1
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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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2
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Mamrutha HM, Zeenat W, Kapil D, Budhagatapalli N, Tikaniya D, Rakesh K, Krishnappa G, Singh G, Singh GP. Evidence and opportunities for developing non-transgenic genome edited crops using site-directed nuclease 1 approach. Crit Rev Biotechnol 2024; 44:1140-1150. [PMID: 37915126 DOI: 10.1080/07388551.2023.2270581] [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: 02/04/2022] [Revised: 07/21/2023] [Accepted: 09/18/2023] [Indexed: 11/03/2023]
Abstract
The innovations and progress in genome editing/new breeding technologies have revolutionized research in the field of functional genomics and crop improvement. This revolution has expanded the horizons of agricultural research, presenting fresh possibilities for creating novel plant varieties equipped with desired traits that can effectively combat the challenges posed by climate change. However, the regulation and social acceptance of genome-edited crops still remain as major barriers. Only a few countries considered the site-directed nuclease 1 (SDN1) approach-based genome-edited plants under less or no regulation. Hence, the present review aims to comprise information on the research work conducted using SDN1 in crops by various genome editing tools. It also elucidates the promising candidate genes that can be used for editing and has listed the studies on non-transgenic crops developed through SDN1 either by Agrobacterium-mediated transformation or by ribo nucleoprotein (RNP) complex. The review also hoards the existing regulatory landscape of genome editing and provides an overview of globally commercialized genome-edited crops. These compilations will enable confidence in researchers and policymakers, across the globe, to recognize the full potential of this technology and reconsider the regulatory aspects associated with genome-edited crops. Furthermore, this compilation serves as a valuable resource for researchers embarking on the development of customized non-transgenic crops through the utilization of SDN1.
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Affiliation(s)
- H M Mamrutha
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Wadhwa Zeenat
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deswal Kapil
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Nagaveni Budhagatapalli
- Institute of Plant Biochemistry, Center for Plant Genome Engineering, Heinrich-Heine-University, Düsseldorf, Germany
| | - Divya Tikaniya
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Kumar Rakesh
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Gyanendra Singh
- ICAR - Indian Institute of Wheat and Barley Research, Karnal, India
| | - G P Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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3
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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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4
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Zhu Y, Wu C, Deng Y, Yuan W, Zhang T, Lu J. Recent advances in virulence of a broad host range plant pathogen Sclerotinia sclerotiorum: a mini-review. Front Microbiol 2024; 15:1424130. [PMID: 38962122 PMCID: PMC11220166 DOI: 10.3389/fmicb.2024.1424130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Sclerotinia sclerotiorum is a typical necrotrophic plant pathogenic fungus, which has a wide host range and can cause a variety of diseases, leading to serious loss of agricultural production around the world. It is difficult to control and completely eliminate the characteristics, chemical control methods is not ideal. Therefore, it is very important to know the pathogenic mechanism of S. sclerotiorum for improving host living environment, relieving agricultural pressure and promoting economic development. In this paper, the life cycle of S. sclerotiorum is introduced to understand the whole process of S. sclerotiorum infection. Through the analysis of the pathogenic mechanism, this paper summarized the reported content, mainly focused on the oxalic acid, cell wall degrading enzyme and effector protein in the process of infection and its mechanism. Besides, recent studies reported virulence-related genes in S. sclerotiorum have been summarized in the paper. According to analysis, those genes were related to the growth and development of the hypha and appressorium, the signaling and regulatory factors of S. sclerotiorum and so on, to further influence the ability to infect the host critically. The application of host-induced gene silencing (HIGS)is considered as a potential effective tool to control various fungi in crops, which provides an important reference for the study of pathogenesis and green control of S. sclerotiorum.
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Affiliation(s)
| | | | | | | | | | - Junxing Lu
- Chongqing Key Laboratory of Plant Environmental Adaptations, College of Life Science, Chongqing Normal University, Chongqing, China
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5
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Mao JC, Yan M, Li JH, Yang JY, Wang HJ. The role of small RNAs in resistant melon cultivar against Phelipanche aegyptiaca parasitization. Front Microbiol 2024; 15:1408926. [PMID: 38774502 PMCID: PMC11106454 DOI: 10.3389/fmicb.2024.1408926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Bidirectional trans-kingdom RNA silencing, a pivotal factor in plant-pathogen interactions, remains less explored in plant host-parasite dynamics. Here, using small RNA sequencing in melon root systems, we investigated microRNA (miRNA) expression variation in resistant and susceptible cultivars pre-and post-infection by the parasitic plant, broomrape. This approach revealed 979 known miRNAs and 110 novel miRNAs across 110 families. When comparing susceptible (F0) and resistant (R0) melon lines with broomrape infection (F25 and R25), 39 significantly differentially expressed miRNAs were observed in F25 vs. F0, 35 in R25 vs. R0, and 5 in R25 vs. F25. Notably, two miRNAs consistently exhibited differential expression across all comparisons, targeting genes linked to plant disease resistance. This suggests their pivotal role in melon's defense against broomrape. The target genes of these miRNAs were confirmed via degradome sequencing and validated by qRT-PCR, ensuring reliable sequencing outcomes. GO and KEGG analyses shed light on the molecular functions and pathways of these differential miRNAs. Furthermore, our study unveiled four trans-kingdom miRNAs, forming a foundation for exploring melon's resistance to broomrape.
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Affiliation(s)
| | | | | | | | - Hao-Jie Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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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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7
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Hao G, Naumann TA, Chen H, Bai G, McCormick S, Kim HS, Tian B, Trick HN, Naldrett MJ, Proctor R. Fusarium graminearum Effector FgNls1 Targets Plant Nuclei to Induce Wheat Head Blight. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:478-488. [PMID: 36853197 DOI: 10.1094/mpmi-12-22-0254-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: 06/18/2023]
Abstract
Fusarium head blight (FHB) caused by Fusarium graminearum is one of the most devastating diseases of wheat and barley worldwide. Effectors suppress host immunity and promote disease development. The genome of F. graminearum contains hundreds of effectors with unknown function. Therefore, investigations of the functions of these effectors will facilitate developing novel strategies to enhance wheat resistance to FHB. We characterized a F. graminearum effector, FgNls1, containing a signal peptide and multiple eukaryotic nuclear localization signals. A fusion protein of green fluorescent protein and FgNls1 accumulated in plant cell nuclei when transiently expressed in Nicotiana benthamiana. FgNls1 suppressed Bax-induced cell death when co-expressed in N. benthamiana. We revealed that the expression of FgNLS1 was induced in wheat spikes infected with F. graminearum. The Fgnls1 mutants significantly reduced initial infection and FHB spread within a spike. The function of FgNLS1 was restored in the Fgnls1-complemented strains. Wheat histone 2B was identified as an interacting protein by FgNls1-affinity chromatography. Furthermore, transgenic wheat plants that silence FgNLS1 expression had significantly lower FHB severity than control plants. This study demonstrates a critical role of FgNls1 in F. graminearum pathogenesis and indicates that host-induced gene silencing targeting F. graminearum effectors is a promising approach to enhance FHB resistance. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Guixia Hao
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Todd A Naumann
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Hui Chen
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, U.S.A
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, U.S.A
| | - Susan McCormick
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Hye-Seon Kim
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
| | - Bin Tian
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Harold N Trick
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Michael J Naldrett
- Nebraska Center for Biotechnology, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE 68588, U.S.A
| | - Robert Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N. University, Peoria, IL 61604, U.S.A
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8
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Diversity, Ecological Characteristics and Identification of Some Problematic Phytopathogenic Fusarium in Soil: A Review. DIVERSITY 2023. [DOI: 10.3390/d15010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The genus Fusarium includes many pathogenic species causing a wide range of plant diseases that lead to high economic losses. In this review, we describe how the Fusarium taxonomy has changed with the development of microbiological methods. We specify the ecological traits of this genus and the methods of its identification in soils, particularly the detection of phytopathogenic representatives of Fusarium and the mycotoxins produced by them. The negative effects of soil-borne phytopathogenic Fusarium on agricultural plants and current methods for its control are discussed. Due to the high complexity and polymorphism of Fusarium species, integrated approaches for the risk assessment of Fusarium diseases are necessary.
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Bharathi JK, Anandan R, Benjamin LK, Muneer S, Prakash MAS. Recent trends and advances of RNA interference (RNAi) to improve agricultural crops and enhance their resilience to biotic and abiotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:600-618. [PMID: 36529010 DOI: 10.1016/j.plaphy.2022.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/04/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Over the last two decades, significant advances have been made using genetic engineering technology to modify genes from various exotic origins and introduce them into plants to induce favorable traits. RNA interference (RNAi) was discovered earlier as a natural process for controlling the expression of genes across all higher species. It aims to enhance precision and accuracy in pest/pathogen resistance, quality improvement, and manipulating the architecture of plants. However, it existed as a widely used technique recently. RNAi technologies could well be used to down-regulate any genes' expression without disrupting the expression of other genes. The use of RNA interference to silence genes in various organisms has become the preferred method for studying gene functions. The establishment of new approaches and applications for enhancing desirable characters is essential in crops by gene suppression and the refinement of knowledge of endogenous RNAi mechanisms in plants. RNAi technology in recent years has become an important and choicest method for controlling insects, pests, pathogens, and abiotic stresses like drought, salinity, and temperature. Although there are certain drawbacks in efficiency of this technology such as gene candidate selection, stability of trigger molecule, choice of target species and crops. Nevertheless, from past decade several target genes has been identified in numerous crops for their improvement towards biotic and abiotic stresses. The current review is aimed to emphasize the research done on crops under biotic and abiotic stress using RNAi technology. The review also highlights the gene regulatory pathways/gene silencing, RNA interference, RNAi knockdown, RNAi induced biotic and abiotic resistance and advancements in the understanding of RNAi technology and the functionality of various components of the RNAi machinery in crops for their improvement.
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Affiliation(s)
- Jothi Kanmani Bharathi
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Ramaswamy Anandan
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India
| | - Lincy Kirubhadharsini Benjamin
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| | - Muthu Arjuna Samy Prakash
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University, Annamalai Nagar, 608 002, Tamil Nadu, India.
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Mapuranga J, Chang J, Zhang L, Zhang N, Yang W. Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions. J Fungi (Basel) 2022; 9:4. [PMID: 36675825 PMCID: PMC9862911 DOI: 10.3390/jof9010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.
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Affiliation(s)
| | | | | | | | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Plant Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding 071001, China
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11
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Xu J, Zhang N, Wang K, Xian Q, Dong J, Chen X. Exploring new strategies in diseases resistance of horticultural crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1021350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Horticultural crops are susceptible to various biotic stressors including fungi, oomycetes, bacteria, viruses, and root-knot nematodes. These pathogens limit the growth, development, yield, and quality of horticultural crops, and also limit their adaptability and geographic distribution. The continuous cropping model in horticultural facilities exacerbates soil-borne diseases, and severely restricts yield, quality, and productivity. Recent progress in the understanding of mechanisms that confer tolerance to different diseases through innovative strategies including host-induced gene silencing (HIGS), targeting susceptibility genes, and rootstocks grafting applications are reviewed to systematically explore the resistance mechanisms against horticultural plant diseases. Future work should successfully breed resistant varieties using these strategies combined with molecular biologic methods.
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12
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Haidoulis JF, Nicholson P. Tissue-specific transcriptome responses to Fusarium head blight and Fusarium root rot. FRONTIERS IN PLANT SCIENCE 2022; 13:1025161. [PMID: 36352885 PMCID: PMC9637937 DOI: 10.3389/fpls.2022.1025161] [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: 08/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Fusarium head blight (FHB) and Fusarium root rot (FRR) are important diseases of small-grain cereals caused by Fusarium species. While host response to FHB has been subject to extensive study, very little is known about response to FRR and the transcriptome responses of FHB and FRR have not been thoroughly compared. Brachypodium distachyon (Bd) is an effective model for investigating host responses to both FHB and FRR. In this study the transcriptome response of Bd to F. graminearum (Fg) infection of heads and roots was investigated. An RNA-seq analysis was performed on both Bd FHB and FRR during the early infection. Additionally, an RNA-seq analysis was performed on in vitro samples of Fg for comparison with Fg gene expression in planta. Differential gene expression and gene-list enrichment analyses were used to compare FHB and FRR transcriptome responses in both Bd and Fg. Differential expression of selected genes was confirmed using RT-qPCR. Most genes associated with receptor signalling, cell-wall modification, oxidative stress metabolism, and cytokinin and auxin biosynthesis and signalling genes were generally upregulated in FHB or were downregulated in FRR. In contrast, Bd genes involved in jasmonic acid and ethylene biosynthesis and signalling, and antimicrobial production were similarly differentially expressed in both tissues in response to infection. A transcriptome analysis of predicted Fg effectors with the same infected material revealed elevated expression of core tissue-independent genes including cell-wall degradation enzymes and the gene cluster for DON production but also several tissue-dependent genes including those for aurofusarin production and cutin degradation. This evidence suggests that Fg modulates its transcriptome to different tissues of the same host.
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Affiliation(s)
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, England
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13
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Ray P, Sahu D, Aminedi R, Chandran D. Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:977502. [PMID: 37746174 PMCID: PMC10512274 DOI: 10.3389/ffunb.2022.977502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/19/2022] [Indexed: 09/26/2023]
Abstract
Existing, emerging, and reemerging strains of phytopathogenic fungi pose a significant threat to agricultural productivity globally. This risk is further exacerbated by the lack of resistance source(s) in plants or a breakdown of resistance by pathogens through co-evolution. In recent years, attenuation of essential pathogen gene(s) via double-stranded (ds) RNA-mediated RNA interference (RNAi) in host plants, a phenomenon known as host-induced gene silencing, has gained significant attention as a way to combat pathogen attack. Yet, due to biosafety concerns regarding transgenics, country-specific GMO legislation has limited the practical application of desirable attributes in plants. The topical application of dsRNA/siRNA targeting essential fungal gene(s) through spray-induced gene silencing (SIGS) on host plants has opened up a transgene-free avenue for crop protection. However, several factors influence the outcome of RNAi, including but not limited to RNAi mechanism in plant/fungi, dsRNA/siRNA uptake efficiency, dsRNA/siRNA design parameters, dsRNA stability and delivery strategy, off-target effects, etc. This review emphasizes the significance of these factors and suggests appropriate measures to consider while designing in silico and in vitro experiments for successful RNAi in open-field conditions. We also highlight prospective nanoparticles as smart delivery vehicles for deploying RNAi molecules in plant systems for long-term crop protection and ecosystem compatibility. Lastly, we provide specific directions for future investigations that focus on blending nanotechnology and RNAi-based fungal control for practical applications.
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Affiliation(s)
- Poonam Ray
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Debashish Sahu
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Raghavendra Aminedi
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Divya Chandran
- Laboratory of Plant-Microbe Interactions, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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14
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S S, Sharma S, Bairwa A, Tomar M, Kumar R, Bhardwaj V, Jeevalatha A, Bakade R, Salaria N, Thakur K, Singh BP, Chakrabarti SK. Spraying of dsRNA molecules derived from Phytophthora infestans, along with nanoclay carriers as a proof of concept for developing novel protection strategy for potato late blight. PEST MANAGEMENT SCIENCE 2022; 78:3183-3192. [PMID: 35478320 DOI: 10.1002/ps.6949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Phytophthora infestans is a late blight-causing oomycetes pathogen. It rapidly evolves and adapts to the host background and new fungicide molecules within a few years of their release, most likely because of the predominance of transposable elements in its genome. Frequent applications of fungicides cause environmental concerns. Here, we developed target-specific RNA interference (RNAi)-based molecules, along with nanoclay carriers, that when sprayed on plants are capable of effectively reducing late blight infection. RESULTS Targeted the genes unique to sporulation, early satge infection and the metabolism pathway stages based on in an our own microarray data. We used nanoclay as a carrier for sorbitol dehydrogenase, heat shock protein 90, translation elongation factor 1-α, phospholipase-D like 3 and glycosylphosphatidylinositol-anchored acidic serine-threonine-rich HAM34-like protein double-stranded (ds)RNAs, which were assessed by culture bioassay, detached leaf assay and spray methods, and revealed a reduction in growth, sporulation and symptom expression. Plants sprayed with multigene targeted dsRNA-nanoclay showed enhanced disease resistance (4% disease severity) and less sporulation (<1 × 103 ) compared with plants sprayed with dsRNA alone. CONCLUSION The use of nanoclay with multigene targeted dsRNA was assumed to be involved in effective delivery, protection and boosting the action of RNAi as a spray-induced gene silencing approach (SIGS). A significant reduction in growth, sporulation, disease severity and decreased gene expression authenticates the effects of SIGS on late blight progression. This study demonstrated as a proof of concept the dsRNA-nanoclay SIGS approach, which could be used as an alternative to chemical fungicides and transgenic approaches to develop an environmentally friendly novel plant protection strategy for late blight. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Sundaresha S
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Sanjeev Sharma
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Aarti Bairwa
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Maharishi Tomar
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
- Plant Biochemistry, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Ravinder Kumar
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Vinay Bhardwaj
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - A Jeevalatha
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
- Plant Protection, ICAR-Indian Institute of Spice Research, Kozhikode, India
| | - Rahul Bakade
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Neha Salaria
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Kajal Thakur
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - Bir Pal Singh
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
| | - S K Chakrabarti
- Plant Protection, ICAR-Central Potato Research Institute, Shimla, India
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15
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Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems. Nat Rev Mol Cell Biol 2022; 23:645-662. [PMID: 35710830 DOI: 10.1038/s41580-022-00496-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 11/08/2022]
Abstract
RNA silencing is a well-established antiviral immunity system in plants, in which small RNAs guide Argonaute proteins to targets in viral RNA or DNA, resulting in virus repression. Virus-encoded suppressors of silencing counteract this defence system. In this Review, we discuss recent findings about antiviral RNA silencing, including the movement of RNA through plasmodesmata and the differentiation between plant self and viral RNAs. We also discuss the emerging role of RNA silencing in plant immunity against non-viral pathogens. This immunity is mediated by transkingdom movement of RNA into and out of the infected plant cells in vesicles or as extracellular nucleoproteins and, like antiviral immunity, is influenced by the silencing suppressors encoded in the pathogens' genomes. Another effect of RNA silencing on general immunity involves host-encoded small RNAs, including microRNAs, that regulate NOD-like receptors and defence signalling pathways in the innate immunity system of plants. These RNA silencing pathways form a network of processes with both positive and negative effects on the immune systems of plants.
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16
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Rössner C, Lotz D, Becker A. VIGS Goes Viral: How VIGS Transforms Our Understanding of Plant Science. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:703-728. [PMID: 35138878 DOI: 10.1146/annurev-arplant-102820-020542] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Virus-induced gene silencing (VIGS) has developed into an indispensable approach to gene function analysis in a wide array of species, many of which are not amenable to stable genetic transformation. VIGS utilizes the posttranscriptional gene silencing (PTGS) machinery of plants to restrain viral infections systemically and is used to downregulate the plant's endogenous genes. Here, we review the molecular mechanisms of DNA- and RNA-virus-based VIGS, its inherent connection to PTGS, and what is known about the systemic spread of silencing. Recently, VIGS-based technologies have been expanded to enable not only gene silencing but also overexpression [virus-induced overexpression (VOX)], genome editing [virus-induced genome editing (VIGE)], and host-induced gene silencing (HIGS). These techniques expand the genetic toolbox for nonmodel organisms even more. Further, we illustrate the versatility of VIGS and the methods derived from it in elucidating molecular mechanisms, using tomato fruit ripening and programmed cell death as examples. Finally, we discuss challenges of and future perspectives on the use of VIGS to advance gene function analysis in nonmodel plants in the postgenomic era.
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Affiliation(s)
- Clemens Rössner
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
| | - Dominik Lotz
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
| | - Annette Becker
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
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17
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Rabuma T, Gupta OP, Chhokar V. Recent advances and potential applications of cross-kingdom movement of miRNAs in modulating plant's disease response. RNA Biol 2022; 19:519-532. [PMID: 35442163 PMCID: PMC9037536 DOI: 10.1080/15476286.2022.2062172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In the recent past, cross-kingdom movement of miRNAs, small (20–25 bases), and endogenous regulatory RNA molecules has emerged as one of the major research areas to understand the potential implications in modulating the plant’s biotic stress response. The current review discussed the recent developments in the mechanism of cross-kingdom movement (long and short distance) and critical cross-talk between host’s miRNAs in regulating gene function in bacteria, fungi, viruses, insects, and nematodes, and vice-versa during host-pathogen interaction and their potential implications in crop protection. Moreover, cross-kingdom movement during symbiotic interaction, the emerging role of plant’s miRNAs in modulating animal’s gene function, and feasibility of spray-induced gene silencing (SIGS) in combating biotic stresses in plants are also critically evaluated. The current review article analysed the horizontal transfer of miRNAs among plants, animals, and microbes that regulates gene expression in the host or pathogenic organisms, contributing to crop protection. Further, it highlighted the challenges and opportunities to harness the full potential of this emerging approach to mitigate biotic stress efficiently.
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Affiliation(s)
- Tilahun Rabuma
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA.,Department of Biotechnology, College of Natural and Computational Science, Wolkite University, Wolkite, Ethiopia
| | - Om Prakash Gupta
- Division of Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, INDIA
| | - Vinod Chhokar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, INDIA
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18
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Successful Silencing of the Mycotoxin Synthesis Gene TRI5 in Fusarium culmorum and Observation of Reduced Virulence in VIGS and SIGS Experiments. Genes (Basel) 2022; 13:genes13030395. [PMID: 35327949 PMCID: PMC8953179 DOI: 10.3390/genes13030395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
Crops constantly experience various biotic stresses during their life cycle, and Fusarium spp. remain one of the most serious groups of pathogens affecting plants. The ability to manipulate the expression of certain microorganism genes via RNAi creates the opportunity for new-generation dsRNA-based preparations to control a large number of diseases. In this study, we applied virus-induced gene silencing (VIGS), and spray-induced gene silencing (SIGS) to silence the trichothecene-producing gene TRI5 in F. culmorum as a means to reduce its aggressiveness on spring wheat. Treatment of the fungus with dsTRI5RNA in vitro reduced deoxynivalenol (DON) and 3-acetyldeoxynivalenol (3-A-DON) accumulations by 53–85% and 61–87%, respectively, and reduced TRI5 expression by 84–97%. VIGS decreased the proportion of infected wheat spikelets by 73%, but upregulation was observed for TRI5. SIGS on wheat leaves and ears using certain dsTRI5RNA amounts negatively impacted F. culmorum growth. However, when performing in vivo analyses of TRI5 mRNA levels, the upregulation of the gene was determined in the variants where fungal colonization was restricted, suggesting a compensatory reaction of the pathogen to RNAi.
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19
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RNAi technology for plant protection and its application in wheat. ABIOTECH 2021; 2:365-374. [PMID: 36304420 PMCID: PMC9590511 DOI: 10.1007/s42994-021-00036-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
The RNAi technology takes advantage of the intrinsic RNA interference (RNAi) mechanism that exists in nearly all eukaryotes in which target mRNAs are degraded or functionally suppressed. Significant progress has been made in recent years where RNAi technology is applied to several crops and economic plants for protection against diseases like fungi, pests, and nematode. RNAi technology is also applied in controlling pathogen damages in wheat, one of the most important crops in the world. In this review, we first give a brief introduction of the RNAi technology and the underneath mechanism. We then review the recent progress of its utilization in crops, particular wheat. Finally, we discuss the existing challenges and prospect future development of this technology in crop protection.
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20
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Hao G, McCormick S, Vaughan MM. Effects of Double-Stranded RNAs Targeting Fusarium graminearum TRI6 on Fusarium Head Blight and Mycotoxins. PHYTOPATHOLOGY 2021; 111:2080-2087. [PMID: 33823648 DOI: 10.1094/phyto-10-20-0468-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium graminearum is the causal agent of Fusarium head blight (FHB), which reduces crop yield and contaminates grains with poisonous trichothecene mycotoxins, including deoxynivalenol (DON). DON functions as an important virulence factor that promotes FHB spread in wheat; therefore, reducing DON production will decrease yield losses to FHB and increase food safety. Recent progress in the topical application of double-stranded RNA (dsRNA) to reduce F. graminearum infection has provided encouraging results. In this study, we designed and synthesized dsRNA targeting the transcription factor TRI6 (TRI6-dsRNA), which is a key regulator of DON biosynthesis. The expression of F. graminearum TRI6 was significantly lower in detached wheat heads treated with TRI6-dsRNA solution compared with the controls. Furthermore, TRI6-dsRNA treatments reduced disease and DON accumulation in inoculated detached wheat heads. Therefore, topical applications of TRI6-dsRNA on wheat heads of intact plants were assessed for their ability to reduce FHB and DON under growth chamber and greenhouse conditions. When wheat heads were treated with TRI6-dsRNA solution in growth chamber conditions, TRI6-dsRNA treatments failed to prevent FHB spread. However, when wheat heads were treated with TRI6-dsRNA solution under greenhouse conditions, FHB and DON were significantly reduced, and infection was restricted to the inoculated floret. In addition, addition of TRI6-dsRNA to toxin induction liquid media had no effect on F. graminearum 15-ADON production. Our study demonstrates that the efficacy of dsRNA applications is strongly dependent on application methods and environmental conditions.
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Affiliation(s)
- Guixia Hao
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604
| | - Susan McCormick
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604
| | - Martha M Vaughan
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604
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21
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Ding Y, Chen Y, Yan B, Liao H, Dong M, Meng X, Wan H, Qian W. Host-Induced Gene Silencing of a Multifunction Gene Sscnd1 Enhances Plant Resistance Against Sclerotinia sclerotiorum. Front Microbiol 2021; 12:693334. [PMID: 34690946 PMCID: PMC8531507 DOI: 10.3389/fmicb.2021.693334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022] Open
Abstract
Sclerotinia sclerotiorum is a devastating necrotrophic fungal pathogen and has a substantial economic impact on crop production worldwide. Magnaporthe appressoria-specific (MAS) proteins have been suggested to be involved in the appressorium formation in Magnaporthe oryzae. Sscnd1, an MAS homolog gene, is highly induced at the early infection stage of S. sclerotiorum. Knock-down the expression of Sscnd1 gene severely reduced the virulence of S. sclerotiorum on intact rapeseed leaves, and their virulence was partially restored on wounded leaves. The Sscnd1 gene-silenced strains exhibited a defect in compound appressorium formation and cell integrity. The instantaneous silencing of Sscnd1 by tobacco rattle virus (TRV)-mediated host-induced gene silencing (HIGS) resulted in a significant reduction in disease development in tobacco. Three transgenic HIGS Arabidopsis lines displayed high levels of resistance to S. sclerotiorum and decreased Sscnd1 expression. Production of specific Sscnd1 siRNA in transgenic HIGS Arabidopsis lines was confirmed by stem-loop qRT-PCR. This study revealed that the compound appressorium-related gene Sscnd1 is required for cell integrity and full virulence in S. sclerotiorum and that Sclerotinia stem rot can be controlled by expressing the silencing constructs of Sscnd1 in host plants.
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Affiliation(s)
- Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Yangui Chen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Baoqin Yan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Hongmei Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Mengquan Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Xinran Meng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Huafang Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China.,Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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22
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Schäfer P. microRNAs - Game-changers in plant symbioses. JOURNAL OF PLANT PHYSIOLOGY 2021; 263:153459. [PMID: 34198125 DOI: 10.1016/j.jplph.2021.153459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Patrick Schäfer
- Institute of Molecular Botany, Faculty of Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
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23
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Recent Progress in Enhancing Fungal Disease Resistance in Ornamental Plants. Int J Mol Sci 2021; 22:ijms22157956. [PMID: 34360726 PMCID: PMC8348885 DOI: 10.3390/ijms22157956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/19/2023] Open
Abstract
Fungal diseases pose a major threat to ornamental plants, with an increasing percentage of pathogen-driven host losses. In ornamental plants, management of the majority of fungal diseases primarily depends upon chemical control methods that are often non-specific. Host basal resistance, which is deficient in many ornamental plants, plays a key role in combating diseases. Despite their economic importance, conventional and molecular breeding approaches in ornamental plants to facilitate disease resistance are lagging, and this is predominantly due to their complex genomes, limited availability of gene pools, and degree of heterozygosity. Although genetic engineering in ornamental plants offers feasible methods to overcome the intrinsic barriers of classical breeding, achievements have mainly been reported only in regard to the modification of floral attributes in ornamentals. The unavailability of transformation protocols and candidate gene resources for several ornamental crops presents an obstacle for tackling the functional studies on disease resistance. Recently, multiomics technologies, in combination with genome editing tools, have provided shortcuts to examine the molecular and genetic regulatory mechanisms underlying fungal disease resistance, ultimately leading to the subsequent advances in the development of novel cultivars with desired fungal disease-resistant traits, in ornamental crops. Although fungal diseases constitute the majority of ornamental plant diseases, a comprehensive overview of this highly important fungal disease resistance seems to be insufficient in the field of ornamental horticulture. Hence, in this review, we highlight the representative mechanisms of the fungal infection-related resistance to pathogens in plants, with a focus on ornamental crops. Recent progress in molecular breeding, genetic engineering strategies, and RNAi technologies, such as HIGS and SIGS for the enhancement of fungal disease resistance in various important ornamental crops, is also described.
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24
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Yang P, Yi SY, Nian JN, Yuan QS, He WJ, Zhang JB, Liao YC. Application of Double-Strand RNAs Targeting Chitin Synthase, Glucan Synthase, and Protein Kinase Reduces Fusarium graminearum Spreading in Wheat. Front Microbiol 2021; 12:660976. [PMID: 34305830 PMCID: PMC8299488 DOI: 10.3389/fmicb.2021.660976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022] Open
Abstract
Controlling the devastating fungal pathogen Fusarium graminearum (Fg) is a challenge due to inadequate resistance in nature. Here, we report on the identification of RNAi molecules and their applications for controlling Fg in wheat through silencing chitin synthase 7 (Chs7), glucan synthase (Gls) and protein kinase C (Pkc). From transgenic Fg strains four RNAi constructs from Chs7 (Chs7RNAi−1, −2, −3, and −4), three RNAi constructs from Gls (GlsRNAi−2, −3, and −6), and one RNAi construct from Pkc (PkcRNAi−5) were identified that displayed effective silencing effects on mycelium growth in medium and pathogenicity in wheat spikes. Transcript levels of Chs7, Gls and Pkc were markedly reduced in those strains. Double-strand RNAs (dsRNAs) of three selected RNAi constructs (Chs7RNAi-4, GlsRNAi-6 and PkcRNA-5) strongly inhibited mycelium growth in vitro. Spray of those dsRNAs on detached wheat leaves significantly reduced lesion sizes; the independent dsRNAs showed comparable effects on lesions with combination of two or three dsRNAs. Expression of three targets Chs7, Gls, and Pkc was substantially down-regulated in Fg-infected wheat leaves. Further application of dsRNAs on wheat spikes in greenhouse significantly reduced infected spikelets. The identified RNAi constructs may be directly used for spray-induced gene silencing and stable expression in plants to control Fusarium pathogens in agriculture.
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Affiliation(s)
- Peng Yang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shu-Yuan Yi
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Forestry and Fruit Tree Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Jun-Na Nian
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qing-Song Yuan
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wei-Jie He
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jing-Bo Zhang
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu-Cai Liao
- Molecular Biotechnology Laboratory of Triticeae Crops, Huazhong Agricultural University, Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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25
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Zivanovic M, Chen ZY. In Vitro Screening of Various Bacterially Produced Double-Stranded RNAs for Silencing Cercospora cf. flagellaris Target Genes and Suppressing Cercosporin Production. PHYTOPATHOLOGY 2021; 111:1228-1237. [PMID: 33289403 DOI: 10.1094/phyto-09-20-0409-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cercospora leaf blight (CLB), primarily caused by Cercospora cf. flagellaris, is one of the most important diseases of soybean (Glycine max) in Louisiana. The pathogen produces cercosporin, a nonspecific toxin and an important virulence factor. There are no commercial cultivars with CLB resistance, and the pathogen has developed substantial resistance to the frequently used fungicides. Consequently, alternative methods are needed to manage CLB. One possibility is the RNA interference-based topical application of double-stranded (ds)RNA. The present study addressed the two most critical steps for this novel approach to be practical: inexpensively producing large quantities of dsRNA and identifying the right target genes for silencing. A screening method was developed to compare the effectiveness of Escherichia coli-produced dsRNAs targeting five fungal genes involved in cercosporin production for silencing in liquid culture. As much as 151.6 mg of dsRNA-containing total nucleic acids (TNAs) was produced from 1 liter of E. coli Luria broth culture using the L4440 vector. All tested dsRNAs reduced cercosporin production. However, significant target gene suppression was only detected in the cultures treated with dsRNAs from Avr4 and CTB8. The most potent dsRNA was from Avr4, which reduced 50% of cercosporin production at an estimated TNA concentration of 10.4 µg/ml (half maximal effective concentration [EC50]), and the least potent dsRNA was from HN-2, with an estimated EC50 of 46.7 µg/ml TNA. The present study paves the road for managing CLB under field conditions using dsRNA. Additionally, this approach could be adapted to identify the best dsRNAs to manage other fungal diseases.
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Affiliation(s)
- Marija Zivanovic
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
| | - Zhi-Yuan Chen
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803
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26
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Koch A, Wassenegger M. Host-induced gene silencing - mechanisms and applications. THE NEW PHYTOLOGIST 2021; 231:54-59. [PMID: 33774815 DOI: 10.1111/nph.17364] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/10/2021] [Indexed: 05/05/2023]
Abstract
Host-induced gene silencing (HIGS) technology has emerged as a powerful alternative to chemical treatments for protecting plants from pathogens or pests. More than 170 HIGS studies have been published so far, and HIGS products have been launched. First, we discuss the strengths and limitations of this technology in a pathosystem-specific context. Next, we highlight the requirement for fundamental knowledge on the molecular mechanisms (i.e. uptake, processing and translocation of transgene-expressed double-stranded RNAs) that determine the efficacy and specificity of HIGS. Additionally, we speculate on the contribution of host and target RNA interference machineries, which may be incompatible depending on the lifestyle of the pathogen or pest. Finally, we predict that closing these gaps in knowledge will lead to the development of novel integrative concepts, precise risk assessment and tailor-made HIGS therapy for plant diseases.
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Affiliation(s)
- Aline Koch
- Institute of Phytomedicine, University of Hohenheim, Otto-Sander-Straße 5, Stuttgart, D-70599, Germany
| | - Michael Wassenegger
- RLP AgroScience, Breitenweg 71, Neustadt, 67435, Germany
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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27
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Habig M, Schotanus K, Hufnagel K, Happel P, Stukenbrock EH. Ago1 Affects the Virulence of the Fungal Plant Pathogen Zymoseptoria tritici. Genes (Basel) 2021; 12:1011. [PMID: 34208898 PMCID: PMC8303167 DOI: 10.3390/genes12071011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/04/2022] Open
Abstract
In host-pathogen interactions RNA interference (RNAi) has emerged as a pivotal mechanism to modify both, the immune responses of the host as well as the pathogenicity and virulence of the pathogen. In addition, in some fungi RNAi is also known to affect chromosome biology via its effect on chromatin conformation. Previous studies reported no effect of the RNAi machinery on the virulence of the fungal plant pathogen Zymoseptoria tritici however the role of RNAi is still poorly understood in this species. Herein, we elucidate whether the RNAi machinery is conserved within the genus Zymoseptoria. Moreover, we conduct functional analyses of Argonaute and Dicer-like proteins and test if the RNAi machinery affects chromosome stability. We show that the RNAi machinery is conserved among closely related Zymoseptoria species while an exceptional pattern of allelic diversity was possibly caused by introgression. The deletion of Ago1 reduced the ability of the fungus to produce asexual propagules in planta in a quantitative matter. Chromosome stability of the accessory chromosome of Z. tritici was not prominently affected by the RNAi machinery. These results indicate, in contrast to previous finding, a role of the RNAi pathway during host infection, but not in the stability of accessory chromosomes in Z. tritici.
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Affiliation(s)
- Michael Habig
- Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 1-11, 24118 Kiel, Germany; (M.H.); (K.S.); (K.H.)
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Klaas Schotanus
- Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 1-11, 24118 Kiel, Germany; (M.H.); (K.S.); (K.H.)
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Kim Hufnagel
- Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 1-11, 24118 Kiel, Germany; (M.H.); (K.S.); (K.H.)
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany;
| | - Eva H. Stukenbrock
- Christian-Albrechts University of Kiel, Environmental Genomics, Am Botanischen Garten 1-11, 24118 Kiel, Germany; (M.H.); (K.S.); (K.H.)
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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Biotechnological Resources to Increase Disease-Resistance by Improving Plant Immunity: A Sustainable Approach to Save Cereal Crop Production. PLANTS 2021; 10:plants10061146. [PMID: 34199861 PMCID: PMC8229257 DOI: 10.3390/plants10061146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/17/2021] [Accepted: 05/29/2021] [Indexed: 12/16/2022]
Abstract
Plant diseases are globally causing substantial losses in staple crop production, undermining the urgent goal of a 60% increase needed to meet the food demand, a task made more challenging by the climate changes. Main consequences concern the reduction of food amount and quality. Crop diseases also compromise food safety due to the presence of pesticides and/or toxins. Nowadays, biotechnology represents our best resource both for protecting crop yield and for a science-based increased sustainability in agriculture. Over the last decades, agricultural biotechnologies have made important progress based on the diffusion of new, fast and efficient technologies, offering a broad spectrum of options for understanding plant molecular mechanisms and breeding. This knowledge is accelerating the identification of key resistance traits to be rapidly and efficiently transferred and applied in crop breeding programs. This review gathers examples of how disease resistance may be implemented in cereals by exploiting a combination of basic research derived knowledge with fast and precise genetic engineering techniques. Priming and/or boosting the immune system in crops represent a sustainable, rapid and effective way to save part of the global harvest currently lost to diseases and to prevent food contamination.
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RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges. PLANTS 2021; 10:plants10040650. [PMID: 33805521 PMCID: PMC8067263 DOI: 10.3390/plants10040650] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Plant pathogenic fungi are the largest group of disease-causing agents on crop plants and represent a persistent and significant threat to agriculture worldwide. Conventional approaches based on the use of pesticides raise social concern for the impact on the environment and human health and alternative control methods are urgently needed. The rapid improvement and extensive implementation of RNA interference (RNAi) technology for various model and non-model organisms has provided the initial framework to adapt this post-transcriptional gene silencing technology for the management of fungal pathogens. Recent studies showed that the exogenous application of double-stranded RNA (dsRNA) molecules on plants targeting fungal growth and virulence-related genes provided disease attenuation of pathogens like Botrytis cinerea, Sclerotinia sclerotiorum and Fusarium graminearum in different hosts. Such results highlight that the exogenous RNAi holds great potential for RNAi-mediated plant pathogenic fungal disease control. Production of dsRNA can be possible by using either in-vitro or in-vivo synthesis. In this review, we describe exogenous RNAi involved in plant pathogenic fungi and discuss dsRNA production, formulation, and RNAi delivery methods. Potential challenges that are faced while developing a RNAi strategy for fungal pathogens, such as off-target and epigenetic effects, with their possible solutions are also discussed.
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Ghosh S, Kant R, Pradhan A, Jha G. RS_CRZ1, a C2H2-Type Transcription Factor Is Required for Pathogenesis of Rhizoctonia solani AG1-IA in Tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:26-38. [PMID: 33030394 DOI: 10.1094/mpmi-05-20-0121-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Rhizoctonia solani is a necrotrophic fungal pathogen that causes disease in diverse plant species. In recent years, the genomic and transcriptomic studies have identified several candidate pathogenicity determinants of R. solani; however, most of them remain to be validated. In this study, we report a viral vector-based host-induced gene silencing (HIGS) as well as a dsRNA (double-stranded RNA)-based approach to effectively downregulate genes of R. solani AG1-IA (BRS1 strain) during pathogenesis in tomato. We tested a few of the in-planta upregulated R. solani genes and observed that silencing of one of them, i.e., RS_CRZ1 (a C2H2 type zinc finger transcription factor) significantly compromises the pathogenesis of R. solani in tomato. The RS_CRZ1-silenced plants not only exhibited significant reduction in disease symptoms, but the depth of pathogen colonization was also compromised. Furthermore, we identified the R. solani genes that were coregulated with RS_CRZ1 during the pathogenicity process. The HIGS-mediated silencing of a few of them [CL1756Contig1; subtilisin-like protease and CL1817Contig2; 2OG-Fe(II) oxygenase] compromised the pathogenesis of R. solani in tomato. The ectopic expression of RS_CRZ1 complemented the crz1 mutant of yeast and restored tolerance against various metal ion stress. Overall, our study reveals the importance of RS_CRZ1 in managing the hostile environment encountered during host colonization. Also, it emphasizes the relevance of the HIGS and dsRNA-based gene silencing approach toward functional characterization of pathogenicity determinants of R. solani.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Ravi Kant
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Amrita Pradhan
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Mahto BK, Singh A, Pareek M, Rajam MV, Dhar-Ray S, Reddy PM. Host-induced silencing of the Colletotrichum gloeosporioides conidial morphology 1 gene (CgCOM1) confers resistance against Anthracnose disease in chilli and tomato. PLANT MOLECULAR BIOLOGY 2020; 104:381-395. [PMID: 32803478 DOI: 10.1007/s11103-020-01046-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/06/2020] [Indexed: 05/22/2023]
Abstract
Host mediated silencing of COM1 gene of Colletotrichum gloeosporioides disables appressorial differentiation and effectively prevents the development of Anthracnose disease in chilli and tomato. Anthracnose disease is caused by the ascomycetes fungal species Colletotrichum, which is responsible for heavy yield losses in chilli and tomato worldwide. Conventionally, harmful pesticides are used to contain anthracnose disease with limited success. In this study, we assessed the potential of Host-Induced Gene Silencing (HIGS) approach to target the Colletotrichum gloeosporioides COM1 (CgCOM1) developmental gene involved in the fungal conidial and appressorium formation, to restrict fungal infection in chilli and tomato fruits. For this study, we have developed stable transgenic lines of chilli and tomato expressing CgCOM1-RNAi construct employing Agrobacterium-mediated transformation. Transgenic plants were characterized by molecular and gene expression analyses. Production of specific CgCOM1 siRNA in transgenic chilli and tomato RNAi lines was confirmed by stem-loop RT-PCR. Fungal challenge assays on leaves and fruits showed that the transgenic lines were resistant to anthracnose disease-causing C. gloeosporioides in comparison to wild type and empty-vector control plants. RT-qPCR analyses in transgenic lines revealed extremely low abundance of CgCOM1 transcripts in the C. gloeosporioides infected tissues, indicating near complete silencing of CgCOM1 gene expression in the pathogen. Microscopic examination of the Cg-challenged leaves of chilli-CgCOM1i lines revealed highly suppressed conidial germination, germ tube development, appressoria formation and mycelial growth of C. gloeosporioides, resulting in reduced infection of plant tissues. These results demonstrated highly efficient use of HIGS in silencing the expression of essential fungal developmental genes to inhibit the growth of pathogenic fungi, thus providing a highly precise approach to arrest the spread of disease.
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Affiliation(s)
- Binod Kumar Mahto
- TERI School of Advanced Studies, 10 Institutional Area, New Delhi, 110070, India
- The Energy and Resources Institute, Lodi Road, New Delhi, 110003, India
| | - Anjulata Singh
- TERI School of Advanced Studies, 10 Institutional Area, New Delhi, 110070, India
- The Energy and Resources Institute, Lodi Road, New Delhi, 110003, India
| | - Manish Pareek
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Manchikatla V Rajam
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | | | - Pallavolu M Reddy
- The Energy and Resources Institute, Lodi Road, New Delhi, 110003, India.
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Tiwari RK, Kumar R, Sharma S, Sagar V, Aggarwal R, Naga KC, Lal MK, Chourasia KN, Kumar D, Kumar M. Potato dry rot disease: current status, pathogenomics and management. 3 Biotech 2020; 10:503. [PMID: 33163322 DOI: 10.1007/s13205-020-02496-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
Potato dry rot disease caused by Fusarium species is a major threat to global potato production. The soil and seed-borne diseases influence the crop stand by inhibiting the development of potato sprouts and cause severe rots in seed tubers, table and processing purpose potatoes in cold stores. The symptoms of the dry rot include sunken and wrinkled brown to black tissue patches on tubers having less dry matter and shriveled flesh. Fungal infection accompanied by toxin development in the rotten tubers raises more concern for consumer health. The widespread dry rot causing fungal species (Fusarium graminearum) is reported to have a hemibiotrophic lifestyle. A cascade of enzymes, toxins and small secreted proteins are involved in the pathogenesis of these hemibiotrophs. With the availability of the genome sequence of the most devastating species Fusarium sambucinum, it is important to identify the potential pathogenicity factors and small secreted proteins that will help in designing management strategies. Limited resistant cultivars and the emergence of fungicide-resistant strains have made it more threatening for potato cultivation and trade. Several novel fungicide molecules (Azoxystrobin, chlorothalonil and fludioxonil), are found very effective as tuber treatment chemicals. Besides, many beneficial bioagents and safer chemicals have shown antibiosis and mycoparasitism against this pathogen. Germplasm screening for dry rot resistance is important to assist the resistance breeding program for the development of resistant cultivars. This review aims to draw attention to the symptomatology, infection process, pathogenomics, the role of toxins and management approaches for potato dry rot disease, which is very much critical in designing better management strategies.
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Affiliation(s)
- Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Vinay Sagar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Rashmi Aggarwal
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | | | - Dharmendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
| | - Manoj Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh 171 001 India
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Abstract
Plant diseases caused by a variety of pathogens can have severe effects on crop plants and even plants in natural ecosystems. Despite many effective conventional approaches to control plant diseases, new, efficacious, environmentally sound and cost-effective approaches are needed, particularly with our increasing human population and the effects on crop production and plant health caused by climate change. RNA interference (RNAi) is a gene regulation and antiviral response mechanism in eukaryotes; transgenic and non transgenic plant-based RNAi approaches have shown great effectiveness and potential to target specific plant pathogens and help control plant diseases, especially when no alternatives are available. Here we discuss ways in which RNAi has been used against different plant pathogens, and some new potential applications for plant disease control.
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Teli B, Purohit J, Rashid MM, Jailani AAK, Chattopadhyay A. Omics Insight on Fusarium Head Blight of Wheat for Translational Research Perspective. Curr Genomics 2020; 21:411-428. [PMID: 33093804 PMCID: PMC7536796 DOI: 10.2174/1389202921999200620222631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/28/2020] [Accepted: 05/13/2020] [Indexed: 01/11/2023] Open
Abstract
In the scenario of global warming and climate change, an outbreak of new pests and pathogens has become a serious concern owing to the rapid emergence of arms races, their epidemic infection, and the ability to break down host resistance, etc. Fusarium head blight (FHB) is one such evidence that depredates major cereals throughout the world. The symptomatological perplexity and aetiological complexity make this disease very severe, engendering significant losses in the yield. Apart from qualitative and quantitative losses, mycotoxin production solemnly deteriorates the grain quality in addition to life endangerment of humans and animals after consumption of toxified grains above the permissible limit. To minimize this risk, we must be very strategic in designing sustainable management practices constituting cultural, biological, chemical, and host resistance approaches. Even though genetic resistance is the most effective and environmentally safe strategy, a huge genetic variation and unstable resistance response limit the holistic deployment of resistance genes in FHB management. Thus, the focus must shift towards the editing of susceptible (S) host proteins that are soft targets of newly evolving effector molecules, which ultimately could be exploited to repress the disease development process. Hence, we must understand the pathological, biochemical, and molecular insight of disease development in a nutshell. In the present time, the availability of functional genomics, proteomics, and metabolomics information on host-pathogen interaction in FHB have constructed various networks which helped in understanding the pathogenesis and coherent host response(s). So now translation of this information for designing of host defense in the form of desirable resistant variety/genotype is the next step. The insights collected and presented in this review will be aiding in the understanding of the disease and apprise a solution to the multi-faceted problems which are related to FHB resistance in wheat and other cereals to ensure global food safety and food security.
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Affiliation(s)
- Basavaraj Teli
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Jyotika Purohit
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Md Mahtab Rashid
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - A Abdul Kader Jailani
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Anirudha Chattopadhyay
- 1Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India; 2Department of Plant Pathology, C.P. College of Agriculture, S.D. Agricultural University, S.K. Nagar, India; 3Plant RNAi Biology Group, I.C.G.E.B., New Delhi, India; 4Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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Forster H, Shuai B. Exogenous siRNAs against chitin synthase gene suppress the growth of the pathogenic fungus Macrophomina phaseolina. Mycologia 2020; 112:699-710. [DOI: 10.1080/00275514.2020.1753467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Heather Forster
- Department of Biological Sciences, Wichita State University, 1845 Fairmount Street, Wichita, Kansas 67260
| | - Bin Shuai
- Department of Biological Sciences, Wichita State University, 1845 Fairmount Street, Wichita, Kansas 67260
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36
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Hu D, Chen Z, Zhang C, Ganiger M. Reduction of Phakopsora pachyrhizi infection on soybean through host- and spray-induced gene silencing. MOLECULAR PLANT PATHOLOGY 2020; 21:794-807. [PMID: 32196911 PMCID: PMC7214474 DOI: 10.1111/mpp.12931] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/23/2020] [Accepted: 02/19/2020] [Indexed: 05/10/2023]
Abstract
Asian soybean rust (ASR), caused by the obligate fungal pathogen Phakopsora pachyrhizi, often leads to significant yield losses and can only be managed through fungicide applications currently. In the present study, eight urediniospore germination or appressorium formation induced P. pachyrhizi genes were investigated for their feasibility to suppress ASR through a bean pod mottle virus (BPMV)-based host-induced gene silencing (HIGS) strategy. Soybean plants expressing three of these modified BPMV vectors suppressed the expression of their corresponding target gene by 45%-80%, fungal biomass accumulation by 58%-80%, and significantly reduced ASR symptom development in soybean leaves after the plants were inoculated with P. pachyrhizi, demonstrating that HIGS can be used to manage ASR. In addition, when the in vitro synthesized double-stranded RNAs (dsRNAs) for three of the genes encoding an acetyl-CoA acyltransferase, a 40S ribosomal protein S16, and glycine cleavage system H protein were sprayed directly onto detached soybean leaves prior to P. pachyrhizi inoculation, they also resulted in an average of over 73% reduction of pustule numbers and 75% reduction in P. pachyrhizi biomass accumulation on the detached leaves compared to the controls. To the best of our knowledge, this is the first report of suppressing P. pachyrhizi infection in soybean through both HIGS and spray-induced gene silencing. It was demonstrated that either HIGS constructs targeting P. pachyrhizi genes or direct dsRNA spray application could be an effective strategy for reducing ASR development on soybean.
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Affiliation(s)
- Dongfang Hu
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Zhi‐Yuan Chen
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
| | - Chunquan Zhang
- Department of AgricultureAlcorn State UniversityLormanMSUSA
| | - Mala Ganiger
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLAUSA
- Present address:
Department of Plant PathologyUniversity of MinnesotaSt. PaulMNUSA
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Ma Z, Xie Q, Li G, Jia H, Zhou J, Kong Z, Li N, Yuan Y. Germplasms, genetics and genomics for better control of disastrous wheat Fusarium head blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1541-1568. [PMID: 31900498 DOI: 10.1007/s00122-019-03525-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/23/2019] [Indexed: 05/20/2023]
Abstract
Fusarium head blight (FHB), or scab, for its devastating nature to wheat production and food security, has stimulated worldwide attention. Multidisciplinary efforts have been made to fight against FHB for a long time, but the great progress has been achieved only in the genomics era of the past 20 years, particularly in the areas of resistance gene/QTL discovery, resistance mechanism elucidation and molecular breeding for better resistance. This review includes the following nine main sections, (1) FHB incidence, epidemic and impact, (2) causal Fusarium species, distribution and virulence, (3) types of host resistance to FHB, (4) germplasm exploitation for FHB resistance, (5) genetic control of FHB resistance, (6) fine mapping of Fhb1, Fhb2, Fhb4 and Fhb5, (7) cloning of Fhb1, (8) omics-based gene discovery and resistance mechanism study and (9) breeding for better FHB resistance. The advancements that have been made are outstanding and exciting; however, judged by the complicated nature of resistance to hemi-biotrophic pathogens like Fusarium species and lack of immune germplasm, it is still a long way to go to overcome FHB.
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Affiliation(s)
- Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Quan Xie
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Guoqiang Li
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Haiyan Jia
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jiyang Zhou
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhongxin Kong
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Na Li
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yang Yuan
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Pathogenomics and Management of Fusarium Diseases in Plants. Pathogens 2020; 9:pathogens9050340. [PMID: 32369942 PMCID: PMC7281180 DOI: 10.3390/pathogens9050340] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
There is an urgency to supplant the heavy reliance on chemical control of Fusarium diseases in different economically important, staple food crops due to development of resistance in the pathogen population, the high cost of production to the risk-averse grower, and the concomitant environmental impacts. Pathogenomics has enabled (i) the creation of genetic inventories which identify those putative genes, regulators, and effectors that are associated with virulence, pathogenicity, and primary and secondary metabolism; (ii) comparison of such genes among related pathogens; (iii) identification of potential genetic targets for chemical control; and (iv) better characterization of the complex dynamics of host–microbe interactions that lead to disease. This type of genomic data serves to inform host-induced gene silencing (HIGS) technology for targeted disruption of transcription of select genes for the control of Fusarium diseases. This review discusses the various repositories and browser access points for comparison of genomic data, the strategies for identification and selection of pathogenicity- and virulence-associated genes and effectors in different Fusarium species, HIGS and successful Fusarium disease control trials with a consideration of loss of RNAi, off-target effects, and future challenges in applying HIGS for management of Fusarium diseases.
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Wang K, Gong Q, Ye X. Recent developments and applications of genetic transformation and genome editing technologies in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1603-1622. [PMID: 31654081 DOI: 10.1007/s00122-019-03464-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/19/2019] [Indexed: 05/24/2023]
Abstract
Wheat (Triticum aestivum) is a staple crop across the world and plays a remarkable role in food supplying security. Over the past few decades, basic and applied research on wheat has lagged behind other cereal crops due to the complex and polyploid genome and difficulties in genetic transformation. A breakthrough called as PureWheat was made in the genetic transformation of wheat in 2014 in Asia, leading to a noticeable progress of wheat genome editing. Due to this great achievement, it is predicated that wheat biotechnology revolution is arriving. Genome editing technologies using zinc finger nucleases, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats-associated endonucleases (CRISR/Cas) are becoming powerful tools for crop modification which can help biologists and biotechnologists better understand the processes of mutagenesis and genomic alteration. Among the three genome editing systems, CRISR/Cas has high specificity and activity, and therefore it is widely used in genetic engineering. Generally, the genome editing technologies depend on an efficient genetic transformation system. In this paper, we summarize recent progresses and applications on genetic transformation and genome editing in wheat. We also examine the future aspects of genetic transformation and genome editing. We believe that the technologies for wheat efficient genetic engineering and functional studies will become routine with the emergence of high-quality genomic sequences.
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Affiliation(s)
- Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Gong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingguo Ye
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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40
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Werner BT, Gaffar FY, Schuemann J, Biedenkopf D, Koch AM. RNA-Spray-Mediated Silencing of Fusarium graminearum AGO and DCL Genes Improve Barley Disease Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:476. [PMID: 32411160 DOI: 10.1101/821868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 03/30/2020] [Indexed: 05/24/2023]
Abstract
Over the last decade, several studies have revealed the enormous potential of RNA-silencing strategies as a potential alternative to conventional pesticides for plant protection. We have previously shown that targeted gene silencing mediated by an in planta expression of non-coding inhibitory double-stranded RNAs (dsRNAs) can protect host plants against various diseases with unprecedented efficiency. In addition to the generation of RNA-silencing (RNAi) signals in planta, plants can be protected from pathogens, and pests by spray-applied RNA-based biopesticides. Despite the striking efficiency of RNA-silencing-based technologies holds for agriculture, the molecular mechanisms underlying spray-induced gene silencing (SIGS) strategies are virtually unresolved, a requirement for successful future application in the field. Based on our previous work, we predict that the molecular mechanism of SIGS is controlled by the fungal-silencing machinery. In this study, we used SIGS to compare the silencing efficiencies of computationally-designed vs. manually-designed dsRNA constructs targeting ARGONAUTE and DICER genes of Fusarium graminearum (Fg). We found that targeting key components of the fungal RNAi machinery via SIGS could protect barley leaves from Fg infection and that the manual design of dsRNAs resulted in higher gene-silencing efficiencies than the tool-based design. Moreover, our results indicate the possibility of cross-kingdom RNA silencing in the Fg-barley interaction, a phenomenon in which sRNAs operate as effector molecules to induce gene silencing between species from different kingdoms, such as a plant host and their interacting pathogens.
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Affiliation(s)
- Bernhard Timo Werner
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Johannes Schuemann
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Dagmar Biedenkopf
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Aline Michaela Koch
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
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41
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Wang M, Dean RA. Movement of small RNAs in and between plants and fungi. MOLECULAR PLANT PATHOLOGY 2020; 21:589-601. [PMID: 32027079 PMCID: PMC7060135 DOI: 10.1111/mpp.12911] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/02/2019] [Accepted: 12/06/2019] [Indexed: 05/12/2023]
Abstract
RNA interference is a biological process whereby small RNAs inhibit gene expression through neutralizing targeted mRNA molecules. This process is conserved in eukaryotes. Here, recent work regarding the mechanisms of how small RNAs move within and between organisms is examined. Small RNAs can move locally and systemically in plants through plasmodesmata and phloem, respectively. In fungi, transportation of small RNAs may also be achieved by septal pores and vesicles. Recent evidence also supports bidirectional cross-kingdom communication of small RNAs between host plants and adapted fungal pathogens to affect the outcome of infection. We discuss several mechanisms for small RNA trafficking and describe evidence for transport through naked form, combined with RNA-binding proteins or enclosed by vesicles.
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Affiliation(s)
- Mengying Wang
- Fungal Genomics LaboratoryCenter for Integrated Fungal ResearchDepartment of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Ralph A. Dean
- Fungal Genomics LaboratoryCenter for Integrated Fungal ResearchDepartment of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
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42
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Höfle L, Biedenkopf D, Werner BT, Shrestha A, Jelonek L, Koch A. Study on the efficiency of dsRNAs with increasing length in RNA-based silencing of the Fusarium CYP51 genes. RNA Biol 2020. [PMID: 31814508 DOI: 10.1101/824953] [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: 05/08/2023] Open
Abstract
Previously, we have demonstrated that transgenic Arabidopsis and barley plants, expressing a 791 nucleotide (nt) dsRNA (CYP3RNA) that targets all three CYP51 genes (FgCYP51A, FgCYP51B, FgCYP51C) in Fusarium graminearum (Fg), inhibited fungal infection via a process designated as host-induced gene silencing (HIGS). More recently, we have shown that spray applications of CYP3RNA also protect barley from fungal infection via a process termed spray-induced gene silencing (SIGS). Thus, RNAi technology may have the potential to revolutionize plant protection in agriculture. Therefore, successful field application will require optimization of RNAi design necessary to maximize the efficacy of the RNA silencing construct for making RNAi-based strategies a realistic and sustainable approach in agriculture. Previous studies indicate that silencing is correlated with the number of siRNAs generated from a dsRNA precursor. To prove the hypothesis that silencing efficiency is correlated with the number of siRNAs processed out of the dsRNA precursor, we tested in a HIGS and SIGS approach dsRNA precursors of increasing length ranging from 400 nt to 1500 nt to assess gene silencing efficiency of individual FgCYP51 genes. Concerning HIGS-mediated disease control, we found that there is no significant correlation between the length of the dsRNA precursor and the reduction of Fg infection on CYP51-dsRNA-expressing Arabidopsis plants. Importantly and in clear contrast to HIGS, we measured a decrease in SIGS-mediated Fg disease resistance that significantly correlates with the length of the dsRNA construct that was sprayed, indicating that the size of the dsRNA interferes with a sufficient uptake of dsRNAs by the fungus.
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Affiliation(s)
- L Höfle
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - D Biedenkopf
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - B T Werner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - A Shrestha
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute, Braunschweig, Germany
| | - L Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - A Koch
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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43
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Omics applications: towards a sustainable protection of tomato. Appl Microbiol Biotechnol 2020; 104:4185-4195. [PMID: 32185431 DOI: 10.1007/s00253-020-10500-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
Abstract
Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.
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Schaefer LK, Parlange F, Buchmann G, Jung E, Wehrli A, Herren G, Müller MC, Stehlin J, Schmid R, Wicker T, Keller B, Bourras S. Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:253. [PMID: 32211008 PMCID: PMC7076181 DOI: 10.3389/fpls.2020.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Cross-kingdom RNA interference (RNAi) is a biological process allowing plants to transfer small regulatory RNAs to invading pathogens to trigger the silencing of target virulence genes. Transient assays in cereal powdery mildews suggest that silencing of one or two effectors could lead to near loss of virulence, but evidence from stable RNAi lines is lacking. We established transient host-induced gene silencing (HIGS) in wheat, and demonstrate that targeting an essential housekeeping gene in the wheat powdery mildew pathogen (Blumeria graminis f. sp. tritici) results in significant reduction of virulence at an early stage of infection. We generated stable transgenic RNAi wheat lines encoding a HIGS construct simultaneously silencing three B.g. tritici effectors including SvrPm3 a1/f1 , a virulence factor involved in the suppression of the Pm3 powdery mildew resistance gene. We show that all targeted effectors are effectively downregulated by HIGS, resulting in reduced fungal virulence on adult wheat plants. Our findings demonstrate that stable HIGS of effector genes can lead to quantitative gain of resistance without major pleiotropic effects in wheat.
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Affiliation(s)
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Andreas Wehrli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jonas Stehlin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Roman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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45
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Guo H, Ji J, Wang J, Sun X. Deoxynivalenol: Masked forms, fate during food processing, and potential biological remedies. Compr Rev Food Sci Food Saf 2020; 19:895-926. [DOI: 10.1111/1541-4337.12545] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 12/24/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Hongyan Guo
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and NutritionJiangnan University Wuxi China
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and NutritionJiangnan University Wuxi China
| | - Jia‐sheng Wang
- Department of Environmental ToxicologyUniversity of Georgia Athens Georgia
| | - Xiulan Sun
- State Key Laboratory of Food Science and Technology, School of Food Science, National Engineering Research Center for Functional Foods, Synergetic Innovation Center of Food Safety and NutritionJiangnan University Wuxi China
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46
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Höfle L, Biedenkopf D, Werner BT, Shrestha A, Jelonek L, Koch A. Study on the efficiency of dsRNAs with increasing length in RNA-based silencing of the Fusarium CYP51 genes. RNA Biol 2020; 17:463-473. [PMID: 31814508 DOI: 10.1080/15476286.2019.1700033] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Previously, we have demonstrated that transgenic Arabidopsis and barley plants, expressing a 791 nucleotide (nt) dsRNA (CYP3RNA) that targets all three CYP51 genes (FgCYP51A, FgCYP51B, FgCYP51C) in Fusarium graminearum (Fg), inhibited fungal infection via a process designated as host-induced gene silencing (HIGS). More recently, we have shown that spray applications of CYP3RNA also protect barley from fungal infection via a process termed spray-induced gene silencing (SIGS). Thus, RNAi technology may have the potential to revolutionize plant protection in agriculture. Therefore, successful field application will require optimization of RNAi design necessary to maximize the efficacy of the RNA silencing construct for making RNAi-based strategies a realistic and sustainable approach in agriculture. Previous studies indicate that silencing is correlated with the number of siRNAs generated from a dsRNA precursor. To prove the hypothesis that silencing efficiency is correlated with the number of siRNAs processed out of the dsRNA precursor, we tested in a HIGS and SIGS approach dsRNA precursors of increasing length ranging from 400 nt to 1500 nt to assess gene silencing efficiency of individual FgCYP51 genes. Concerning HIGS-mediated disease control, we found that there is no significant correlation between the length of the dsRNA precursor and the reduction of Fg infection on CYP51-dsRNA-expressing Arabidopsis plants. Importantly and in clear contrast to HIGS, we measured a decrease in SIGS-mediated Fg disease resistance that significantly correlates with the length of the dsRNA construct that was sprayed, indicating that the size of the dsRNA interferes with a sufficient uptake of dsRNAs by the fungus.
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Affiliation(s)
- L Höfle
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - D Biedenkopf
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - B T Werner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - A Shrestha
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute, Braunschweig, Germany
| | - L Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - A Koch
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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47
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Su X, Lu G, Li X, Rehman L, Liu W, Sun G, Guo H, Wang G, Cheng H. Host-Induced Gene Silencing of an Adenylate Kinase Gene Involved in Fungal Energy Metabolism Improves Plant Resistance to Verticillium dahliae. Biomolecules 2020; 10:E127. [PMID: 31940882 PMCID: PMC7023357 DOI: 10.3390/biom10010127] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
Verticillium wilt, caused by the ascomycete fungus Verticillium dahliae (Vd), is a devastating disease of numerous plant species. However, the pathogenicity/virulence-related genes in this fungus, which may be potential targets for improving plant resistance, remain poorly elucidated. For the study of these genes in Vd, we used a well-established host-induced gene silencing (HIGS) approach and identified 16 candidate genes, including a putative adenylate kinase gene (VdAK). Transiently VdAK-silenced plants developed milder wilt symptoms than control plants did. VdAK-knockout mutants were more sensitive to abiotic stresses and had reduced germination and virulence on host plants. Transgenic Nicotiana benthamiana and Arabidopsis thaliana plants that overexpressed VdAK dsRNAs had improved Vd resistance than the wild-type. RT-qPCR results showed that VdAK was also crucial for energy metabolism. Importantly, in an analysis of total small RNAs from Vd strains isolated from the transgenic plants, a small interfering RNA (siRNA) targeting VdAK was identified in transgenic N. benthamiana. Our results demonstrate that HIGS is a promising strategy for efficiently screening pathogenicity/virulence-related genes of Vd and that VdAK is a potential target to control this fungus.
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Affiliation(s)
- Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Guoqing Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Xiaokang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Latifur Rehman
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
- Department of Biotechnology, University of Swabi, Khyber Pakhtunkhwa 23561, Pakistan
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Huiming Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
| | - Guoliang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
| | - Hongmei Cheng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.S.); (G.L.); (X.L.); (L.R.); (G.S.); (H.G.)
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48
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Werner BT, Gaffar FY, Schuemann J, Biedenkopf D, Koch AM. RNA-Spray-Mediated Silencing of Fusarium graminearum AGO and DCL Genes Improve Barley Disease Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:476. [PMID: 32411160 PMCID: PMC7202221 DOI: 10.3389/fpls.2020.00476] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 03/30/2020] [Indexed: 05/21/2023]
Abstract
Over the last decade, several studies have revealed the enormous potential of RNA-silencing strategies as a potential alternative to conventional pesticides for plant protection. We have previously shown that targeted gene silencing mediated by an in planta expression of non-coding inhibitory double-stranded RNAs (dsRNAs) can protect host plants against various diseases with unprecedented efficiency. In addition to the generation of RNA-silencing (RNAi) signals in planta, plants can be protected from pathogens, and pests by spray-applied RNA-based biopesticides. Despite the striking efficiency of RNA-silencing-based technologies holds for agriculture, the molecular mechanisms underlying spray-induced gene silencing (SIGS) strategies are virtually unresolved, a requirement for successful future application in the field. Based on our previous work, we predict that the molecular mechanism of SIGS is controlled by the fungal-silencing machinery. In this study, we used SIGS to compare the silencing efficiencies of computationally-designed vs. manually-designed dsRNA constructs targeting ARGONAUTE and DICER genes of Fusarium graminearum (Fg). We found that targeting key components of the fungal RNAi machinery via SIGS could protect barley leaves from Fg infection and that the manual design of dsRNAs resulted in higher gene-silencing efficiencies than the tool-based design. Moreover, our results indicate the possibility of cross-kingdom RNA silencing in the Fg-barley interaction, a phenomenon in which sRNAs operate as effector molecules to induce gene silencing between species from different kingdoms, such as a plant host and their interacting pathogens.
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Affiliation(s)
- Bernhard Timo Werner
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | | | - Johannes Schuemann
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Dagmar Biedenkopf
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
| | - Aline Michaela Koch
- Centre for BioSystems, Land Use and Nutrition, Institute of Phytopathology, Justus Liebig University Giessen, Giessen, Germany
- *Correspondence: Aline Michaela Koch,
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49
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Janowska-Sejda EI, Lysenko A, Urban M, Rawlings C, Tsoka S, Hammond-Kosack KE. PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. Front Microbiol 2019; 10:2721. [PMID: 31866958 PMCID: PMC6908471 DOI: 10.3389/fmicb.2019.02721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 11/08/2019] [Indexed: 12/28/2022] Open
Abstract
Interactions between proteins underlie all aspects of complex biological mechanisms. Therefore, methodologies based on complex network analyses can facilitate identification of promising candidate genes involved in phenotypes of interest and put this information into appropriate contexts. To facilitate discovery and gain additional insights into globally important pathogenic fungi, we have reconstructed computationally inferred interactomes using an interolog and domain-based approach for 15 diverse Ascomycete fungal species, across nine orders, specifically Aspergillus fumigatus, Bipolaris sorokiniana, Blumeria graminis f. sp. hordei, Botrytis cinerea, Colletotrichum gloeosporioides, Colletotrichum graminicola, Fusarium graminearum, Fusarium oxysporum f. sp. lycopersici, Fusarium verticillioides, Leptosphaeria maculans, Magnaporthe oryzae, Saccharomyces cerevisiae, Sclerotinia sclerotiorum, Verticillium dahliae, and Zymoseptoria tritici. Network cartography analysis was associated with functional patterns of annotated genes linked to the disease-causing ability of each pathogen. In addition, for the best annotated organism, namely F. graminearum, the distribution of annotated genes with respect to network structure was profiled using a random walk with restart algorithm, which suggested possible co-location of virulence-related genes in the protein–protein interaction network. In a second ‘use case’ study involving two networks, namely B. cinerea and F. graminearum, previously identified small silencing plant RNAs were mapped to their targets. The F. graminearum phenotypic network analysis implicates eight B. cinerea targets and 35 F. graminearum predicted interacting proteins as prime candidate virulence genes for further testing. All 15 networks have been made accessible for download at www.phi-base.org providing a rich resource for major crop plant pathogens.
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Affiliation(s)
- Elzbieta I Janowska-Sejda
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom.,Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom.,Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Artem Lysenko
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Chris Rawlings
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
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50
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Koch A, Höfle L, Werner BT, Imani J, Schmidt A, Jelonek L, Kogel K. SIGS vs HIGS: a study on the efficacy of two dsRNA delivery strategies to silence Fusarium FgCYP51 genes in infected host and non-host plants. MOLECULAR PLANT PATHOLOGY 2019; 20:1636-1644. [PMID: 31603277 PMCID: PMC6859480 DOI: 10.1111/mpp.12866] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CYP3RNA, a double-stranded (ds)RNA designed to concomitantly target the two sterol 14α-demethylase genes FgCYP51A and FgCYP51B and the fungal virulence factor FgCYP51C, inhibits the growth of the ascomycete fungus Fusarium graminearum (Fg) in vitro and in planta. Here we compare two different methods (setups) of dsRNA delivery, viz. transgene expression (host-induced gene silencing, HIGS) and spray application (spray-induced gene silencing, SIGS), to assess the activity of CYP3RNA and novel dsRNA species designed to target one or two FgCYP51 genes. Using Arabidopsis and barley, we found that dsRNA designed to target two FgCYP51 genes inhibited fungal growth more efficiently than dsRNA targeting a single gene, although both dsRNA species reduced fungal infection. Either dsRNA delivery method reduced fungal growth stronger than anticipated from previous mutational knock-out (KO) strategies, where single gene KO had no significant effect on fungal viability. Consistent with the strong inhibitory effects of the dsRNAs on fungal development in both setups, we detected to a large extent dsRNA-mediated co-silencing of respective non-target FgCYP51 genes. Together, our data further support the valuation that dsRNA applications have an interesting potential for pesticide target validation and gene function studies, apart from their potential for crop protection.
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Affiliation(s)
- Aline Koch
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Lisa Höfle
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Bernhard Timo Werner
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Jafargholi Imani
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Alexandra Schmidt
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems BiologyJustus Liebig UniversityHeinrich‐Buff‐Ring 58D‐35392GiessenGermany
| | - Karl‐Heinz Kogel
- Institute of PhytopathologyCentre for BioSystemsLand Use and NutritionJustus Liebig UniversityHeinrich‐Buff‐Ring 26D‐35392GiessenGermany
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