector family containing a 68 amino acid conserved domain unique in basidiomycetous fungi was characterized. Two effectors containing the conserved domain in AG4-JY were identified, and named as RsUEB1 and RsUEB2. Furthermore, the spray-induced gene silencing strategy was used to generate a dsRNA capable of silencing the conserved domain sequence of RsUEB1 and RsUEB2. This dsRNA can significantly reduce the expression of RsUEB1 and RsUEB2 and the pathogenicity of AG4-JY on foxtail millet, maize, rice and wheat. In conclusion, this study provides significant insights into the pathogenicity mechanisms of R. solani. The identification of the conserved domain and the successful use of dsRNA silencing of the gene containing the conserved domain will offer a new strategy for controlling sheath blight in cereal crops.
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Affiliation(s)
- Yuwei Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Jiayue Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Mingqing Sun
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Yanan Mao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shang Feng
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Shen Shen
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China
| | - Tingting Liu
- Shijiazhuang Agricultural Technology Extension Center, Shijiazhuang, 050051, China
| | - Zhiyan Cao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhiyong Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Genetic Improvement and Utilization for Featured Coarse Cereals (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs/Key Laboratory of Minor Cereal Crops of Hebei Province, Shijiazhuang, Hebei, 050035, China.
| | - Zhimin Hao
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China.
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Hebei Bioinformatic Utilization and Technological Innovation Center for Agricultural Microbes, Hebei Agricultural University, Hebei 071001, China; College of Plant Protection/Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei 071001, China.
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Liu C, Kogel K, Ladera‐Carmona M. Harnessing RNA interference for the control of Fusarium species: A critical review. MOLECULAR PLANT PATHOLOGY 2024; 25:e70011. [PMID: 39363756 PMCID: PMC11450251 DOI: 10.1111/mpp.70011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/13/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024]
Abstract
Fusarium fungi are a pervasive threat to global agricultural productivity. They cause a spectrum of plant diseases that result in significant yield losses and threaten food safety by producing mycotoxins that are harmful to human and animal health. In recent years, the exploitation of the RNA interference (RNAi) mechanism has emerged as a promising avenue for the control of Fusarium-induced diseases, providing both a mechanistic understanding of Fusarium gene function and a potential strategy for environmentally sustainable disease management. However, despite significant progress in elucidating the presence and function of the RNAi pathway in different Fusarium species, a comprehensive understanding of its individual protein components and underlying silencing mechanisms remains elusive. Accordingly, while a considerable number of RNAi-based approaches to Fusarium control have been developed and many reports of RNAi applications in Fusarium control under laboratory conditions have been published, the applicability of this knowledge in agronomic settings remains an open question, and few convincing data on RNAi-based disease control under field conditions have been published. This review aims to consolidate the current knowledge on the role of RNAi in Fusarium disease control by evaluating current research and highlighting important avenues for future investigation.
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Affiliation(s)
- Caihong Liu
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Karl‐Heinz Kogel
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
- Institut de Biologie Moléculaire des Plantes, CNRSUniversité de StrasbourgStrasbourgFrance
| | - Maria Ladera‐Carmona
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig University GiessenGiessenGermany
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LeBoldus JM, Lynch SC, Newhouse AE, Søndreli KL, Newcombe G, Bennett PI, Muchero W, Chen JG, Busby PE, Gordon M, Liang H. Biotechnology and Genomic Approaches to Mitigating Disease Impacts on Forest Health. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:309-335. [PMID: 39251210 DOI: 10.1146/annurev-phyto-021622-114434] [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: 09/11/2024]
Abstract
Outbreaks of insects and diseases are part of the natural disturbance regime of all forests. However, introduced pathogens have had outsized impacts on many dominant forest tree species over the past century. Mitigating these impacts and restoring these species are dilemmas of the modern era. Here, we review the ecological and economic impact of introduced pathogens, focusing on examples in North America. We then synthesize the successes and challenges of past biotechnological approaches and discuss the integration of genomics and biotechnology to help mitigate the effects of past and future pathogen invasions. These questions are considered in the context of the transgenic American chestnut, which is the most comprehensive example to date of how biotechnological tools have been used to address the impacts of introduced pathogens on naïve forest ecosystems.
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Affiliation(s)
- Jared M LeBoldus
- Department of Botany and Plant Pathology and Department of Forest Engineering, Resources, and Management, Oregon State University, Corvallis, Oregon, USA;
| | - Shannon C Lynch
- Faculty of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Andrew E Newhouse
- Faculty of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Kelsey L Søndreli
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - George Newcombe
- Department of Forest, Rangeland and Fire Sciences, University of Idaho, Moscow, Idaho, USA
| | - Patrick I Bennett
- Rocky Mountain Research Station, United States Forest Service, Moscow, Idaho, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michael Gordon
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, USA
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, USA
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6
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Balassa K, Balassa G, Almási A, Visnovitz T, Rudnóy S. Detection of exogenous siRNA inside sweet corn bundle sheath cells and the RNAi dynamics in the early stage of Maize dwarf mosaic virus infection. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1265-1276. [PMID: 39184556 PMCID: PMC11341793 DOI: 10.1007/s12298-024-01500-2] [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: 05/29/2024] [Revised: 07/10/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
Maize dwarf mosaic virus (MDMV) is one of the most serious viruses of sweet corn. Utilising the process of RNA interference, the exogenous introduction of small RNA molecules mimicking virus-derived small interfering RNA (siRNA) into the plant prior to infection triggers the antiviral RNA silencing effect, thereby promoting more effective antiviral protection. Hence, a treatment with MDMV-derived small RNA was applied to sweet corn plants one day before MDMV virus inoculation. ALEXA FLUOR®488 fluorophore-bound exogenous siRNA was successfully detected inside intact sweet corn cells using confocal fluorescence microscopy. Furthermore, it was demonstrated that the exogenous siRNA treatment led to a notable upregulation of the AGO1, AGO2b, AGO10b, AGO18a, DCL1, DCL3a, DCL4, RDR1, and MOP1 genes within 24 h of the treatment. Overall, exogenous siRNA treatment resulted in better virus control of infected sweet corn plants, as indicated by the lower viral RNA and coat protein levels compared to the infected group without pre-treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01500-2.
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Affiliation(s)
- Kinga Balassa
- Doctoral School of Biology, Institute of Biology, Eötvös Loránd University, Budapest, 1117 Hungary
- Department of Plant Physiology and Molecular Plant Biology, Faculty of Science, Eötvös Loránd University, Budapest, 1117 Hungary
| | - György Balassa
- Doctoral School of Biology, Institute of Biology, Eötvös Loránd University, Budapest, 1117 Hungary
- Department of Plant Physiology and Molecular Plant Biology, Faculty of Science, Eötvös Loránd University, Budapest, 1117 Hungary
| | - Asztéria Almási
- Department of Plant Pathology, Plant Protection Institute, HUN-REN Centre for Agricultural Research, Budapest, 1022 Hungary
| | - Tamás Visnovitz
- Department of Plant Physiology and Molecular Plant Biology, Faculty of Science, Eötvös Loránd University, Budapest, 1117 Hungary
- Institute of Genetics, Cell and Immunobiology, Semmelweis University, Budapest, 1085 Hungary
| | - Szabolcs Rudnóy
- Department of Plant Physiology and Molecular Plant Biology, Faculty of Science, Eötvös Loránd University, Budapest, 1117 Hungary
- Eurofins BIOMI Ltd, Gödöllő, 2100 Hungary
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Webb RJ, Roberts AA, Rush C, Skerratt LF, Tizard ML, Berger L. Small Interfering RNA Mediated Messenger RNA Knockdown in the Amphibian Pathogen Batrachochytrium dendrobatidis. J Basic Microbiol 2024; 64:e2400081. [PMID: 39031701 DOI: 10.1002/jobm.202400081] [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: 02/14/2024] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 07/22/2024]
Abstract
RNA interference (RNAi) has not been tested in the pandemic amphibian pathogen, Batrachochytrium dendrobatidis, but developing this technology could be useful to elucidate virulence mechanisms, identify therapeutic targets, and may present a novel antifungal treatment option for chytridiomycosis. To manipulate and decipher gene function, rationally designed small interfering RNA (siRNA) can initiate the destruction of homologous messenger RNA (mRNA), resulting in the "knockdown" of target gene expression. Here, we investigate whether siRNA can be used to manipulate gene expression in B. dendrobatidis via RNAi using differing siRNA strategies to target genes involved in glutathione and ornithine synthesis. To determine the extent and duration of mRNA knockdown, target mRNA levels were monitored for 24-48 h after delivery of siRNA targeting glutamate-cysteine ligase, with a maximum of ~56% reduction in target transcripts occurring at 36 h. A second siRNA design targeting glutamate-cysteine ligase also resulted in ~53% knockdown at this time point. siRNA directed toward a different gene target, ornithine decarboxylase, achieved 17% reduction in target transcripts. Although no phenotypic effects were observed, these results suggest that RNAi is possible in B. dendrobatidis, and that gene expression can be manipulated in this pathogen. We outline ideas for further optimization steps to increase knockdown efficiency to better harness RNAi techniques for control of B. dendrobatidis.
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Affiliation(s)
- Rebecca J Webb
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Alexandra A Roberts
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Catherine Rush
- Australian Institute of Tropical Health and Medicine, James Cook Univiersity, Townsville, Queensland, Australia
| | - Lee F Skerratt
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
| | - Mark L Tizard
- Australian Centre for Disease Preparedness, CSIRO Health and Biosecurity, Geelong, Victoria, Australia
| | - Lee Berger
- One Health Research Group, Melbourne Veterinary School, University of Melbourne, Werribee, Victoria, Australia
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Capriotti L, Molesini B, Pandolfini T, Jin H, Baraldi E, Cecchin M, Mezzetti B, Sabbadini S. RNA interference-based strategies to control Botrytis cinerea infection in cultivated strawberry. PLANT CELL REPORTS 2024; 43:201. [PMID: 39048858 PMCID: PMC11269516 DOI: 10.1007/s00299-024-03288-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
KEY MESSAGE Gene silencing of BcDCL genes improves gray mold disease control in the cultivated strawberry. Gene silencing technology offers new opportunities to develop new formulations or new pathogen-resistant plants for reducing impacts of agricultural systems. Recent studies offered the proof of concept that the symptoms of gray mold can be reduced by downregulating Dicer-like 1 (DCL1) and 2 (DCL2) genes of Botrytis cinerea. In this study, we demonstrate that both solutions based on dsRNA topical treatment and in planta expression targeting BcDCL1 and BcDCL2 genes can be used to control the strawberry gray mold, the most harmful disease for different fruit crops. 50, 70 and 100 ng μL-1 of naked BcDCL1/2 dsRNA, sprayed on plants of Fragaria x ananassa cultivar Romina in the greenhouse, displayed significant reduction of susceptibility, compared to the negative controls, but to a lesser extent than the chemical fungicide. Three independent lines of Romina cultivar were confirmed for their stable expression of the hairpin gene construct that targets the Bc-DCL1 and 2 sequences (hp-Bc-DCL1/2), and for the production of hp construct-derived siRNAs, by qRT-PCR and Northern blot analyses. In vitro and in vivo detached leaves, and fruits from the hp-Bc-DCL1/2 lines showed significantly enhanced tolerance to this fungal pathogen compared to the control. This decreased susceptibility was correlated to the reduced fungal biomass and the downregulation of the Bc-DCL1 and 2 genes in B. cinerea. These results confirm the potential of both RNAi-based products and plants for protecting the cultivated strawberry from B. cinerea infection, reducing the impact of chemical pesticides on the environment and the health of consumers.
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Affiliation(s)
- Luca Capriotti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Barbara Molesini
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Tiziana Pandolfini
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Elena Baraldi
- Department of Agricultural and Food Science, DISTAL, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Michela Cecchin
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134, Verona, Italy
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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Spada M, Pugliesi C, Fambrini M, Pecchia S. Challenges and Opportunities Arising from Host- Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. Int J Mol Sci 2024; 25:6798. [PMID: 38928507 PMCID: PMC11203536 DOI: 10.3390/ijms25126798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The necrotrophic plant pathogenic fungus Botrytis cinerea (Pers., 1794), the causative agent of gray mold disease, causes significant losses in agricultural production. Control of this fungal pathogen is quite difficult due to its wide host range and environmental persistence. Currently, the management of the disease is still mainly based on chemicals, which can have harmful effects not only on the environment and on human health but also because they favor the development of strains resistant to fungicides. The flexibility and plasticity of B. cinerea in challenging plant defense mechanisms and its ability to evolve strategies to escape chemicals require the development of new control strategies for successful disease management. In this review, some aspects of the host-pathogen interactions from which novel and sustainable control strategies could be developed (e.g., signaling pathways, molecules involved in plant immune mechanisms, hormones, post-transcriptional gene silencing) were analyzed. New biotechnological tools based on the use of RNA interference (RNAi) are emerging in the crop protection scenario as versatile, sustainable, effective, and environmentally friendly alternatives to the use of chemicals. RNAi-based fungicides are expected to be approved soon, although they will face several challenges before reaching the market.
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Affiliation(s)
- Maria Spada
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Susanna Pecchia
- Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
- Interdepartmental Research Center Nutrafood “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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10
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Vatanparast M, Merkel L, Amari K. Exogenous Application of dsRNA in Plant Protection: Efficiency, Safety Concerns and Risk Assessment. Int J Mol Sci 2024; 25:6530. [PMID: 38928236 PMCID: PMC11204322 DOI: 10.3390/ijms25126530] [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: 05/17/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
The use of double-stranded RNA (dsRNA) for plant protection shows great potential as a sustainable alternative to traditional pesticides. This review summarizes the current state of knowledge on using exogenous dsRNA in plant protection and includes the latest findings on the safety and efficiency of this strategy. The review also emphasizes the need for a cautious and comprehensive approach, considering safety considerations such as off-target effects and formulation challenges. The regulatory landscape in different regions is also discussed, underscoring the need for specific guidelines tailored to dsRNA-based pesticides. The review provides a crucial resource for researchers, regulators, and industry stakeholders, promoting a balanced approach incorporating innovation with thorough safety assessments. The continuous dialog emphasized in this review is essential for shaping the future of dsRNA-based plant protection. As the field advances, collaboration among scientists, regulators, and industry partners will play a vital role in establishing guidelines and ensuring the responsible, effective, and sustainable use of dsRNA in agriculture.
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Affiliation(s)
| | | | - Khalid Amari
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plant, Institute for Biosafety in Plant Biotechnology, D-06484 Quedlinburg, Germany
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11
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Jain H, Kaur R, Sain SK, Siwach P. Development, Design, and Application of Efficient siRNAs Against Cotton Leaf Curl Virus-Betasatellite Complex to Mediate Resistance Against Cotton Leaf Curl Disease. Indian J Microbiol 2024; 64:558-571. [PMID: 39011016 PMCID: PMC11246389 DOI: 10.1007/s12088-024-01191-z] [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: 11/18/2023] [Accepted: 01/01/2024] [Indexed: 07/17/2024] Open
Abstract
Cotton leaf curl disease (CLCuD), caused by the Cotton leaf curl virus, is one of the most irrepressible diseases in cotton due to high recombination in the virus. RNA interference (RNAi) is widely used as a biotechnological approach for sequence-specific gene silencing guided by small interfering RNAs (siRNAs) to generate resistance against viruses. The success of RNAi depends upon the fact that the target site of the designed siRNA must be conserved even if the genome undergoes recombination. Thus, the present study designs the most efficient siRNA against the conserved sites of the Cotton leaf curl Multan virus (CLCuMuV) and the Cotton leaf curl Multan betasatellite (CLCuMB). From an initial prediction of 9 and 7 siRNAs against CLCuMuV and CLCuMB, respectively, the final selection was made for 2 and 1 siRNA based on parameters such as no off-targets, good GC content, high validity score, and targeting coding region. The target sites of siRNA were observed to lie in the AC3 and an overlapping region of AC2-AC1 of CLCuMuV and βC1 of CLCuMB; all target sites showed a highly conserved nature in recombination analysis. Docking the designed siRNAs with the Argonaute-2 protein of Gossypium hirsutum showed stable binding. Finally, BLASTn of siRNA-target positions in genomes of other BGVs indicated the suitability of designed siRNAs against a broad range of BGVs. The designed siRNAs of the present study could help gain complete control over the virus, though experimental validation is highly required to suggest predicted siRNAs for CLCuD resistance. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-024-01191-z.
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Affiliation(s)
- Heena Jain
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
| | - Ramandeep Kaur
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
| | - Satish Kumar Sain
- Central Institute of Cotton Research, Regional Station, Sirsa, Haryana 125055 India
| | - Priyanka Siwach
- Department of Biotechnology, Chaudhary Devi Lal University, Sirsa, Haryana 125055 India
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12
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Kallavus T, Kaasik R, Leemet T, Soots K, Soonvald L, Sulg S, Veromann E. Laboratory sprayer for dsRNA application: Design and bioassay validation. MethodsX 2024; 12:102734. [PMID: 38707218 PMCID: PMC11068844 DOI: 10.1016/j.mex.2024.102734] [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: 08/11/2023] [Accepted: 04/25/2024] [Indexed: 05/07/2024] Open
Abstract
The shortage of commercially available and reliable laboratory spraying equipment for testing different preparations can be a major obstacle to achieve field-comparable results in the laboratory conditions. RNA interference is natural biological process which, when used for plant protection, can be designed method combining sustainability and minimal environmental side effects. Spraying of dsRNA is a field-relevant method that should ensure consistency and repeatability if conducted in laboratory. We built a portable spray device for laboratory use and tested its suitability for dsRNA application. For that, we carried out bioassay on three plant species with different leaf surface textures. DsRNA were detected in all samples 3 days post-treatment indicating its suitability for dsRNA delivery. We built a portable spray device for laboratory use and tested its suitability for dsRNA application. For that, we carried out:•Bioassay on three plant species with different leaf surface textures. DsRNA were detected in all samples 3 days post-treatment indicating its suitability for dsRNA delivery.
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Affiliation(s)
- Triin Kallavus
- Chair of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent 9000, Belgium
| | - Riina Kaasik
- Chair of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Tõnu Leemet
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Kaarel Soots
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Liina Soonvald
- Chair of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Silva Sulg
- Chair of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
| | - Eve Veromann
- Chair of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu 51006, Estonia
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13
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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14
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Wang Y, Guo Y, Guo S, Qi L, Li B, Jiang L, Xu C, An M, Wu Y. RNA interference-based exogenous double-stranded RNAs confer resistance to Rhizoctonia solani AG-3 on Nicotiana tabacum. PEST MANAGEMENT SCIENCE 2024; 80:2170-2178. [PMID: 38284497 DOI: 10.1002/ps.7962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Rhizoctonia solani Kühn is a pathogenic fungus causing tobacco target spot disease, and leads to great losses worldwide. At present, resistant varieties and effective control strategy on tobacco target spot disease are very limited. Host-induced gene silencing (HIGS) as well as the exogenous dsRNA can be used to suppress disease progression, and reveal the function of crucial genes involved in the growth and pathogenesis of the fungus. RESULTS The silencing of endoPGs or RPMK1 in host plants by TRV-based HIGS resulted in a significant reduction in disease development in Nicotiana benthamiana. In vitro analysis validated that red fluorescence signals were consistently observed in the hyphae treated with Cy3-fluorescein-labeled dsRNA at 12, 24, 48 and 72 h postinoculation (hpi). Additionally, application of dsRNA-endoPGs, dsRNA-RPMK1 and dsRNA-PGMK (fusion of partial endoPGs and RPMK1 sequences) effectively inhibited the hyphal growth of R. solani YC-9 in vitro and suppressed disease progression in the leaves, and quantitative real-time PCR confirmed that the application of dsRNAs significantly reduced the expression levels of endoPGs and RPMK1. CONCLUSION These results provide theoretical basis and new direction for RNAi approaches on the prevention and control of disease caused by R. solani. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yan Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yi Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shiping Guo
- Sichuan Province Tobacco Company, Chengdu, China
| | - Lin Qi
- Sichuan Province Tobacco Company, Chengdu, China
| | - Bin Li
- Sichuan Province Tobacco Company, Chengdu, China
| | - Lianqiang Jiang
- Liangshanzhou Branch of Sichuan Province Tobacco Company, Xichang, China
| | - Chuantao Xu
- Luzhou Branch of Sichuan Province Tobacco Company, Luzhou, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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15
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Gyawali B, Rahimi R, Alizadeh H, Mohammadi M. Graphene Quantum Dots (GQD)-Mediated dsRNA Delivery for the Control of Fusarium Head Blight Disease in Wheat. ACS APPLIED BIO MATERIALS 2024; 7:1526-1535. [PMID: 38422985 DOI: 10.1021/acsabm.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Graphene quantum dots (GQDs), a class of fluorescent carbon materials, have displayed significant potential in various fields such as energy devices, catalysis, sensing, bioimaging, and drug delivery. Because of their extremely small size, generally less than 100 nm, they also have tremendous potential in plant science research, especially for the delivery of nucleic acids, breaking the barrier of cell walls. In this study, we synthesized GQDs with a size range of 2-5 nm, characterized them, and surface-functionalized them with branched polyethylenimine (bPEI). We then used the surface-functionalized GQDs as carriers to deliver double-stranded RNA (dsRNA) that target two growth-and-development-related genes in Fusarium graminearum─the causative organism of the Fusarium head blight disease of wheat. The successful binding of dsRNA to GQDs-bPEIs was demonstrated through gel-shifting assays, showcasing the potential for efficient dsRNA delivery. We designed dsRNAs targeting the MGV1 and RAS1 genes of F. graminearum by using the pssRNAit pipeline, ensuring high specificity and no off-target effects. The coding sequences of the designed dsRAS1 and dsMGV1 were cloned into the L4440 vector and transformed into the Escherichia coli HT115 strain for dsRNA production. Fungal culture analysis revealed that the inclusion of dsRNAs in potato dextrose agar (PDA) media effectively slowed down the growth. Exogenous spraying experiments both in plate cultures and in intact wheat spikes demonstrated that the dsRNA:GQDs-bPEIs treatment was more effective in restricting fungal mycelium growth or the number of infected spikelets compared to naked dsRNA treatment. Our study demonstrates the promising potential of graphene quantum dots as carriers for dsRNA-based fungal disease management in wheat and other crops.
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Affiliation(s)
- Binod Gyawali
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rahim Rahimi
- School of Materials Engineering, Purdue University, West Lafayette, Indiana 47907, United States
| | - Houshang Alizadeh
- Campus of Agriculture and Natural Resources, University of Tehran, Tehran 11366, Iran
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, United States
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16
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Ortolá B, Daròs JA. RNA Interference in Insects: From a Natural Mechanism of Gene Expression Regulation to a Biotechnological Crop Protection Promise. BIOLOGY 2024; 13:137. [PMID: 38534407 DOI: 10.3390/biology13030137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Insect pests rank among the major limiting factors in agricultural production worldwide. In addition to direct effect on crops, some phytophagous insects are efficient vectors for plant disease transmission. Large amounts of conventional insecticides are required to secure food production worldwide, with a high impact on the economy and environment, particularly when beneficial insects are also affected by chemicals that frequently lack the desired specificity. RNA interference (RNAi) is a natural mechanism gene expression regulation and protection against exogenous and endogenous genetic elements present in most eukaryotes, including insects. Molecules of double-stranded RNA (dsRNA) or highly structured RNA are the substrates of cellular enzymes to produce several types of small RNAs (sRNAs), which play a crucial role in targeting sequences for transcriptional or post-transcriptional gene silencing. The relatively simple rules that underlie RNAi regulation, mainly based in Watson-Crick complementarity, have facilitated biotechnological applications based on these cellular mechanisms. This includes the promise of using engineered dsRNA molecules, either endogenously produced in crop plants or exogenously synthesized and applied onto crops, as a new generation of highly specific, sustainable, and environmentally friendly insecticides. Fueled on this expectation, this article reviews current knowledge about the RNAi pathways in insects, and some other applied questions such as production and delivery of recombinant RNA, which are critical to establish RNAi as a reliable technology for insect control in crop plants.
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Affiliation(s)
- Beltrán Ortolá
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain
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17
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Kiselev KV, Suprun AR, Aleynova OA, Ogneva ZV, Dubrovina AS. Simultaneous Application of Several Exogenous dsRNAs for the Regulation of Anthocyanin Biosynthesis in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2024; 13:541. [PMID: 38498529 PMCID: PMC10893326 DOI: 10.3390/plants13040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Plant surface treatment with double-stranded RNAs (dsRNAs) has gained recognition as a promising method for inducing gene silencing and combating plant pathogens. However, the regulation of endogenous plant genes by external dsRNAs has not been sufficiently investigated. Also, the effect of the simultaneous application of multiple gene-specific dsRNAs has not been analyzed. The aim of this study was to exogenously target five genes in Arabidopsis thaliana, namely, three transcription factor genes (AtCPC, AtMybL2, AtANAC032), a calmodulin-binding protein gene (AtCBP60g), and an anthocyanidin reductase gene (AtBAN), which are known as negative regulators of anthocyanin accumulation. Exogenous dsRNAs encoding these genes were applied to the leaf surface of A. thaliana either individually or in mixtures. The mRNA levels of the five targets were analyzed using qRT-PCR, and anthocyanin content was evaluated through HPLC-MS. The results demonstrated significant downregulation of all five target genes by the exogenous dsRNAs, resulting in enhanced expression of chalcone synthase (AtCHS) gene and increased anthocyanin content. The simultaneous foliar application of the five dsRNAs proved to be more efficient in activating anthocyanin accumulation compared to the application of individual dsRNAs. These findings hold considerable importance in plant biotechnology and gene function studies.
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Affiliation(s)
- Konstantin V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Andrey R Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Olga A Aleynova
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Zlata V Ogneva
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Alexandra S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
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18
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Xi Y, Long X, Song M, Liu Y, Yan J, Lv Y, Yang H, Zhang Y, Miao W, Lin C. The fatty acid 2-hydroxylase CsSCS7 is a key hyphal growth factor and potential control target in Colletotrichum siamense. mBio 2024; 15:e0201523. [PMID: 38197633 PMCID: PMC10865788 DOI: 10.1128/mbio.02015-23] [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: 07/28/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
SCS7 is a fatty acid 2-hydroxylase required for the synthesis of inositol phosphorylceramide but is not essential for normal growth in Saccharomyces cerevisiae. Here, we demonstrate that the Colletotrichum siamense SCS7 homolog CsSCS7 plays a key role in hyphal growth. The CsSCS7 deletion mutant showed strong hyphal growth inhibition, small conidia, and marginally reduced sporulation and also resulted in a sharp reduction in the full virulence and increasing the fungicide sensitivity. The three protein domains (a cytochrome b5 domain, a transmembrane domain, and a hydroxylase domain) are important to CsSCS7 protein function in hyphal growth. The fatty acid assay results revealed that the CsSCS7 gene is important for balancing the contents of multiple mid-long- and short-chain fatty acids. Additionally, the retarded growth and virulence of C. siamense ΔCsSCS7 can be recovered partly by the reintroduction of homologous sequences from Magnaporthe oryzae and Fusarium graminearum but not SCS7 of S. cerevisiae. In addition, the spraying of C. siamense with naked CsSCS7-double-stranded RNA (dsRNAs), which leads to RNAi, increases the inhibition of hyphal growth and slightly decreases disease lesions. Then, we used nano material Mg-Al-layered double hydroxide as carriers to deliver dsRNA, which significantly enhanced the control effect of dsRNA, and the lesion area was obviously reduced. These data indicated that CsSCS7 is an important factor for hyphal growth and affects virulence and may be a potential control target in C. siamense and even in filamentous plant pathogenic fungi.IMPORTANCECsSCS7, which is homologous to yeast fatty acid 2-hydroxylase SCS7, was confirmed to play a key role in the hyphal growth of Colletotrichum siamense and affect its virulence. The CsSCS7 gene is involved in the synthesis and metabolism of fatty acids. Homologs from the filamentous fungi Magnaporthe oryzae and Fusarium graminearum can recover the retarded growth and virulence of C. siamense ΔCsSCS7. The spraying of double-stranded RNAs targeting CsSCS7 can inhibit hyphal growth and reduce the disease lesion area to some extent. After using nano material Mg-Al layered double hydroxide as carrier, the inhibition rates were significantly increased. We demonstrated that CsSCS7 is an important factor for hyphal growth and affects virulence and may be a potential control target in C. siamense and even in filamentous plant pathogenic fungi.
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Affiliation(s)
- Yitao Xi
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xiping Long
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Miao Song
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yu Liu
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Jingting Yan
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yanyun Lv
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Hong Yang
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, Haikou, China
| | - Yu Zhang
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Weiguo Miao
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chunhua Lin
- Sanya Institute of Breeding and Mutiplication, Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pest (Ministry of Education)/School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
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19
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Septiani P, Pramesti Y, Ningsih DU, Pancaningtyas S, Meitha K. Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease. Sci Rep 2024; 14:3272. [PMID: 38332251 PMCID: PMC10853554 DOI: 10.1038/s41598-024-53685-x] [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: 07/24/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defence genes. The objective of this study is to identify differentially expressed miRNAs in black pod-resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao's defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.
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Affiliation(s)
- Popi Septiani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Yonadita Pramesti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Devi Ulfa Ningsih
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Sulistyani Pancaningtyas
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jl. PB. Sudirman 90, Jember, 68118, Indonesia
| | - Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia.
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20
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Singh VK, Ahmed S, Saini DK, Gahlaut V, Chauhan S, Khandare K, Kumar A, Sharma PK, Kumar J. Manipulating epigenetic diversity in crop plants: Techniques, challenges and opportunities. Biochim Biophys Acta Gen Subj 2024; 1868:130544. [PMID: 38104668 DOI: 10.1016/j.bbagen.2023.130544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Epigenetic modifications act as conductors of inheritable alterations in gene expression, all while keeping the DNA sequence intact, thereby playing a pivotal role in shaping plant growth and development. This review article presents an overview of techniques employed to investigate and manipulate epigenetic diversity in crop plants, focusing on both naturally occurring and artificially induced epialleles. The significance of epigenetic modifications in facilitating adaptive responses is explored through the examination of how various biotic and abiotic stresses impact them. Further, environmental chemicals are explored for their role in inducing epigenetic changes, particularly focusing on inhibitors of DNA methylation like 5-AzaC and zebularine, as well as inhibitors of histone deacetylation including trichostatin A and sodium butyrate. The review delves into various approaches for generating epialleles, including tissue culture techniques, mutagenesis, and grafting, elucidating their potential to induce heritable epigenetic modifications in plants. In addition, the ground breaking CRISPR/Cas is emphasized for its accuracy in targeting specific epigenetic changes. This presents a potent tools for deciphering the intricacies of epigenetic mechanisms. Furthermore, the intricate relationship between epigenetic modifications and non-coding RNA expression, including siRNAs and miRNAs, is investigated. The emerging role of exo-RNAi in epigenetic regulation is also introduced, unveiling its promising potential for future applications. The article concludes by addressing the opportunities and challenges presented by these techniques, emphasizing their implications for crop improvement. Conclusively, this extensive review provides valuable insights into the intricate realm of epigenetic changes, illuminating their significance in phenotypic plasticity and their potential in advancing crop improvement.
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Affiliation(s)
| | - Shoeb Ahmed
- Ch. Charan Singh University, Meerut 250004, India
| | - Dinesh Kumar Saini
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Vijay Gahlaut
- University Centre for Research and Development, Chandigarh University, Mohali 140413, Punjab, India
| | | | - Kiran Khandare
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Ashutosh Kumar
- Center of Innovative and Applied Bioprocessing, Mohali 140308, Punjab, India
| | - Pradeep Kumar Sharma
- Ch. Charan Singh University, Meerut 250004, India; Maharaja Suhel Dev State University, Azamgarh 276404, U.P., India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali 140306, Punjab, India.
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Abbas H, Nahid N, Nawaz ul Rehman MS, Shaheen T, Liaquat S. Assessment of Resistance Induction in Mungbean against Alternaria alternata through RNA Interference. THE PLANT PATHOLOGY JOURNAL 2024; 40:59-72. [PMID: 38326959 PMCID: PMC10850528 DOI: 10.5423/ppj.oa.03.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/01/2024] [Accepted: 01/02/2024] [Indexed: 02/09/2024]
Abstract
A comprehensive survey of mungbean-growing areas was conducted to observe leaf spot disease caused by Alternaria alternata. Alternaria leaf spot symptoms were observed on the leaves. Diversity of 50 genotypes of mungbean was assessed against A. alternata and data on pathological traits was subjected to cluster analysis. The results showed that genotypes of mungbean were grouped into four clusters based on resistance parameters under the influence of disease. The principal component biplot demonstrated that all the disease-related parameters (% disease incidence, % disease intensity, lesion area, and % of infection) were strongly correlated with each other. Alt a 1 gene that is precisely found in Alternaria species and is responsible for virulence and pathogenicity. Alt a 1 gene was amplified using gene specific primers. The isolated pathogen produced similar symptoms when inoculated on mungbean and tobacco. The sequence analysis of the internal transcribed spacer (ITS) region, a 600 bp fragment amplified using specific primers, ITS1 and ITS2 showed 100% identity with A. alternata. Potato virus X (PVX) -based silencing vector expressing Alt a 1 gene was constructed to control this pathogen through RNA interference in tobacco. Out of 50 inoculated plants, 9 showed delayed onset of disease. Furthermore, to confirm our findings at molecular level semi-quantitative reverse transcriptase polymerase chain reaction was used. Both phenotypic and molecular investigation indicated that RNAi induced through the VIGS vector was efficacious in resisting the pathogen in the model host, Tobacco (Nicotiana tabacum). To the best of our knowledge, this study has been reported for the first time.
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Affiliation(s)
- Hira Abbas
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shah Nawaz ul Rehman
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Tayyaba Shaheen
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Sadia Liaquat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
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22
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Levanova AA, Poranen MM. Utilization of Bacteriophage phi6 for the Production of High-Quality Double-Stranded RNA Molecules. Viruses 2024; 16:166. [PMID: 38275976 PMCID: PMC10818839 DOI: 10.3390/v16010166] [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: 12/24/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Double-stranded RNA (dsRNA) molecules are mediators of RNA interference (RNAi) in eukaryotic cells. RNAi is a conserved mechanism of post-transcriptional silencing of genes cognate to the sequences of the applied dsRNA. RNAi-based therapeutics for the treatment of rare hereditary diseases have recently emerged, and the first sprayable dsRNA biopesticide has been proposed for registration. The range of applications of dsRNA molecules will likely expand in the future. Therefore, cost-effective methods for the efficient large-scale production of high-quality dsRNA are in demand. Conventional approaches to dsRNA production rely on the chemical or enzymatic synthesis of single-stranded (ss)RNA molecules with a subsequent hybridization of complementary strands. However, the yield of properly annealed biologically active dsRNA molecules is low. As an alternative approach, we have developed methods based on components derived from bacteriophage phi6, a dsRNA virus encoding RNA-dependent RNA polymerase (RdRp). Phi6 RdRp can be harnessed for the enzymatic production of high-quality dsRNA molecules. The isolated RdRp efficiently synthesizes dsRNA in vitro on a heterologous ssRNA template of any length and sequence. To scale up dsRNA production, we have developed an in vivo system where phi6 polymerase complexes produce target dsRNA molecules inside Pseudomonas cells.
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Affiliation(s)
- Alesia A. Levanova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
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Gao D, Abdullah S, Baldwin T, Caspersen A, Williams E, Carlson A, Petersen M, Hu G, Klos KE, Bregitzer P. Agrobacterium-mediated transfer of the Fusarium graminearum Tri6 gene into barley using mature seed-derived shoot tips as explants. PLANT CELL REPORTS 2024; 43:40. [PMID: 38244048 PMCID: PMC10799836 DOI: 10.1007/s00299-023-03129-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
KEY MESSAGE We transferred the Tri6 gene into the elite barley GemCraft via new transformation method through shoot organogenesis and identified the rearrangements of transgenes and phenotypic variations in the transgenic plants. Despite its agronomic and economic importance, barley transformation is still very challenging for many elite varieties. In this study, we used direct shoot organogenesis to transform the elite barley cultivar GemCraft with the RNAi constructs containing Tri6 gene of Fusarium graminearum, which causes fusarium head blight (FHB). We isolated 4432 shoot tips and co-cultured these explants with Agrobacterium tumefaciens. A total of 25 independent T0 transgenic plants were generated including 15 events for which transgene-specific PCR amplicons were observed. To further determine the presence of transgenes, the T1 progenies of all 15 T0 plants were analyzed, and the expected PCR products were obtained in 10 T1 lines. Droplet digital (dd) PCR analysis revealed various copy numbers of transgenes in the transgenic plants. We determined the insertion site of transgenes using long-read sequencing data and observed the rearrangements of transgenes. We found phenotypic variations in both T1 and T2 generation plants. FHB disease was evaluated under growth chamber conditions, but no significant differences in disease severity or deoxynivalenol accumulation were observed between two Tri6 transgenic lines and the wildtype. Our results demonstrate the feasibility of the shoot tip transformation and may open the door for applying this system for genetic improvement and gene function research in other barley genotypes.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA.
| | - Sidrat Abdullah
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
| | - Thomas Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Ann Caspersen
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
| | - Edward Williams
- Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Middleton, WI, 53562, USA
| | - Alvar Carlson
- Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Middleton, WI, 53562, USA
| | - Mike Petersen
- Wisconsin Crop Innovation Center, University of Wisconsin-Madison, Middleton, WI, 53562, USA
| | - Gongshe Hu
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
| | - Phil Bregitzer
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
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Chaudhary D, Jeena AS, Rohit, Gaur S, Raj R, Mishra S, Kajal, Gupta OP, Meena MR. Advances in RNA Interference for Plant Functional Genomics: Unveiling Traits, Mechanisms, and Future Directions. Appl Biochem Biotechnol 2024:10.1007/s12010-023-04850-x. [PMID: 38175411 DOI: 10.1007/s12010-023-04850-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
RNA interference (RNAi) is a conserved molecular mechanism that plays a critical role in post-transcriptional gene silencing across diverse organisms. This review delves into the role of RNAi in plant functional genomics and its applications in crop improvement, highlighting its mechanistic insights and practical implications. The review begins with the foundational discovery of RNAi's mechanism, tracing its origins from petunias to its widespread presence in various organisms. Various classes of regulatory non-coding small RNAs, including siRNAs, miRNAs, and phasiRNAs, have been uncovered, expanding the scope of RNAi-mediated gene regulation beyond conventional understanding. These RNA classes participate in intricate post-transcriptional and epigenetic processes that influence gene expression. In the context of crop enhancement, RNAi has emerged as a powerful tool for understanding gene functions. It has proven effective in deciphering gene roles related to stress resistance, metabolic pathways, and more. Additionally, RNAi-based approaches hold promise for integrated pest management and sustainable agriculture, contributing to global efforts in food security. This review discusses RNAi's diverse applications, such as modifying plant architecture, extending shelf life, and enhancing nutritional content in crops. The challenges and future prospects of RNAi technology, including delivery methods and biosafety concerns, are also explored. The global landscape of RNAi research is highlighted, with significant contributions from regions such as China, Europe, and North America. In conclusion, RNAi remains a versatile and pivotal tool in modern plant research, offering novel avenues for understanding gene functions and improving crop traits. Its integration with other biotechnological approaches such as gene editing holds the potential to shape the future of agriculture and sustainable food production.
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Affiliation(s)
- Divya Chaudhary
- Department of Genetics and Plant Breeding, College of Agriculture, G B Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Anand Singh Jeena
- Department of Genetics and Plant Breeding, College of Agriculture, G B Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India.
| | - Rohit
- Department of Genetics and Plant Breeding, College of Agriculture, G B Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Sonali Gaur
- Department of Genetics and Plant Breeding, College of Agriculture, G B Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Rishi Raj
- ICAR- Sugarcane Breeding Institute-Regional Centre, Karnal, 132001, Haryana, India
| | | | - Kajal
- Department of Biotechnology, Chandigarh University, Chandigarh, 140143, India
| | - Om Prakash Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, Haryana, India.
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25
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Peng J, Wang X, Wang H, Li X, Zhang Q, Wang M, Yan J. Advances in understanding grapevine downy mildew: From pathogen infection to disease management. MOLECULAR PLANT PATHOLOGY 2024; 25:e13401. [PMID: 37991155 PMCID: PMC10788597 DOI: 10.1111/mpp.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023]
Abstract
Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.
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Affiliation(s)
- Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hui Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qi Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Meng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
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Duan S, Wang G. Inducible Expression of dsRNA in Escherichia coli. Methods Mol Biol 2024; 2771:57-64. [PMID: 38285391 DOI: 10.1007/978-1-0716-3702-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Double-stranded RNA (dsRNA) is a valuable tool for reverse genetics research and gene silencing applications. It is also an important management method for pests and diseases in agriculture. It can be synthesized both in vivo and in vitro. The latter presents the drawback of high production cost, the former is less expensive and suitable for scalable production. In general, dsRNAs are obtained in vivo from Escherichia coli heterologous systems that require the IPTG-inducible T7 RNA polymerase. In this report, we describe the construction of an RNAi system for the expression of dsRNA using the HT115 bacterial strain and the L4440 plasmid, and the extraction and identification of dsRNA.
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Affiliation(s)
- Saiya Duan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China
| | - Guangjun Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
- Scientific Observation and Experimental Station of Pests in Xilin Gol Rangeland, Ministry of Agriculture and Rural Affairs, Xilinhot, China.
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27
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Tang T, Wang Y, Niu D. Application of dsRNA for Fungi Disease Management Sclerotinia sclerotiorum and Botrytis cinerea. Methods Mol Biol 2024; 2771:127-132. [PMID: 38285399 DOI: 10.1007/978-1-0716-3702-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are two closely related necrotrophic plant pathogenic fungi that have garnered significant attention due to their broad host range and persistent environmental presence. The use of double-stranded RNA (dsRNA) to inhibit specific genes has demonstrated promising potential in disease management. Various RNA interference (RNAi) strategies have been developed and applied in disease management, including the use of dsRNA to silence specific genes, as well as other RNA-based approaches. These strategies show promise in controlling fungal diseases and have the potential for broader application in plant protection. Here, we present a protocol that outlines techniques for preparing dsRNA and spraying it directly to control fungal diseases. This protocol offers a practical and effective solution for managing plant diseases and has the potential to be widely applied in disease management.
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Affiliation(s)
- Tao Tang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Yumeng Wang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Dongdong Niu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.
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Kim S, Lee R, Jeon H, Lee N, Park J, Moon H, Shin J, Min K, Kim JE, Yang JW, Son H. Identification of Essential Genes for the Establishment of Spray-Induced Gene Silencing-Based Disease Control in Fusarium graminearum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19302-19311. [PMID: 38018120 DOI: 10.1021/acs.jafc.3c04557] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
As resistance to chemical fungicides continues to increase inFusarium graminearum, there is a growing need to develop novel disease control strategies. To discover essential genes that could serve as new disease control targets, we selected essential gene candidates that had failed to be deleted in previous studies. Thirteen genes were confirmed to be essential, either by constructing conditional promoter replacement mutants or by employing a clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated editing strategy. We synthesized double-stranded RNAs (dsRNAs) targeting these essential genes and analyzed their protective effects in plants using a spray-induced gene silencing (SIGS) method. When dsRNAs targeting Fg10360, Fg13150, and Fg06123 were applied to detached barley leaves prior to fungal inoculation, disease lesions were greatly reduced. Our findings provide evidence of the potential of essential genes identified by a SIGS method to be effective targets for the control of fungal diseases.
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Affiliation(s)
- Sieun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Rowoon Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Hosung Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Nahyun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jiyeun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Heeji Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jiyoung Shin
- Division of Bioresources Bank, Honam National Institute of Biological Resources, Mokpo 58762, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Eun Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Jeju 63240, Republic of Korea
| | - Jung-Wook Yang
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon 16429, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Chen A, Halilovic L, Shay JH, Koch A, Mitter N, Jin H. Improving RNA-based crop protection through nanotechnology and insights from cross-kingdom RNA trafficking. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102441. [PMID: 37696727 PMCID: PMC10777890 DOI: 10.1016/j.pbi.2023.102441] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/21/2023] [Accepted: 08/06/2023] [Indexed: 09/13/2023]
Abstract
Spray-induced gene silencing (SIGS) is a powerful and eco-friendly method for crop protection. Based off the discovery of RNA uptake ability in many fungal pathogens, the application of exogenous RNAs targeting pathogen/pest genes results in gene silencing and infection inhibition. However, SIGS remains hindered by the rapid degradation of RNA in the environment. As extracellular vesicles are used by plants, animals, and microbes in nature to transport RNAs for cross-kingdom/species RNA interference between hosts and microbes/pests, nanovesicles and other nanoparticles have been used to prevent RNA degradation. Efforts examining the effect of nanoparticles on RNA stability and internalization have identified key attributes that can inform better nanocarrier designs for SIGS. Understanding sRNA biogenesis, cross-kingdom/species RNAi, and how plants and pathogens/pests naturally interact are paramount for the design of SIGS strategies. Here, we focus on nanotechnology advancements for the engineering of innovative RNA-based disease control strategies against eukaryotic pathogens and pests.
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Affiliation(s)
- Angela Chen
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Lida Halilovic
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Jia-Hong Shay
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Aline Koch
- Institute of Plant Sciences Cell Biology and Plant Biochemistry, Plant RNA Transport, University of Regensburg, Regensburg, Germany
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Science, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Hailing Jin
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
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Moonjely S, Ebert M, Paton-Glassbrook D, Noel ZA, Roze L, Shay R, Watkins T, Trail F. Update on the state of research to manage Fusarium head blight. Fungal Genet Biol 2023; 169:103829. [PMID: 37666446 DOI: 10.1016/j.fgb.2023.103829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023]
Abstract
Fusarium head blight (FHB) is one of the most devastating diseases of cereal crops, causing severe reduction in yield and quality of grain worldwide. In the United States, the major causal agent of FHB is the mycotoxigenic fungus, Fusarium graminearum. The contamination of grain with mycotoxins, including deoxynivalenol and zearalenone, is a particularly serious concern due to its impact on the health of humans and livestock. For the past few decades, multidisciplinary studies have been conducted on management strategies designed to reduce the losses caused by FHB. However, effective management is still challenging due to the emergence of fungicide-tolerant strains of F. graminearum and the lack of highly resistant wheat and barley cultivars. This review presents multidisciplinary approaches that incorporate advances in genomics, genetic-engineering, new fungicide chemistries, applied biocontrol, and consideration of the disease cycle for management of FHB.
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Affiliation(s)
- Soumya Moonjely
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Malaika Ebert
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Drew Paton-Glassbrook
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA
| | - Zachary A Noel
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Ludmila Roze
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Rebecca Shay
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA
| | - Tara Watkins
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI 48823, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
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Subha D, AnuKiruthika R, Sreeraj H, Tamilselvi KS. Plant exosomes: nano conveyors of pathogen resistance. DISCOVER NANO 2023; 18:146. [PMID: 38032422 PMCID: PMC10689327 DOI: 10.1186/s11671-023-03931-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/26/2023] [Indexed: 12/01/2023]
Abstract
The entry of a pathogen into a plant host is a complex process involving multiple steps. Survival techniques from the pathogen and the defense mechanisms of the plant lead to a plethora of molecular interactions during the operation. Plant extracellular vesicles, especially the exosomes in the size range of 50-150 nm play a crucial role in plant defense. They act as signalosomes capable of transporting bioactive lipids, proteins, RNA and metabolites between the host and the pathogen. Recent research works have revealed that anti-microbial compounds, stress response proteins and small RNA are among the contents of these extracellular vesicles. The current review article analyses the cruciality of the cross-talk between the host and the pathogen organized through trafficking of small RNA via exosomes towards RNA induced gene silencing in the pathogenic organisms. Recent studies have shown that extracellular vesicles released by both plants and the pathogens, play a crucial role in cross-kingdom communication, thereby regulating the host response and contributing to plant immunity. An in-depth understanding of the mechanism by which the EVs mediate this inter-species and cross-kingdom regulation is currently needed to develop sustainable plant-protection strategies. The review highlights on the latest advances in understanding the role of EVs in establishing host-pathogen relationship, modulating plant immunity and approaches for how these findings can be developed into innovative strategies for crop protection.
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Affiliation(s)
- D Subha
- Department of Biotechnology, PSGR Krishnammal College for Women, Coimbatore, India.
| | - R AnuKiruthika
- Department of Botany, PSGR Krishnammal College for Women, Coimbatore, India
| | - Harsha Sreeraj
- Department of Botany, PSGR Krishnammal College for Women, Coimbatore, India
| | - K S Tamilselvi
- Department of Botany, PSGR Krishnammal College for Women, Coimbatore, India.
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McLaughlin MS, Roy M, Abbasi PA, Carisse O, Yurgel SN, Ali S. Why Do We Need Alternative Methods for Fungal Disease Management in Plants? PLANTS (BASEL, SWITZERLAND) 2023; 12:3822. [PMID: 38005718 PMCID: PMC10675458 DOI: 10.3390/plants12223822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Fungal pathogens pose a major threat to food production worldwide. Traditionally, chemical fungicides have been the primary means of controlling these pathogens, but many of these fungicides have recently come under increased scrutiny due to their negative effects on the health of humans, animals, and the environment. Furthermore, the use of chemical fungicides can result in the development of resistance in populations of phytopathogenic fungi. Therefore, new environmentally friendly alternatives that provide adequate levels of disease control are needed to replace chemical fungicides-if not completely, then at least partially. A number of alternatives to conventional chemical fungicides have been developed, including plant defence elicitors (PDEs); biological control agents (fungi, bacteria, and mycoviruses), either alone or as consortia; biochemical fungicides; natural products; RNA interference (RNAi) methods; and resistance breeding. This article reviews the conventional and alternative methods available to manage fungal pathogens, discusses their strengths and weaknesses, and identifies potential areas for future research.
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Affiliation(s)
- Michael S. McLaughlin
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 4H5, Canada
| | - Maria Roy
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Pervaiz A. Abbasi
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
| | - Odile Carisse
- Saint-Jean-sur-Richelieu Research Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 7B5, Canada;
| | - Svetlana N. Yurgel
- United States Department of Agriculture (USDA), Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Shawkat Ali
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5, Canada; (M.S.M.); (M.R.); (P.A.A.)
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Nalla MK, Schafleitner R, Pappu HR, Barchenger DW. Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223982. [PMID: 37936944 PMCID: PMC10626458 DOI: 10.3389/fpls.2023.1223982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023]
Abstract
Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.
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Affiliation(s)
- Manoj Kumar Nalla
- World Vegetable Center, South and Central Asia Regional Office, Hyderabad, India
| | | | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Cheng AP, Kwon S, Adeshara T, Göhre V, Feldbrügge M, Weiberg A. Extracellular RNAs released by plant-associated fungi: from fundamental mechanisms to biotechnological applications. Appl Microbiol Biotechnol 2023; 107:5935-5945. [PMID: 37572124 PMCID: PMC10485130 DOI: 10.1007/s00253-023-12718-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/15/2023] [Accepted: 07/19/2023] [Indexed: 08/14/2023]
Abstract
Extracellular RNAs are an emerging research topic in fungal-plant interactions. Fungal plant pathogens and symbionts release small RNAs that enter host cells to manipulate plant physiology and immunity. This communication via extracellular RNAs between fungi and plants is bidirectional. On the one hand, plants release RNAs encapsulated inside extracellular vesicles as a defense response as well as for intercellular and inter-organismal communication. On the other hand, recent reports suggest that also full-length mRNAs are transported within fungal EVs into plants, and these fungal mRNAs might get translated inside host cells. In this review article, we summarize the current views and fundamental concepts of extracellular RNAs released by plant-associated fungi, and we discuss new strategies to apply extracellular RNAs in crop protection against fungal pathogens. KEY POINTS: • Extracellular RNAs are an emerging topic in plant-fungal communication. • Fungi utilize RNAs to manipulate host plants for colonization. • Extracellular RNAs can be engineered to protect plants against fungal pathogens.
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Affiliation(s)
- An-Po Cheng
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany
| | - Seomun Kwon
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Trusha Adeshara
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Vera Göhre
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Heinrich Heine Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Arne Weiberg
- Faculty of Biology, Ludwig-Maximilians Universität München (LMU), 82152, Martinsried, Germany.
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O'Mara SP, Broz K, Schwister EM, Singh L, Dong Y, Elmore JM, Kistler HC. The Fusarium graminearum Transporters Abc1 and Abc6 Are Important for Xenobiotic Resistance, Trichothecene Accumulation, and Virulence to Wheat. PHYTOPATHOLOGY 2023; 113:1916-1923. [PMID: 37260101 DOI: 10.1094/phyto-09-22-0345-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: 06/02/2023]
Abstract
The plant pathogenic fungus Fusarium graminearum is the causal agent of Fusarium head blight (FHB) disease on small-grain cereals. F. graminearum produces trichothecene mycotoxins such as deoxynivalenol (DON) that are required for full virulence. DON must be exported outside the cell to cause FHB disease, a process that may require the involvement of membrane-bound transporters. In this study, we show that the deletion of membrane-bound transporters results in reduced DON accumulation as well as reduced FHB symptoms on wheat. Deletion of the ATP-binding cassette (ABC) transporter gene Abc1 results in the greatest reduction in DON accumulation and virulence. Deletion of another ABC transporter gene, Abc6, also reduces FHB symptoms to a lesser degree. Combining deletions fails to reduce DON accumulation or virulence in an additive fashion, even when a ∆abc1 deletion is included. Heterologous expression of F. graminearum transporters in a DON-sensitive strain of yeast confirms Abc1 as a major DON resistance mechanism; furthermore, it suggests that Abc1 is directly participating in DON transport rather than facilitating DON transport though other means. Yeast expression further indicates that multiple transporters, including Abc1, play an important role in resistance to the wheat phytoalexin 2-benzoxazolinone (BOA) and other xenobiotics. Thus, Abc1 may contribute to virulence on wheat both by facilitating export of DON and by providing resistance to the wheat phytoalexin BOA. This research provides useful information that may aid in designing novel management techniques of FHB or other destructive plant diseases.
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Affiliation(s)
- Sean P O'Mara
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Karen Broz
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
| | - Erin M Schwister
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
| | - Lovepreet Singh
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - J Mitch Elmore
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - H Corby Kistler
- U.S. Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Bhagta S, Bhardwaj V, Kant A. Exogenous dsRNA trigger RNAi in Venturia inaequalis resulting in down regulation of target genes and growth reduction. Mol Biol Rep 2023; 50:8421-8429. [PMID: 37620739 DOI: 10.1007/s11033-023-08736-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/02/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Venturia inaequalis is an apple scab causing fungal pathogen. It is a highly contagious and destructive pathogen which rapidly spreads infection in the surrounding orchards if not managed. The management and control of disease require multiple fungicides to be sprayed at different development stages of the apple. Persistent applications of fungicides also raises environmental concerns. Here, we demonstrate the potential of using spray induced gene silencing (SIGS) by developing target specific gene constructs for the synthesis of corresponding double-stranded RNA (dsRNA). METHODS AND RESULTS The exogenous application of dsRNAs was found to reduce mycelial growth and spore formation of V. inaequalis on culture plates. Four genes of V. inaequalis viz. CIN1, CE5, VICE12 and VICE16 which get upregulated during infection, were selected as targets for the development of gene construct expressing the corresponding dsRNA. The effect of exogenously supplied in vitro synthesized dsRNA on V. inaequalis was assessed in culture bioassay experiments with respect to growth, and spore formation. The expression level of the target genes in treated and control fungus was evaluated using quantitative PCR. Fungus treated with VICE12 targeted dsRNA showed maximum reduction in colony size (~ 55%), conidia formation (~ 93%) and expression level of the corresponding gene (2.2 fold), which was followed by CIN1-dsRNA. VICE16-dsRNA treatment was least effective with 32% reduction in growth, the non-significant effect of conidial spore formation and 1.13 fold down regulation of corresponding target gene expression level. CONCLUSION The result of this investigation validates the hypothesis that RNAi is evoked in V. inaequalis by exogenously supplied dsRNA and spray induced gene silencing (SIGS) based solutions may reduce burden of fungicide usage on apple crop against apple scab disease in future.
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Affiliation(s)
- Suhani Bhagta
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Anil Kant
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India.
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Huang C, Sede AR, Elvira-González L, Yan Y, Rodriguez ME, Mutterer J, Boutant E, Shan L, Heinlein M. dsRNA-induced immunity targets plasmodesmata and is suppressed by viral movement proteins. THE PLANT CELL 2023; 35:3845-3869. [PMID: 37378592 PMCID: PMC10533371 DOI: 10.1093/plcell/koad176] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 05/24/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Emerging evidence indicates that in addition to its well-recognized functions in antiviral RNA silencing, dsRNA elicits pattern-triggered immunity (PTI), likely contributing to plant resistance against virus infections. However, compared to bacterial and fungal elicitor-mediated PTI, the mode-of-action and signaling pathway of dsRNA-induced defense remain poorly characterized. Here, using multicolor in vivo imaging, analysis of GFP mobility, callose staining, and plasmodesmal marker lines in Arabidopsis thaliana and Nicotiana benthamiana, we show that dsRNA-induced PTI restricts the progression of virus infection by triggering callose deposition at plasmodesmata, thereby likely limiting the macromolecular transport through these cell-to-cell communication channels. The plasma membrane-resident SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1, the BOTRYTIS INDUCED KINASE1/AVRPPHB SUSCEPTIBLE1-LIKE KINASE1 kinase module, PLASMODESMATA-LOCATED PROTEINs 1/2/3, as well as CALMODULIN-LIKE 41 and Ca2+ signals are involved in the dsRNA-induced signaling leading to callose deposition at plasmodesmata and antiviral defense. Unlike the classical bacterial elicitor flagellin, dsRNA does not trigger a detectable reactive oxygen species (ROS) burst, substantiating the idea that different microbial patterns trigger partially shared immune signaling frameworks with distinct features. Likely as a counter strategy, viral movement proteins from different viruses suppress the dsRNA-induced host response leading to callose deposition to achieve infection. Thus, our data support a model in which plant immune signaling constrains virus movement by inducing callose deposition at plasmodesmata and reveals how viruses counteract this layer of immunity.
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Affiliation(s)
- Caiping Huang
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Ana Rocío Sede
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Laura Elvira-González
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Yan Yan
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Miguel Eduardo Rodriguez
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Jérôme Mutterer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Emmanuel Boutant
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Libo Shan
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Manfred Heinlein
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67000 Strasbourg, France
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Wen HG, Zhao JH, Zhang BS, Gao F, Wu XM, Yan YS, Zhang J, Guo HS. Microbe-induced gene silencing boosts crop protection against soil-borne fungal pathogens. NATURE PLANTS 2023; 9:1409-1418. [PMID: 37653339 DOI: 10.1038/s41477-023-01507-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
Small RNA (sRNA)-mediated trans-kingdom RNA interference (RNAi) between host and pathogen has been demonstrated and utilized. However, interspecies RNAi in rhizospheric microorganisms remains elusive. In this study, we developed a microbe-induced gene silencing (MIGS) technology by using a rhizospheric beneficial fungus, Trichoderma harzianum, to exploit an RNAi engineering microbe and two soil-borne pathogenic fungi, Verticillium dahliae and Fusarium oxysporum, as RNAi recipients. We first detected the feasibility of MIGS in inducing GFP silencing in V. dahliae. Then by targeting a fungal essential gene, we further demonstrated the effectiveness of MIGS in inhibiting fungal growth and protecting dicotyledon cotton and monocotyledon rice plants against V. dahliae and F. oxysporum. We also showed steerable MIGS specificity based on a selected target sequence. Our data verify interspecies RNAi in rhizospheric fungi and the potential application of MIGS in crop protection. In addition, the in situ propagation of a rhizospheric beneficial microbe would be optimal in ensuring the stability and sustainability of sRNAs, avoiding the use of nanomaterials to carry chemically synthetic sRNAs. Our finding reveals that exploiting MIGS-based biofungicides would offer straightforward design and implementation, without the need of host genetic modification, in crop protection against phytopathogens.
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Affiliation(s)
- Han-Guang Wen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China.
| | - Bo-Sen Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Feng Gao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Xue-Ming Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Yong-Sheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, Beijing, China.
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McRae AG, Taneja J, Yee K, Shi X, Haridas S, LaButti K, Singan V, Grigoriev IV, Wildermuth MC. Spray-induced gene silencing to identify powdery mildew gene targets and processes for powdery mildew control. MOLECULAR PLANT PATHOLOGY 2023; 24:1168-1183. [PMID: 37340595 PMCID: PMC10423327 DOI: 10.1111/mpp.13361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/22/2023]
Abstract
Spray-induced gene silencing (SIGS) is an emerging tool for crop pest protection. It utilizes exogenously applied double-stranded RNA to specifically reduce pest target gene expression using endogenous RNA interference machinery. In this study, SIGS methods were developed and optimized for powdery mildew fungi, which are widespread obligate biotrophic fungi that infect agricultural crops, using the known azole-fungicide target cytochrome P450 51 (CYP51) in the Golovinomyces orontii-Arabidopsis thaliana pathosystem. Additional screening resulted in the identification of conserved gene targets and processes important to powdery mildew proliferation: apoptosis-antagonizing transcription factor in essential cellular metabolism and stress response; lipid catabolism genes lipase a, lipase 1, and acetyl-CoA oxidase in energy production; and genes involved in manipulation of the plant host via abscisic acid metabolism (9-cis-epoxycarotenoid dioxygenase, xanthoxin dehydrogenase, and a putative abscisic acid G-protein coupled receptor) and secretion of the effector protein, effector candidate 2. Powdery mildew is the dominant disease impacting grapes and extensive powdery mildew resistance to applied fungicides has been reported. We therefore developed SIGS for the Erysiphe necator-Vitis vinifera system and tested six successful targets identified using the G. orontii-A. thaliana system. For all targets tested, a similar reduction in powdery mildew disease was observed between systems. This indicates screening of broadly conserved targets in the G. orontii-A. thaliana pathosystem identifies targets and processes for the successful control of other powdery mildew fungi. The efficacy of SIGS on powdery mildew fungi makes SIGS an exciting prospect for commercial powdery mildew control.
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Affiliation(s)
- Amanda G. McRae
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jyoti Taneja
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kathleen Yee
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Xinyi Shi
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Sajeet Haridas
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Kurt LaButti
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Vasanth Singan
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Igor V. Grigoriev
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
- US Department of Energy Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Mary C. Wildermuth
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023; 24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.
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Affiliation(s)
- Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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42
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Jiang C, Li Z, Zheng L, Yu Y, Niu D. Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions. MOLECULAR PLANT PATHOLOGY 2023; 24:999-1013. [PMID: 37026481 PMCID: PMC10346379 DOI: 10.1111/mpp.13329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
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Affiliation(s)
- Chun‐Hao Jiang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zi‐Jie Li
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Li‐Yu Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Yi‐Yang Yu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dong‐Dong Niu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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43
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Ghosh S, Patra S, Ray S. A Combinatorial Nanobased Spray-Induced Gene Silencing Technique for Crop Protection and Improvement. ACS OMEGA 2023; 8:22345-22351. [PMID: 37396279 PMCID: PMC10308407 DOI: 10.1021/acsomega.3c01968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/29/2023] [Indexed: 07/04/2023]
Abstract
Recent research reports have shown that plant pests and pathogens have depleted the crop yield widely, which has led to an increased dependence on commercial pesticides and fungicides. Increased usage of these pesticides has also shown adverse effects on the environment, therefore many techniques have been implemented for solving the issue, some of which include using nanobioconjugates, RNA(i), which put into use double-stranded RNAs to inhibit gene expression. A more innovative and eco-friendly strategy includes spray induced gene silencing, which is being increasingly implemented. This review delves into the eco-friendly approach of spray induced gene silencing (SIGS) in combination with nanobioconjugates, which have been used concerning various plant hosts and their pathogens to provide improved protection. Furthermore, nanotechnological advancements have been understood by addressing the scientific gaps to provide a rationale for the development of updated techniques in crop protection.
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Affiliation(s)
- Snigdha Ghosh
- Amity
Institute of Biotechnology, Amity University,
Kolkata, Plot No: 36, 37, and 38 Major Arterial Road, Action Area II, Kadampukur
Village, Rajarhat, Newtown, Kolkata, West Bengal-700135, India
| | - Snehanjana Patra
- Amity
Institute of Biotechnology, Amity University,
Kolkata, Plot No: 36, 37, and 38 Major Arterial Road, Action Area II, Kadampukur
Village, Rajarhat, Newtown, Kolkata, West Bengal-700135, India
| | - Sarmistha Ray
- Amity
Institute of Biotechnology, Amity University,
Kolkata, Plot No: 36, 37, and 38 Major Arterial Road, Action Area II, Kadampukur
Village, Rajarhat, Newtown, Kolkata, West Bengal-700135, India
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Ouyang SQ, Ji HM, Feng T, Luo SJ, Cheng L, Wang N. Artificial trans-kingdom RNAi of FolRDR1 is a potential strategy to control tomato wilt disease. PLoS Pathog 2023; 19:e1011463. [PMID: 37339156 DOI: 10.1371/journal.ppat.1011463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023] Open
Abstract
Tomato is cultivated worldwide as a nutrient-rich vegetable crop. Tomato wilt disease caused by Fusarium oxysporum f.sp. Lycopersici (Fol) is one of the most serious fungal diseases posing threats to tomato production. Recently, the development of Spray-Induced Gene Silencing (SIGS) directs a novel plant disease management by generating an efficient and environmental friendly biocontrol agent. Here, we characterized that FolRDR1 (RNA-dependent RNA polymerase 1) mediated the pathogen invasion to the host plant tomato, and played as an essential regulator in pathogen development and pathogenicity. Our fluorescence tracing data further presented that effective uptakes of FolRDR1-dsRNAs were observed in both Fol and tomato tissues. Subsequently, exogenous application of FolRDR1-dsRNAs on pre-Fol-infected tomato leaves resulted in significant alleviation of tomato wilt disease symptoms. Particularly, FolRDR1-RNAi was highly specific without sequence off-target in related plants. Our results of pathogen gene-targeting RNAi have provided a new strategy for tomato wilt disease management by developing an environmentally-friendly biocontrol agent.
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Affiliation(s)
- Shou-Qiang Ouyang
- College of Life Sciences, Zhejiang Normal University, Jinhua, China
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hui-Min Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Tao Feng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Shu-Jie Luo
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Lu Cheng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Nan Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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Koeppe S, Kawchuk L, Kalischuk M. RNA Interference Past and Future Applications in Plants. Int J Mol Sci 2023; 24:ijms24119755. [PMID: 37298705 DOI: 10.3390/ijms24119755] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Antisense RNA was observed to elicit plant disease resistance and post-translational gene silencing (PTGS). The universal mechanism of RNA interference (RNAi) was shown to be induced by double-stranded RNA (dsRNA), an intermediate produced during virus replication. Plant viruses with a single-stranded positive-sense RNA genome have been instrumental in the discovery and characterization of systemic RNA silencing and suppression. An increasing number of applications for RNA silencing have emerged involving the exogenous application of dsRNA through spray-induced gene silencing (SIGS) that provides specificity and environmentally friendly options for crop protection and improvement.
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Affiliation(s)
- Sarah Koeppe
- Department of Plant Agriculture, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Lawrence Kawchuk
- Research Centre, Agriculture and Agri-Food Canada, 5403 1 Ave S., Lethbridge, AB T1J 4B1, Canada
| | - Melanie Kalischuk
- Department of Plant Agriculture, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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Singewar K, Fladung M. Double-stranded RNA (dsRNA) technology to control forest insect pests and fungal pathogens: challenges and opportunities. Funct Integr Genomics 2023; 23:185. [PMID: 37243792 PMCID: PMC10220346 DOI: 10.1007/s10142-023-01107-y] [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: 07/04/2022] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023]
Abstract
Climate change alters the seasonal synchronization between plants and respective pests plus pathogens. The geographical infiltration helps to shift their hosts, resulting in novel outbreaks that damage forests and ecology. Traditional management schemes are unable to control such outbreaks, therefore unconventional and competitive governance is needed to manage forest pests and pathogens. RNA interference (RNAi) mediated double-stranded RNA (dsRNA) treatment method can be implemented to protect forest trees. Exogenous dsRNA triggers the RNAi-mediated gene silencing of a vital gene, and suspends protein production, resulting in the death of targeted pathogens and pests. The dsRNA treatment method is successful for many crop insects and fungi, however, studies of dsRNA against forest pests and pathogens are depleting. Pesticides and fungicides based on dsRNA could be used to combat pathogens that caused outbreaks in different parts of the world. Although the dsRNA has proved its potential, the crucial dilemma and risks including species-specific gene selection, and dsRNA delivery methods cannot be overlooked. Here, we summarized the major fungi pathogens and insect pests that have caused outbreaks, their genomic information, and studies on dsRNA fungi-and pesticides. Current challenges and opportunities in dsRNA target decision, delivery using nanoparticles, direct applications, and a new method using mycorrhiza for forest tree protection are discussed. The importance of affordable next-generation sequencing to minimize the impact on non-target species is discussed. We suggest that collaborative research among forest genomics and pathology institutes could develop necessary dsRNA strategies to protect forest tree species.
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Affiliation(s)
- Kiran Singewar
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Großhansdorf, Germany.
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Suprun AR, Kiselev KV, Dubrovina AS. Exogenously Induced Silencing of Four MYB Transcription Repressor Genes and Activation of Anthocyanin Accumulation in Solanum lycopersicum. Int J Mol Sci 2023; 24:ijms24119344. [PMID: 37298295 DOI: 10.3390/ijms24119344] [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: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
RNA interference (RNAi) is a natural post-transcriptional regulatory mechanism that can be artificially induced by exogenous application of double-stranded RNAs (dsRNAs) to the plant surfaces. Recent studies show that it is possible to silence plant genes and change plant properties using plant RNA spraying and other approaches for dsRNA delivery. In this study, we investigated the effect of exogenous gene-specific dsRNAs on the silencing of four tomato genes encoding MYB-family transcription repressors of anthocyanin biosynthesis in the leaves of tomato Solanum lycopersicum L. We found that the exogenous application of dsRNAs encoding for the SlMYBATV1, SlMYB32, SlMYB76, and SlTRY genes downregulated mRNA levels of these endogenous repressors of anthocyanin production, upregulated the expression of anthocyanin biosynthesis-related genes, and enhanced anthocyanin content in the leaves of S. lycopersicum. The data demonstrated that exogenous gene-specific dsRNAs can induce post-transcriptional gene silencing in tomato leaves by direct foliar application of dsRNAs. This approach may be used for plant secondary metabolism induction and as a silencing tool for gene function studies without the need to produce genetically modified plants.
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Affiliation(s)
- Andrey R Suprun
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Konstantin V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Alexandra S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok 690022, Russia
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Padilla-Roji I, Ruiz-Jiménez L, Bakhat N, Vielba-Fernández A, Pérez-García A, Fernández-Ortuño D. RNAi Technology: A New Path for the Research and Management of Obligate Biotrophic Phytopathogenic Fungi. Int J Mol Sci 2023; 24:ijms24109082. [PMID: 37240427 DOI: 10.3390/ijms24109082] [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: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Powdery mildew and rust fungi are major agricultural problems affecting many economically important crops and causing significant yield losses. These fungi are obligate biotrophic parasites that are completely dependent on their hosts for growth and reproduction. Biotrophy in these fungi is determined by the presence of haustoria, specialized fungal cells that are responsible for nutrient uptake and molecular dialogue with the host, a fact that undoubtedly complicates their study under laboratory conditions, especially in terms of genetic manipulation. RNA interference (RNAi) is the biological process of suppressing the expression of a target gene through double-stranded RNA that induces mRNA degradation. RNAi technology has revolutionized the study of these obligate biotrophic fungi by enabling the analysis of gene function in these fungal. More importantly, RNAi technology has opened new perspectives for the management of powdery mildew and rust diseases, first through the stable expression of RNAi constructs in transgenic plants and, more recently, through the non-transgenic approach called spray-induced gene silencing (SIGS). In this review, the impact of RNAi technology on the research and management of powdery mildew and rust fungi will be addressed.
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Affiliation(s)
- Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Laura Ruiz-Jiménez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Nisrine Bakhat
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandra Vielba-Fernández
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
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Raruang Y, Omolehin O, Hu D, Wei Q, Promyou S, Parekattil LJ, Rajasekaran K, Cary JW, Wang K, Chen ZY. Targeting the Aspergillus flavus p2c gene through host-induced gene silencing reduces A. flavus infection and aflatoxin contamination in transgenic maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1150086. [PMID: 37229129 PMCID: PMC10203651 DOI: 10.3389/fpls.2023.1150086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/11/2023] [Indexed: 05/27/2023]
Abstract
Aspergillus flavus is an opportunistic fungal pathogen that infects maize and produces aflatoxins. Using biocontrol or developing resistant cultivars to reduce aflatoxin contamination has only achieved limited success. Here, the A. flavus polygalacturonase gene (p2c) was targeted for suppression through host-induced gene silencing (HIGS) to reduce aflatoxin contamination in maize. An RNAi vector carrying a portion of the p2c gene was constructed and transformed into maize B104. Thirteen out of fifteen independent transformation events were confirmed to contain p2c. The T2 generation kernels containing the p2c transgene had less aflatoxin than those without the transgene in six out of eleven events we examined. Homozygous T3 transgenic kernels from four events produced significantly less aflatoxins (P ≤ 0.02) than the kernels from the null or B104 controls under field inoculation conditions. The F1 kernels from the crosses between six elite inbred lines with P2c5 and P2c13 also supported significantly less aflatoxins (P ≤ 0.02) than those from the crosses with null plants. The reduction in aflatoxin ranged from 93.7% to 30.3%. Transgenic leaf (T0 and T3) and kernel tissues (T4) were also found to have significantly higher levels of p2c gene-specific small RNAs. Further, homozygous transgenic maize kernels had significantly less fungal growth (27~40 fold) than the null control kernels 10 days after fungal inoculation in the field. The calculated suppression of p2c gene expression based on RNAseq data was 57.6% and 83.0% in P2c5 and P2c13 events, respectively. These results indicate clearly that the reduced aflatoxin production in the transgenic kernels is due to RNAi-based suppression of p2c expression, which results in reduced fungal growth and toxin production.
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Affiliation(s)
- Yenjit Raruang
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Olanike Omolehin
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Dongfang Hu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Qijian Wei
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Surassawadee Promyou
- Faculty of Natural Resources and Agro-Industry, Kasetsart University, Sakonnakhon, Thailand
| | - Lidiya J. Parekattil
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jeffrey W. Cary
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Borniego ML, Innes RW. Extracellular RNA: mechanisms of secretion and potential functions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2389-2404. [PMID: 36609873 PMCID: PMC10082932 DOI: 10.1093/jxb/erac512] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/21/2022] [Indexed: 06/06/2023]
Abstract
Extracellular RNA (exRNA) has long been considered as cellular waste that plants can degrade and utilize to recycle nutrients. However, recent findings highlight the need to reconsider the biological significance of RNAs found outside of plant cells. A handful of studies suggest that the exRNA repertoire, which turns out to be an extremely heterogenous group of non-coding RNAs, comprises species as small as a dozen nucleotides to hundreds of nucleotides long. They are found mostly in free form or associated with RNA-binding proteins, while very few are found inside extracellular vesicles (EVs). Despite their low abundance, small RNAs associated with EVs have been a focus of exRNA research due to their putative role in mediating trans-kingdom RNAi. Therefore, non-vesicular exRNAs have remained completely under the radar until very recently. Here we summarize our current knowledge of the RNA species that constitute the extracellular RNAome and discuss mechanisms that could explain the diversity of exRNAs, focusing not only on the potential mechanisms involved in RNA secretion but also on post-release processing of exRNAs. We will also share our thoughts on the putative roles of vesicular and extravesicular exRNAs in plant-pathogen interactions, intercellular communication, and other physiological processes in plants.
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Affiliation(s)
- M Lucía Borniego
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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