RNA Interference Strategies for Future Management of Plant Pathogenic Fungi: Prospects and Challenges

RNAi-biofungicides: a quantum leap for tree fungal pathogen management

Fungal diseases threaten the forest ecosystem, impacting tree health, productivity, and biodiversity. Conventional approaches to combating diseases, such as biological control or fungicides, often reach limits regarding efficacy, resistance, non-target organisms, and environmental impact, enforcing alternative approaches. From an environmental and ecological standpoint, an RNA interference (RNAi) mediated double-stranded RNA (dsRNA)-based strategy can effectively manage forest fungal pathogens. The RNAi approach explicitly targets and suppresses gene expression through a conserved regulatory mechanism. Recently, it has evolved to be an effective tool in combating fungal diseases and promoting sustainable forest management approaches. RNAi bio-fungicides provide efficient and eco-friendly disease control alternatives using species-specific gene targeting, minimizing the off-target effects. With accessible data on fungal disease outbreaks, genomic resources, and effective delivery systems, RNAi-based biofungicides can be a promising tool for managing fungal pathogens in forests. However, concerns regarding the environmental fate of RNAi molecules and their potential impact on non-target organisms require an extensive investigation on a case-to-case basis. The current review critically evaluates the feasibility of RNAi bio-fungicides against forest pathogens by delving into the accessible delivery methods, environmental persistence, regulatory aspects, cost-effectiveness, community acceptance, and plausible future of RNAi-based forest protection products.

Advances on polymeric nanocarriers for sustainable agriculture: Enhancing dsRNA/siRNA delivery to combat agricultural pests

The application of exogenous RNA for gene-silencing strategies has gained significant traction in agriculture, offering a highly efficient and eco-friendly alternative to conventional plant protection methods. This success has been driven by advances in biotechnology, from the design of long double-stranded RNA (dsRNA) and small interfering RNA (siRNA) molecules to the development of nanocarrier systems that address the challenge of RNA delivery into plant cells. In particular, polymer-based nanocarriers have emerged as a promising solution for enhancing the stability and delivery efficiency of RNA molecules. This review provides a comprehensive overview of the current state of research on the use of polymeric nanocarriers in RNA interference (RNAi) systems for crop protection. It examines key technological developments that have enabled the effective delivery of dsRNA/siRNA to target organisms, with a focus on the unique advantages polymers offer as carriers. Recent studies highlight significant progress in the preparation, characterization, and application of polymeric nanocarriers for RNA encapsulation and delivery. The review also explores the environmental and health challenges posed by these technologies, emphasizing the need for sustainable approaches in their development. Specifically, the production of nanocarriers must adhere to the principles of green chemistry, prioritizing chemical modification routes that reduce harmful residues, such as toxic solvents. Finally, this paper discusses both the current challenges and future prospects of using polymer-based nanocarriers in sustainable agriculture, offering critical insights into their potential to transform crop protection through RNAi technologies.

RNA interference: a promising biotechnological approach to combat plant pathogens, mechanism and future prospects

Plant pathogens and other biological pests represent significant obstacles to crop Protection worldwide. Even though there are many effective conventional methods for controlling plant diseases, new methods that are also effective, environmentally safe, and cost-effective are required. While plant breeding has traditionally been used to manipulate the plant genome to develop resistant cultivars for controlling plant diseases, the emergence of genetic engineering has introduced a completely new approach to render plants resistant to bacteria, nematodes, fungi, and viruses. The RNA interference (RNAi) approach has recently emerged as a potentially useful tool for mitigating the inherent risks associated with the development of conventional transgenics. These risks include the use of specific transgenes, gene control sequences, or marker genes. Utilizing RNAi to silence certain genes is a promising solution to this dilemma as disease-resistant transgenic plants can be generated within a legislative structure. Recent investigations have shown that using target double stranded RNAs via an effective vector system can produce significant silencing effects. Both dsRNA-containing crop sprays and transgenic plants carrying RNAi vectors have proven effective in controlling plant diseases that threaten commercially significant crop species. This article discusses the methods and applications of the most recent RNAi technology for reducing plant diseases to ensure sustainable agricultural yields.

RNA interference-based strategies to control Botrytis cinerea infection in cultivated strawberry

KEY MESSAGE

Gene silencing of BcDCL genes improves gray mold disease control in the cultivated strawberry. Gene silencing technology offers new opportunities to develop new formulations or new pathogen-resistant plants for reducing impacts of agricultural systems. Recent studies offered the proof of concept that the symptoms of gray mold can be reduced by downregulating Dicer-like 1 (DCL1) and 2 (DCL2) genes of Botrytis cinerea. In this study, we demonstrate that both solutions based on dsRNA topical treatment and in planta expression targeting BcDCL1 and BcDCL2 genes can be used to control the strawberry gray mold, the most harmful disease for different fruit crops. 50, 70 and 100 ng μL-1 of naked BcDCL1/2 dsRNA, sprayed on plants of Fragaria x ananassa cultivar Romina in the greenhouse, displayed significant reduction of susceptibility, compared to the negative controls, but to a lesser extent than the chemical fungicide. Three independent lines of Romina cultivar were confirmed for their stable expression of the hairpin gene construct that targets the Bc-DCL1 and 2 sequences (hp-Bc-DCL1/2), and for the production of hp construct-derived siRNAs, by qRT-PCR and Northern blot analyses. In vitro and in vivo detached leaves, and fruits from the hp-Bc-DCL1/2 lines showed significantly enhanced tolerance to this fungal pathogen compared to the control. This decreased susceptibility was correlated to the reduced fungal biomass and the downregulation of the Bc-DCL1 and 2 genes in B. cinerea. These results confirm the potential of both RNAi-based products and plants for protecting the cultivated strawberry from B. cinerea infection, reducing the impact of chemical pesticides on the environment and the health of consumers.

Advancements in genetic studies of mushrooms: a comprehensive review

Genetic studies in mushrooms, driven by innovations such as CRISPR-Cas9 genome editing and RNA interference, transform our understanding of these enigmatic fungi and their multifaceted roles in agriculture, medicine, and conservation. This comprehensive review explores the rationale and significance of genetic research in mushrooms, delving into the ethical, regulatory, and ecological dimensions of this field. CRISPR-Cas9 emerges as a game-changing technology, enabling precise genome editing, targeted gene knockouts, and pathway manipulation. RNA interference complements these efforts by downregulating genes for improved crop yield and enhanced pest and disease resistance. Genetic studies also contribute to the conservation of rare species and developing more robust mushroom strains, fostering sustainable cultivation practices. Moreover, they unlock the potential for discovering novel medicinal compounds, offering new horizons in pharmaceuticals and nutraceuticals. As emerging technologies and ethical considerations shape the future of mushroom research, these studies promise to revolutionize our relationship with these fungi, paving the way for a more sustainable and innovative world.

Agriculture and environmental management through nanotechnology: Eco-friendly nanomaterial synthesis for soil-plant systems, food safety, and sustainability

Through the advancement of nanotechnology, agricultural and food systems are undergoing strategic enhancements, offering innovative solutions to complex problems. This scholarly essay thoroughly examines nanotechnological innovations and their implications within these critical industries. Traditional practices are undergoing radical transformation as nanomaterials emerge as novel agents in roles traditionally filled by fertilizers, pesticides, and biosensors. Micronutrient management and preservation techniques are further enhanced, indicating a shift towards more nutrient-dense and longevity-oriented food production. Nanoparticles (NPs), with their unique physicochemical properties, such as an extraordinary surface-to-volume ratio, find applications in healthcare, diagnostics, agriculture, and other fields. However, concerns about their potential overuse and bioaccumulation raise unanswered questions about their health effects. Molecule-to-molecule interactions and physicochemical dynamics create pathways through which nanoparticles cause toxicity. The combination of nanotechnology and environmental sustainability principles leads to the examination of green nanoparticle synthesis. The discourse extends to how nanomaterials penetrate biological systems, their applications, toxicological effects, and dissemination routes. Additionally, this examination delves into the ecological consequences of nanomaterial contamination in natural ecosystems. Employing robust risk assessment methodologies, including the risk allocation framework, is recommended to address potential dangers associated with nanotechnology integration. Establishing standardized, universally accepted guidelines for evaluating nanomaterial toxicity and protocols for nano-waste disposal is urged to ensure responsible stewardship of this transformative technology. In conclusion, the article summarizes global trends, persistent challenges, and emerging regulatory strategies shaping nanotechnology in agriculture and food science. Sustained, in-depth research is crucial to fully benefit from nanotechnology prospects for sustainable agriculture and food systems.

Establishment of RNAi-Mediated Pest Control Method for Red Imported Fire Ant, Solenopsis invicta

RNAi plays a crucial role in insect gene function research and pest control field. Nonetheless, the variable efficiency of RNAi across diverse insects and off-target effects also limited its further application. In this study, we cloned six essential housekeeping genes from Solenopsis invicta and conducted RNAi experiments by orally administering dsRNA. Then, we found that mixing with liposomes significantly enhanced the RNAi efficiency by targeting for SiV-ATPaseE. Additionally, we observed a certain lethal effect of this dsRNA on queens by our established RNAi system. Furthermore, no strict sequence-related off-target effects were detected. Finally, the RNAi effect of large-scale bacteria expressing dsRNA was successfully confirmed for controlling S. invicta. In summary, this study established an RNAi system for S. invicta and provided a research template for the future development of nucleic acid drugs based on RNAi.

Effective Control of Sclerotinia Stem Rot in Canola Plants Through Application of Exogenous Hairpin RNA of Multiple Sclerotinia sclerotiorum Genes

Sclerotinia stem rot is a globally destructive plant disease caused by Sclerotinia sclerotiorum. Current management of Sclerotinia stem rot primarily relies on chemical fungicides and crop rotation, raising environmental concerns. In this study, we developed an eco-friendly RNA bio-fungicide targeting S. sclerotiorum. Six S. sclerotiorum genes were selected for double-stranded RNA (dsRNA) synthesis. Four genes, a chitin-binding domain, mitogen-activated protein kinase, oxaloacetate acetylhydrolase, and abhydrolase-3, were combined to express hairpin RNA in Escherichia coli HT115. The effect of application of total RNA extracted from E. coli HT115 expressing hairpin RNA on disease progressive and necrosis lesions was evaluated. Gene expression analysis using real-time PCR showed silencing of the target genes using 5 ng/µl of dsRNA in a fungal liquid culture. A detached leaf assay and greenhouse application of dsRNA on canola stem and leaves showed variation in the reduction of necrosis symptoms by dsRNA of different genes, with abhydrolase-3 being the most effective. The dsRNA from a combination of four genes reduced disease severity significantly (P = 0.01). Plants sprayed with hairpin RNA from four genes had lesions that were almost 30% smaller than those of plants treated with abhydrolase-3 alone, in lab and greenhouse assays. The results of this study highlight the potential of RNA interference to manage diseases caused by S. sclerotiorum; however, additional research is necessary to optimize its efficacy.

A review on regulatory aspects, challenges and public perception in acceptance of genetically modified foods

A clear vision for the future of the world's food supply must be developed by all stakeholders, including consumers, farmers, and governments, especially in light of the rapid improvements in the production of genetically modified crops. It has been possible through biotechnology and genetic engineering, genetically modified (GM) crops have been engineered to have certain qualities, such as resistance to pests, illnesses, or herbicides. Concerns about risks and unintended effects of GM crops include ecosystem impacts, new pests or diseases, and health effects on humans and animals. There is mounting evidence that consumers may respond unfavourably to the introduction of genetically altered foods. This research focuses at how genetic engineering can raise agricultural yields, improve nutrient content, and lessen the use for hazardous pesticides and herbicides in food production. Regulatory framework for GM foods may impact on perception and acceptance of consumers.

Biotechnological and Biocontrol Approaches for Mitigating Postharvest Diseases Caused by Fungal Pathogens and Their Mycotoxins in Fruits: A Review

Postharvest diseases caused by fungal pathogens are significant contributors to the postharvest losses of fruits. Moreover, some fungal pathogens produce mycotoxins, which further compromise the safety and quality of fruits. In this review, the potential of biotechnological and biocontrol approaches for mitigating postharvest diseases and mycotoxins in fruits is explored. The review begins by discussing the impact of postharvest diseases on fruit quality and postharvest losses. Next, it provides an overview of major postharvest diseases caused by fungal pathogens. Subsequently, it delves into the role of biotechnological approaches in controlling these diseases. The review also explored the application of biocontrol agents, such as antagonistic yeasts, bacteria, and fungi, which can suppress pathogen growth. Furthermore, future trends and challenges in these two approaches are discussed in detail. Overall, this review can provide insights into promising biotechnological and biocontrol strategies for managing postharvest diseases and mycotoxins in fruits.

A Combinatorial Nanobased Spray-Induced Gene Silencing Technique for Crop Protection and Improvement

Recent research reports have shown that plant pests and pathogens have depleted the crop yield widely, which has led to an increased dependence on commercial pesticides and fungicides. Increased usage of these pesticides has also shown adverse effects on the environment, therefore many techniques have been implemented for solving the issue, some of which include using nanobioconjugates, RNA(i), which put into use double-stranded RNAs to inhibit gene expression. A more innovative and eco-friendly strategy includes spray induced gene silencing, which is being increasingly implemented. This review delves into the eco-friendly approach of spray induced gene silencing (SIGS) in combination with nanobioconjugates, which have been used concerning various plant hosts and their pathogens to provide improved protection. Furthermore, nanotechnological advancements have been understood by addressing the scientific gaps to provide a rationale for the development of updated techniques in crop protection.

Establishment, optimization, and application of genetic technology in Aspergillus spp

Aspergillus is widely distributed in nature and occupies a crucial ecological niche, which has complex and diverse metabolic pathways and can produce a variety of metabolites. With the deepening of genomics exploration, more Aspergillus genomic informations have been elucidated, which not only help us understand the basic mechanism of various life activities, but also further realize the ideal functional transformation. Available genetic engineering tools include homologous recombinant systems, specific nuclease based systems, and RNA techniques, combined with transformation methods, and screening based on selective labeling. Precise editing of target genes can not only prevent and control the production of mycotoxin pollutants, but also realize the construction of economical and efficient fungal cell factories. This paper reviewed the establishment and optimization process of genome technologies, hoping to provide the theoretical basis of experiments, and summarized the recent progress and application in genetic technology, analyzes the challenges and the possibility of future development with regard to Aspergillus.

Biotrophic Fungal Pathogens: a Critical Overview

Biotrophic fungi are one group of heterogeneous organisms and these fungi differ in their traits like mode of nutrition, types of reproduction, and dispersal systems. Generally, based on the nutritional mode, fungi are classified into three broad categories, viz. biotrophs, necrotrophs, and hemi-biotrophs. Biotrophs derive their nutrients and energy from living plant cells and survive within the interstitial space of the cells. Biotrophic fungi cause serious crop diseases but are highly challenging to investigate and develop a treatment strategy. Blumeria (Erysiphe) graminis, Uromyces fabae, Ustilago maydis, Cladosporium fulvum, Puccinia graminis, and Phytophthora infestans are some of the significant biotrophic fungi that affect mainly plants. One among the biotrophic fungus, Pneumocystis jirovecii (Taphrinomycotina subphylum of the Ascomycota) exclusively a human pathogen, can cause lung diseases such as "pneumocystis." Biotrophic fungus widely parasitizing Solanaceae family crops (Tomato and potato) has done massive damage to the crops and has led to economic impact worldwide. During infection and for nutrient absorption, biotrophs develops external appendages such as appressoria or haustoria. The hyphae or appressorium adheres to the plant cell wall and collapses the layers for their nutrient absorption. The pathogen also secretes effector molecules to escape from the plant defense mechanism. Later, plants activate their primary and secondary defense mechanisms; however, the pathogen induces virulence genes to escape the host immune responses. Obligate biotrophic fungi pathogenicity has not been fully understood at the molecular level because of the complex interaction, recognition, and signaling with the host. This review summarizes the mechanism of infection in the host, and immune response to emphasize the understanding of the biotrophic fungal biology and pathogenesis in crops. Thus, the detailed review will pave the way to design methods to overcome the resistance of biotrophic fungi and develop disease-free crops.

Biotechnological approaches for reducing fruit losses caused by pathogenic infection

Fruit loss due to disease occurs in both the field and postharvest. Knowledge of host immune responses and pathogen virulence is enabling the formulation of increasingly sophisticated strategies for disease control. Traditional genetic modification, typically involving overexpression of genes involved in pathogen perception and defence responses, is beginning to be superseded by CRISPR-Cas9 manipulation of host susceptibility targets. Moreover, the refinement of RNA interference (RNAi) strategies, including spray-induced gene silencing (SIGS), is allowing more nuanced control options. These latter approaches have the advantage over earlier technologies in that either they do not result in the generation of genetically modified organisms (RNAi-based SIGS), or the genetic manipulation used leaves no trace of introduced genetic material (gene editing). Thus, these strategies may be more widely acceptable for deployment for future disease control.

Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops

Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

RNA-Based Vaccination of Plants for Control of Viruses

Plant viruses cause nearly half of the emerging plant diseases worldwide, contributing to 10-15% of crop yield losses. Control of plant viral diseases is mainly accomplished by extensive chemical applications targeting the vectors (i.e., insects, nematodes, fungi) transmitting these viruses. However, these chemicals have a significant negative effect on human health and the environment. RNA interference is an endogenous, cellular, sequence-specific RNA degradation mechanism in eukaryotes induced by double-stranded RNA molecules that has been exploited as an antiviral strategy through transgenesis. Because genetically modified crop plants are not accepted for cultivation in several countries globally, there is an urgent demand for alternative strategies. This has boosted research on exogenous application of the RNA-based biopesticides that are shown to exhibit significant protective effect against viral infections. Such environment-friendly and efficacious antiviral agents for crop protection will contribute to global food security, without adverse effects on human health.

Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems

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.

Management of Post-Harvest Anthracnose: Current Approaches and Future Perspectives

Anthracnose is a severe disease caused by Colletotrichum spp. on several crop species. Fungal infections can occur both in the field and at the post-harvest stage causing severe lesions on fruits and economic losses. Physical treatments and synthetic fungicides have traditionally been the preferred means to control anthracnose adverse effects; however, the urgent need to decrease the use of toxic chemicals led to the investigation of innovative and sustainable protection techniques. Evidence for the efficacy of biological agents and vegetal derivates has been reported; however, their introduction into actual crop protection strategies requires the solutions of several critical issues. Biotechnology-based approaches have also been explored, revealing the opportunity to develop innovative and safe methods for anthracnose management through genome editing and RNA interference technologies. Nevertheless, besides the number of advantages related to their use, e.g., the putative absence of adverse effects due to their high specificity, a number of aspects remain to be clarified to enable their introduction into Integrated Pest Management (IPM) protocols against Colletotrichum spp. disease.

Exogenous dsRNA Induces RNA Interference of a Chalcone Synthase Gene in Arabidopsis thaliana

Recent investigations have shown the possibility of artificial induction of RNA interference (RNAi) via plant foliar treatments with naked double-stranded RNA (dsRNA) to silence essential genes in plant fungal pathogens or to target viral RNAs. Furthermore, several studies have documented the downregulation of plant endogenous genes via external application of naked gene-specific dsRNAs and siRNAs to the plant surfaces. However, there are limited studies on the dsRNA processing and gene silencing mechanisms after external dsRNA application. Such studies would assist in the development of innovative tools for crop improvement and plant functional studies. In this study, we used exogenous gene-specific dsRNA to downregulate the gene of chalcone synthase (CHS), the key enzyme in the flavonoid/anthocyanin biosynthesis pathway, in Arabidopsis. The nonspecific NPTII-dsRNA encoding the nonrelated neomycin phosphotransferase II bacterial gene was used to treat plants in order to verify that any observed effects and processing of AtCHS mRNA were sequence specific. Using high-throughput small RNA (sRNA) sequencing, we obtained six sRNA-seq libraries for plants treated with water, AtCHS-dsRNA, or NPTII-dsRNA. After plant foliar treatments, we detected the emergence of a large number of AtCHS- and NPTII-encoding sRNAs, while there were no such sRNAs after control water treatment. Thus, the exogenous AtCHS-dsRNAs were processed into siRNAs and induced RNAi-mediated AtCHS gene silencing. The analysis showed that gene-specific sRNAs mapped to the AtCHS and NPTII genes unevenly with peak read counts at particular positions, involving primarily the sense strand, and documented a gradual decrease in read counts from 17-nt to 30-nt sRNAs. Results of the present study highlight a significant potential of exogenous dsRNAs as a promising strategy to induce RNAi-based downregulation of plant gene targets for plant management and gene functional studies.

RNA Interference-Based Pesticides and Antiviral Agents: Microbial Overproduction Systems for Double-Stranded RNA for Applications in Agriculture and Aquaculture

RNA interference (RNAi)-based pesticides are pest control agents that use RNAi mechanisms as the basis of their action. They are regarded as environmentally friendly and are a promising alternative to conventional chemical pesticides. The effective substance in RNAi-based pesticides is double-stranded RNA (dsRNA) designed to match the nucleotide sequence of a target essential gene of the pest of concern. When taken up by the pest, this exerts an RNAi effect and inhibits some vital biochemical/biological process in the pest. dsRNA products are also expected to be applied for the control of viral diseases in aquaculture by RNAi, especially in shrimp farming. A critical issue in the practical application of RNAi agents is that production of the dsRNA must be low-cost. Here, we review recent methods for microbial production of dsRNAs using representative microorganisms (Escherichia coli, Pseudomonas syringae, Corynebacterium glutamicum, Chlamydomonas reinhardtii, and others) as host strains. The characteristics of each dsRNA production system are discussed.

The Specificity of Transgene Suppression in Plants by Exogenous dsRNA

The phenomenon of RNA interference (RNAi) is widely used to develop new approaches for crop improvement and plant protection. Recent investigations show that it is possible to downregulate plant transgenes, as more prone sequences to silencing than endogenous genes, by exogenous application of double-stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs). However, there are scarce data on the specificity of exogenous RNAs. In this study, we explored whether plant transgene suppression is sequence-specific to exogenous dsRNAs and whether similar effects can be caused by exogenous DNAs that are known to be perceived by plants and induce certain epigenetic and biochemical changes. We treated transgenic plants of Arabidopsis thaliana bearing the neomycin phosphotransferase II (NPTII) transgene with specific synthetic NPTII-dsRNAs and non-specific dsRNAs, encoding enhanced green fluorescent protein (EGFP), as well as with DNA molecules mimicking the applied RNAs. None of the EGFP-dsRNA doses resulted in a significant decrease in NPTII transgene expression in the NPTII-transgenic plants, while the specific NPTII-dsRNA significantly reduced NPTII expression in a dose-dependent manner. Long DNAs mimicking dsRNAs and short DNA oligonucleotides mimicking siRNAs did not exhibit a significant effect on NPTII transgene expression. Thus, exogenous NPTII-dsRNAs induced a sequence-specific and RNA-specific transgene-suppressing effect, supporting external application of dsRNAs as a promising strategy for plant gene regulation.

RNAi-mediated silencing of PEX6 and GAS1 genes of Fusarium oxysporum f. sp. lycopersici confers resistance against Fusarium wilt in tomato

In the present study, we have explored the potential of the RNAi mediated silencing of genes encoding peroxisomal biogenesis factor and β-1,3-glucanosyltransferase in Fusarium oxysporum f. sp. lycopersici (Fol) to confer resistance to Fusarium wilt in transgenic tomato plants. The partial gene fragments from these genes were utilized independently to generate hairpin RNAi constructs in appropriate silencing vectors and used for Agrobacterium-mediated transformation of tomato. The presence of gene-specific siRNAs was confirmed by stem-loop RT-PCR analysis of selected transgenic tomato lines. Transgenic lines expressing gene-specific dsRNA displayed enhanced resistance to Fol with delayed development of disease symptoms. The survival rate of transgenic tomato lines after fungal infection was higher as compared to that of the untransformed tomato plants.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02973-8.

Game-changing alternatives to conventional fungicides: small RNAs and short peptides

Fungicide use is one of the core elements of intensive agriculture because it is necessary to fight pathogens that would otherwise cause large production losses. Oomycete and fungal pathogens are kept under control using several active compounds, some of which are predicted to be banned in the near future owing to serious concerns about their impact on the environment, non-targeted organisms, and human health. To avoid detrimental repercussions for food security, it is essential to develop new biomolecules that control existing and emerging pathogens but are innocuous to human health and the environment. This review presents and discusses the use of novel low-risk biological compounds based on small RNAs and short peptides that are attractive alternatives to current contentious fungicides.

External dsRNA Downregulates Anthocyanin Biosynthesis-Related Genes and Affects Anthocyanin Accumulation in Arabidopsis thaliana

Exogenous application of double-stranded RNAs (dsRNAs) and small-interfering RNAs (siRNAs) to plant surfaces has emerged as a promising method for regulation of essential genes in plant pathogens and for plant disease protection. Yet, regulation of plant endogenous genes via external RNA treatments has not been sufficiently investigated. In this study, we targeted the genes of chalcone synthase (CHS), the key enzyme in the flavonoid/anthocyanin biosynthesis pathway, and two transcriptional factors, MYBL2 and ANAC032, negatively regulating anthocyanin biosynthesis in Arabidopsis. Direct foliar application of AtCHS-specific dsRNAs and siRNAs resulted in an efficient downregulation of the AtCHS gene and suppressed anthocyanin accumulation in A. thaliana under anthocyanin biosynthesis-modulating conditions. Targeting the AtMYBL2 and AtANAC032 genes by foliar dsRNA treatments markedly reduced their mRNA levels and led to a pronounced upregulation of the AtCHS gene. The content of anthocyanins was increased after treatment with AtMYBL2-dsRNA. Laser scanning microscopy showed a passage of Cy3-labeled AtCHS-dsRNA into the A. thaliana leaf vessels, leaf parenchyma cells, and stomata, indicating the dsRNA uptake and spreading into leaf tissues and plant individual cells. Together, these data show that exogenous dsRNAs were capable of downregulating Arabidopsis genes and induced relevant biochemical changes, which may have applications in plant biotechnology and gene functional studies.

Spray-Induced Silencing of Pathogenicity Gene MoDES1 via Exogenous Double-Stranded RNA Can Confer Partial Resistance Against Fungal Blast in Rice

Over the past years, RNA interference (RNAi) has been used as a promising combat strategy against a wide range of pests and pathogens in ensuring global food security. It involves the induction of highly specific posttranscriptional regulation of target essential genes from an organism, via the application of precursor long, non-coding double-stranded RNA (dsRNA) molecules that share sequence-complementarity with the mRNAs of the targets. Fungal blast disease caused by Magnaporthe oryzae is one of the most deadly diseases of rice and wheat incurring huge losses in global crop yield. To date, the host-induced gene silencing (HIGS) and virus-induced gene silencing (VIGS) aspects of RNAi have been successfully exploited in developing resistance against M. oryzae in rice. Spray-induced gene silencing (SIGS) is a current, potential, non-transformative, and environment-friendly pest and pathogen management strategy, where naked or nanomaterial-bound dsRNA are sprayed on leaves to cause selective knockdown of pathogenicity genes. Although it relies on the ability of fungal pathogens to uptake sprayed RNA, its efficiency varies largely across phytopathogens and their genes, targeted for silencing. Here, we report a transient dsRNA supplementation system for the targeted knockdown of MoDES1, a host-defense suppressor pathogenicity gene from M. oryzae. We validate the feasibility of in vivo SIGS and post-uptake transfer of RNA signals to distal plant parts in rice-M. oryzae pathosystem through a GFP-based reporter system. A protocol for efficient silencing via direct foliar spray of naked dsRNA was optimized. As proof-of-concept, we demonstrate the phenotypic impacts of in vitro dsDES1 treatment on growth, conidiation, ROS-scavenging ability, and pathogenic potential of M. oryzae. Furthermore, our extrapolatory dsDES1 spray experiments on wounded leaves and whole rice plants indicate resultant silencing of MoDES1 that conferred significant resistance against the fungal blast disease. The evaluation of primary and secondary host defense responses provides evidence supporting the notion that spray of sequence-specific dsRNA on wounded leaf tissue can cause systemic and sustained silencing of a M. oryzae target gene. For the first time, we establish a transgene-free SIGS approach as a promising crop protection strategy against the notorious rice-blast fungus.