RNAi as a Foliar Spray: Efficiency and Challenges to Field Applications

Silence is not always golden: A closer look at potential environmental and ecotoxicological impacts of large-scale dsRNA application

RNA interference (RNAi) technology has emerged as a pivotal strategy in sustainable pest management, offering a targeted approach that significantly mitigates the environmental and health risks associated with traditional insecticides. Originally implemented through genetically modified organisms (GMOs) to produce specific RNAi constructs, the technology has evolved in response to public and regulatory concerns over GMOs. This evolution has spurred the development of non-transgenic RNAi applications such as spray-induced gene silencing (SIGS), which employs double-stranded RNA (dsRNA) to silence pest genes directly without altering the plant's genetic makeup. Despite its advantages in specificity and reduced ecological footprint, SIGS faces significant obstacles, particularly the instability of dsRNA in field conditions, which limits its practical efficacy. To overcome these limitations, innovative delivery mechanisms have been developed. These include nanotechnology-based systems, minicells, and nanovesicles, which are designed to protect dsRNA from degradation and enhance its delivery to target organisms. While these advancements have improved the stability and application efficiency of dsRNA, comprehensive assessments of their environmental safety and the potential for increased exposure risks to non-target organisms remain incomplete. This comprehensive review aims to elucidate the environmental fate of dsRNA and evaluate the potential risks associated with its widespread application on non-target organisms, encompassing soil microorganisms, beneficial insects, host plants, and mammals. The objective is to establish a more refined framework for RNAi risk assessment within environmental and ecotoxicological contexts, thereby fostering the development of safer, non-transgenic RNAi-based pest control strategies.

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.

Harnessing RNA interference for the control of Fusarium species: A critical review

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.

Cross-Kingdom RNA Transport Based on Extracellular Vesicles Provides Innovative Tools for Plant Protection

RNA interference (RNAi) shows great potential in plant defense against pathogens through RNA-mediated sequence-specific gene silencing. Among RNAi-based plant protection strategies, spray-induced gene silencing (SIGS) is considered a more promising approach because it utilizes the transfer of exogenous RNA between plants and microbes to silence target pathogen genes. The application of nanovesicles significantly enhances RNA stability and delivery efficiency, thereby improving the effectiveness of SIGS and further enhancing plant resistance to diseases and pathogens. This review explores the role of RNAi in plant protection, focusing on the cross-kingdom transport of small RNAs (sRNAs) via extracellular vesicles. It also explores the potential of nanotechnology to further optimize RNA-based plant protection, offering innovative tools and methods in modern plant biotechnology.

Suppression of Thrips palmi population by spray-on application of dsRNA targeting V-ATPase-B

The RNA interference (RNAi)-based gene silencing technique has enormous potential as a non-chemical and eco-friendly alternative to hazardous pesticides. This study reports a spray-induced gene silencing (SIGS) approach for managing Thrips palmi by lowering survival and offspring development. Vacuolar ATP synthases (V-ATPases) are responsible for survival, egg-laying, and viability of eggs in insects. In the current study, T. palmi V-ATPase-B was targeted to suppress the pest population by spray-on application of double-stranded RNA (dsRNA). Silencing of V-ATPase-B was first validated by oral administration of dsV-ATPase-B. The expression of V-ATPase-B was reduced by 5.40-fold post-dsRNA feeding leading to increased mortality (57.03 %) and reduced reproductive fitness (67.73 %). Spray-on application of naked dsV-ATPase-B at concentrations of 3.0 μg/mL and 5.0 μg/mL effectively suppressed the population by 30.00 % and 43.33 %, respectively. The expression of the target gene was downregulated by up to 4.24-fold. Two consecutive sprays at a concentration of 5.0 μg/mL provided substantial protection against the fresh release of T. palmi for up to 10 days. The spray-on application of dsV-ATPase-B would be an eco-friendly alternative for managing T. palmi populations thereby reducing crop damage and limiting the spread of orthotospoviruses.

Comparative analysis of RNA interference and pattern-triggered immunity induced by dsRNA reveals different efficiencies in the antiviral response to potato virus X

Antiviral responses induced by double-stranded RNA (dsRNA) include RNA interference (RNAi) and pattern-triggered immunity (PTI), but their relative contributions to antiviral defence are not well understood. We aimed at testing the impact of exogenous applied dsRNA on both layers of defence against potato virus X expressing GFP (PVX-GFP) in Nicotiana benthamiana. Co-inoculation of PVX-GFP with either sequence-specific (RNAi) or nonspecific dsRNA (PTI) showed that nonspecific dsRNA reduced virus accumulation in both inoculated and systemic leaves. However, nonspecific dsRNA was a poor inducer of antiviral immunity compared to a sequence-specific dsRNA capable of triggering the RNAi response, and plants became susceptible to systemic infection. Studies with a PVX mutant unable to move from cell to cell indicated that the interference with PVX-GFP triggered by nonspecific dsRNA operated at the single-cell level. Next, we performed RNA-seq analysis to examine similarities and differences in the transcriptome triggered by dsRNA alone or in combination with viruses harbouring sequences targeted or not by dsRNA. Enrichment analysis showed an over-representation of plant-pathogen signalling pathways, such as calcium, ethylene and MAPK signalling, which are typical of antimicrobial PTI. Moreover, the transcriptomic response to the virus targeted by dsRNA had a greater impact on defence than the non-targeted virus, highlighting qualitative differences between sequence-specific RNAi and nonspecific PTI responses. Together, these results further our understanding of plant antiviral defence, particularly the contribution of nonspecific dsRNA-mediated PTI. We envisage that both sequence-specific RNAi and nonspecific PTI pathways may be triggered via topical application of dsRNA, contributing cumulatively to plant protection against viruses.

Resistance of the CRISPR-Cas13a Gene-Editing System to Potato Spindle Tuber Viroid Infection in Tomato and Nicotiana benthamiana

Gene-editing technology, specifically the CRISPR-Cas13a system, has shown promise in breeding plants resistant to RNA viruses. This system targets RNA and, theoretically, can also combat RNA-based viroids. To test this, the CRISPR-Cas13a system was introduced into tomato plants via transient expression and into Nicotiana benthamiana through transgenic methods, using CRISPR RNAs (crRNAs) targeting the conserved regions of both sense and antisense genomes of potato spindle tuber viroid (PSTVd). In tomato plants, the expression of CRISPR-Cas13a and crRNAs substantially reduced PSTVd accumulation and alleviated disease symptoms. In transgenic N. benthamiana plants, the PSTVd levels were lower as compared to wild-type plants. Several effective crRNAs targeting the PSTVd genomic RNA were also identified. These results demonstrate that the CRISPR-Cas13a system can effectively target and combat viroid RNAs, despite their compact structures.

Impact of Exogenous dsRNA on miRNA Composition in Arabidopsis thaliana

The application of double-stranded RNAs (dsRNAs) to plant surfaces has emerged as a promising tool for manipulating gene expression in plants and pathogens, offering new opportunities for crop improvement. While research has shown the capability of exogenous dsRNAs to silence genes, the full spectrum of their impact, particularly on the intricate network of microRNAs (miRNAs), remains largely unexplored. Here, we show that the exogenous application of chalcone synthase (CHS)-encoding dsRNA to the rosette leaves of Arabidopsis thaliana induced extensive alterations in the miRNA profile, while non-specific bacterial neomycin phosphotransferase II (NPTII) dsRNA had a minimal effect. Two days after treatment, we detected 60 differentially expressed miRNAs among the 428 miRNAs found in the A. thaliana genome. A total of 59 miRNAs were significantly changed after AtCHS-dsRNA treatment compared with water and NPTII-dsRNA, and 1 miRNA was significantly changed after AtCHS-dsRNA and NPTII-dsRNA compared with the water control. A comprehensive functional enrichment analysis revealed 17 major GO categories enriched among the genes potentially targeted by the up- and downregulated miRNAs. These categories included processes such as aromatic compound biosynthesis (a pathway directly related to CHS activity), heterocycle biosynthesis, RNA metabolism and biosynthesis, DNA transcription, and plant development. Several predicted targets of upregulated and downregulated miRNAs, including APETALA2, SCL27, SOD1, GRF1, AGO2, PHB, and PHV, were verified by qRT-PCR. The analysis showed a negative correlation between the expression of miRNAs and the expression of their predicted targets. Thus, exogenous plant gene-specific dsRNAs induce substantial changes in the plant miRNA composition, ultimately affecting the expression of a wide range of genes. These findings have profound implications for our understanding of the effects of exogenously induced RNA interference, which can have broader effects beyond targeted mRNA degradation, affecting the expression of other genes through miRNA regulation.

Enhancing tomato disease resistance through endogenous antifungal proteins and introduced nematode-targeting dsRNA of biocontrol agent Bacillus velezensis HS-3

BACKGROUND

As a type of biological control agent (BCA), Bacillus velezensis possesses the efficacy of inhibiting pathogenic microorganisms, promoting plant growth, and overcoming continuous cropping obstacles (CCOs). However, there is limited reporting on the optimization of the cultivation conditions for such biocontrol agents and their role as double-stranded RNA (dsRNA) delivery vectors.

RESULTS

In this study, a Bacillus velezensis strain HS-3 was isolated from the root zone of tomato plants with in vitro anti-Botrytis cinerea activity. The investigation into active compounds revealed that HS-3 predominantly employs proteins with molecular weights greater than 3 kDa for its antifungal activity. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified various proteases and chitosanase, further suggesting that HS-3 most likely employs these enzymes to degrade fungal cell walls for its antifungal effect. To optimize the production of extracellular proteins, fermentation parameters for HS-3 were systematically optimized, leading to an optimized medium (OP-M). HS-3 cultured in OP-M demonstrated enhanced capacity to assist tomato plants in withstanding CCOs. However, the presence of excessive nematodes in diseased soil resulted in the disease severity index (DSI) remaining high. An RNA interference mechanism was further introduced to HS-3, targeting the nematode tyrosine phosphatase (TP) gene. Ultimately, HS-3 expressing dsRNA of TP in OP-M effectively assisted tomatoes in mitigating CCOs, reducing DSI to 2.2% and 17.8% of the control after 45 and 90 days of growth, respectively.

CONCLUSION

The advantages of Bacillus velezensis in crop disease management and the mitigation of CCOs become even more pronounced when utilizing both optimized levels of endogenous enzymes and introduced nematode-targeting dsRNA. © 2024 Society of Chemical Industry.

Transgenic poplar (Populus davidiana×P. bolleana Loucne) expressing dsRNA of insect chitinase gene: lines identification and resistance assay

Poplar is a valuable tree species that is distributed all over the world. However, many insect pests infest poplar trees and have caused significant damage. To control poplar pests, we transformed a poplar species, Populus davidiana × P. bolleana Loucne, with the dsRNA of the chitinase gene of a poplar defoliator, Clostera anastomosis (Linnaeus) (Lepidoptera: Notodontidae), employing an Agrobaterium-mediated approach. The transgenic plant has been identified by cloning the T-DNA flanking sequences using TAIL-PCR and quantifying the expression of the dsRNA using qPCR. The toxicity assay of the transgenic poplar lines was carried out by feeding the target insect species (C. anastomosis). The results showed that, in C. anastomosis, the activity of chitinase was significantly decreased, consistent with the expression on mRNA levels, and the larval mortality was significantly increased. These results suggested that the transgenic poplar of dsRNA could be used for pest control.

Structure, ultrastructure and cation accumulation in quinoa epidermal bladder cell complex under high saline stress

Quinoa is a facultative halophyte with excellent tolerance to salinity. In this study, the epidermal bladder cell complex (EBCc) of quinoa leaves was studied to determine their cellular characteristics and involvement in salt tolerance. We used light microscopy, confocal RAMAN microscopy, confocal fluorescence microscopy, transmission electron microscopy, and environmental scanning electron microscopy complemented by energy dispersive X-ray analysis. Ionic content was quantified with flame atomic absorption spectroscopy and with flame emission photometry. Results show that: (i) the number of EBCcs remains constant but their density and area vary with leaf age; (ii) stalk cells store lipids and exhibit thick walls, bladder cells present carotenes in small vesicles, oxalate crystals in vacuoles and lignin in their walls and both stalk and bladder cells have cuticles that differ in wax and cutin content; (iii) chloroplasts containing starch can be found on both stalk and bladder cells, and the latter also presents grana; (iv) plasmodesmata are observed between the stalk cell and the bladder cell, and between the epidermal cell and the stalk cell, and ectodesmata-like structures are observed on the bladder cell. Under high salinity conditions, (v) there is a clear tendency to accumulate greater amounts of K+ with respect to Na+ in the bladder cell; (vi) stalk cells accumulate similar amounts of K+ and Na+; (vii) Na+ accumulates mainly in the medullary parenchyma of the stem. These results add knowledge about the structure, content, and role of EBCc under salt stress, and surprisingly present the parenchyma of the stem as the main area of Na+ accumulation.

Challenges and Opportunities Arising from Host-Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference

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.

Development, Design, and Application of Efficient siRNAs Against Cotton Leaf Curl Virus-Betasatellite Complex to Mediate Resistance Against Cotton Leaf Curl Disease

Cotton leaf curl disease (CLCuD), caused by the Cotton leaf curl virus, is one of the most irrepressible diseases in cotton due to high recombination in the virus. RNA interference (RNAi) is widely used as a biotechnological approach for sequence-specific gene silencing guided by small interfering RNAs (siRNAs) to generate resistance against viruses. The success of RNAi depends upon the fact that the target site of the designed siRNA must be conserved even if the genome undergoes recombination. Thus, the present study designs the most efficient siRNA against the conserved sites of the Cotton leaf curl Multan virus (CLCuMuV) and the Cotton leaf curl Multan betasatellite (CLCuMB). From an initial prediction of 9 and 7 siRNAs against CLCuMuV and CLCuMB, respectively, the final selection was made for 2 and 1 siRNA based on parameters such as no off-targets, good GC content, high validity score, and targeting coding region. The target sites of siRNA were observed to lie in the AC3 and an overlapping region of AC2-AC1 of CLCuMuV and βC1 of CLCuMB; all target sites showed a highly conserved nature in recombination analysis. Docking the designed siRNAs with the Argonaute-2 protein of Gossypium hirsutum showed stable binding. Finally, BLASTn of siRNA-target positions in genomes of other BGVs indicated the suitability of designed siRNAs against a broad range of BGVs. The designed siRNAs of the present study could help gain complete control over the virus, though experimental validation is highly required to suggest predicted siRNAs for CLCuD resistance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01191-z.

Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals

At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.

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.

Simultaneous Application of Several Exogenous dsRNAs for the Regulation of Anthocyanin Biosynthesis in Arabidopsis thaliana

Plant surface treatment with double-stranded RNAs (dsRNAs) has gained recognition as a promising method for inducing gene silencing and combating plant pathogens. However, the regulation of endogenous plant genes by external dsRNAs has not been sufficiently investigated. Also, the effect of the simultaneous application of multiple gene-specific dsRNAs has not been analyzed. The aim of this study was to exogenously target five genes in Arabidopsis thaliana, namely, three transcription factor genes (AtCPC, AtMybL2, AtANAC032), a calmodulin-binding protein gene (AtCBP60g), and an anthocyanidin reductase gene (AtBAN), which are known as negative regulators of anthocyanin accumulation. Exogenous dsRNAs encoding these genes were applied to the leaf surface of A. thaliana either individually or in mixtures. The mRNA levels of the five targets were analyzed using qRT-PCR, and anthocyanin content was evaluated through HPLC-MS. The results demonstrated significant downregulation of all five target genes by the exogenous dsRNAs, resulting in enhanced expression of chalcone synthase (AtCHS) gene and increased anthocyanin content. The simultaneous foliar application of the five dsRNAs proved to be more efficient in activating anthocyanin accumulation compared to the application of individual dsRNAs. These findings hold considerable importance in plant biotechnology and gene function studies.

RNA Interference-Screening of Potentially Lethal Gene Targets in the White-Backed Planthopper Sogatella furcifera via a Spray-Induced and Nanocarrier-Delivered Gene Silencing System

RNA interference (RNAi) is a widespread post-transcriptional silencing mechanism that targets homologous mRNA sequences for specific degradation. An RNAi-based pest management strategy is target-specific and considered a sustainable biopesticide. However, the specific genes targeted and the efficiency of the delivery methods can vary widely across species. In this study, a spray-induced and nanocarrier-delivered gene silencing (SI-NDGS) system that incorporated gene-specific dsRNAs targeting conserved genes was used to evaluate phenotypic effects in white-backed planthopper (WBPH). At 2 days postspraying, transcript levels for all target genes were significantly reduced and knockdown of two gene orthologs, hsc70-3 and PP-α, resulted in an elevated mortality (>60%) and impaired ecdysis. These results highlight the utility of the SI-NDGS system for identifying genes involved in WBPH growth and development that could be potentially exploitable as high mortality target genes to develop an alternative method for WBPH control.

Improving RNA-based crop protection through nanotechnology and insights from cross-kingdom RNA trafficking

Spray-induced gene silencing (SIGS) is a powerful and eco-friendly method for crop protection. Based off the discovery of RNA uptake ability in many fungal pathogens, the application of exogenous RNAs targeting pathogen/pest genes results in gene silencing and infection inhibition. However, SIGS remains hindered by the rapid degradation of RNA in the environment. As extracellular vesicles are used by plants, animals, and microbes in nature to transport RNAs for cross-kingdom/species RNA interference between hosts and microbes/pests, nanovesicles and other nanoparticles have been used to prevent RNA degradation. Efforts examining the effect of nanoparticles on RNA stability and internalization have identified key attributes that can inform better nanocarrier designs for SIGS. Understanding sRNA biogenesis, cross-kingdom/species RNAi, and how plants and pathogens/pests naturally interact are paramount for the design of SIGS strategies. Here, we focus on nanotechnology advancements for the engineering of innovative RNA-based disease control strategies against eukaryotic pathogens and pests.

Characterisation and functionalisation of chitosan nanoparticles as carriers for double-stranded RNA (dsRNA) molecules towards sustainable crop protection

The need to minimise the impact of phytosanitary treatments for disease control boosted researchers to implement techniques with less environmental impact. The development of technologies using molecular mechanisms based on the modulation of metabolism by short dsRNA sequences appears promising. The intrinsic fragility of polynucleotides and the high cost of these techniques can be circumvented by nanocarriers that protect the bioactive molecule enabling high efficiency delivery to the leaf surface and extending its half-life. In this work, a specific protocol was developed aiming to assess the best methodological conditions for the synthesis of low-size chitosan nanoparticles (NPs) to be loaded with nucleotides. In particular, NPs have been functionalised with partially purified Green Fluorescent Protein dsRNAs (GFP dsRNA) and their size, surface charge and nucleotide retention capacity were analysed. Final NPs were also stained with FITC and sprayed on Nicotiana benthamiana leaves to assess, by confocal microscopy, both a distribution protocol and the fate of NPs up to 6 days after application. Finally, to confirm the ability of NPs to increase the efficacy of dsRNA interference, specific tests were performed: by means of GFP dsRNA-functionalised NPs, the nucleotide permanence during time was assessed both in vitro on detached wild-type N. benthamiana leaves and in planta; lastly, the inhibition of Botrytis cinerea on single leaves was also evaluated, using a specific fungal sequence (Bc dsRNA) as the NPs' functionalising agent. The encouraging results obtained are promising in the perspective of long-lasting application of innovative treatments based on gene silencing.

Nanoplatforms for the Delivery of Nucleic Acids into Plant Cells

Nanocarriers are widely used for efficient delivery of different cargo into mammalian cells; however, delivery into plant cells remains a challenging issue due to physical and mechanical barriers such as the cuticle and cell wall. Here, we discuss recent progress on biodegradable and biosafe nanomaterials that were demonstrated to be applicable to the delivery of nucleic acids into plant cells. This review covers studies the object of which is the plant cell and the cargo for the nanocarrier is either DNA or RNA. The following nanoplatforms that could be potentially used for nucleic acid foliar delivery via spraying are discussed: mesoporous silica nanoparticles, layered double hydroxides (nanoclay), carbon-based materials (carbon dots and single-walled nanotubes), chitosan and, finally, cell-penetrating peptides (CPPs). Hybrid nanomaterials, for example, chitosan- or CPP-functionalized carbon nanotubes, are taken into account. The selected nanocarriers are analyzed according to the following aspects: biosafety, adjustability for the particular cargo and task (e.g., organelle targeting), penetration efficiency and ability to protect nucleic acid from environmental and cellular factors (pH, UV, nucleases, etc.) and to mediate the gradual and timely release of cargo. In addition, we discuss the method of application, experimental system and approaches that are used to assess the efficiency of the tested formulation in the overviewed studies. This review presents recent progress in developing the most promising nanoparticle-based materials that are applicable to both laboratory experiments and field applications.

A Non-Canonical Pathway Induced by Externally Applied Virus-Specific dsRNA in Potato Plants

The external application of double-stranded RNA (dsRNA) has recently been developed as a non-transgenic approach for crop protection against pests and pathogens. This novel and emerging approach has come to prominence due to its safety and environmental benefits. It is generally assumed that the mechanism of dsRNA-mediated antivirus RNA silencing is similar to that of natural RNA interference (RNAi)-based defence against RNA-containing viruses. There is, however, no direct evidence to support this idea. Here, we provide data on the high-throughput sequencing (HTS) analysis of small non-coding RNAs (sRNA) as hallmarks of RNAi induced by infection with the RNA-containing potato virus Y (PVY) and also by exogenous application of dsRNA which corresponds to a fragment of the PVY genome. Intriguingly, in contrast to PVY-induced production of discrete 21 and 22 nt sRNA species, the externally administered PVY dsRNA fragment led to generation of a non-canonical pool of sRNAs, which were present as ladders of ~18-30 nt in length; suggestive of an unexpected sRNA biogenesis pathway. Interestingly, these non-canonical sRNAs are unable to move systemically and also do not induce transitive amplification. These findings may have significant implications for further developments in dsRNA-mediated crop protection.

Probing the Nucleic Acid Flexibility to Disarm the Viral Counter-Defense Machinery: Design and Characterization of Potent p19 Inhibitors

Plant viruses are highly destructive and significant contributors to several global pandemics and epidemics in plants. A viral disease outbreak in plants can cause a scarcity of food supply and is a severe concern to humanity. The siRNA (small interfering RNA)-mediated RNA-induced silencing complex (RISC) formation is a primary defense mechanism in plants against viruses, where the RISC binds and degrades viral mRNAs. As a counter-defense, many viruses encode RNA-silencing suppressor proteins (e.g., the p19 protein from the Tombusviridae family) for viral proliferation in plants. The functional form of p19 (homodimer) binds to plant siRNA with high affinities, thereby interrupting the RISC formation and thus preventing the viral mRNA silencing in plants. By altering the RISC formation, the p19 protein helps the virus invasion in the plant and ultimately stunts host growth. In this study, we designed several modified siRNA-based molecules for p19 inhibition. The viral p19 protein is known to interact predominantly through H-bonds with 2'-OH and phosphates of the plant siRNA. We utilized this information and in silico-designed flexible substituents of siRNA, where we removed the C2'-C3' bond in each nucleotide unit. We performed all-atom explicit-solvent molecular dynamics simulations (400 ns, 3 replicates each) for control/modified siRNA─p19 complexes (8 in total) followed by energetic estimations. Strikingly, in a few modified complexes, the siRNA not only retained the double-helical structural integrity but also displayed remarkably enhanced p19 binding compared to the control siRNA; hence, we consider it important to perform biological and chemical in vitro and in vivo studies on proposed flexible nucleic acids as p19 inhibitors for crop protection.

CRISPR/Cas, Multiomics, and RNA Interference in Virus Disease Management

Plant viruses infect a wide range of commercially important crop plants and cause significant crop production losses worldwide. Numerous alterations in plant physiology related to the reprogramming of gene expression may result from viral infections. Although conventional integrated pest management-based strategies have been effective in reducing the impact of several viral diseases, continued emergence of new viruses and strains, expanding host ranges, and emergence of resistance-breaking strains necessitate a sustained effort toward the development and application of new approaches for virus management that would complement existing tactics. RNA interference-based techniques, and more recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing technologies have paved the way for precise targeting of viral transcripts and manipulation of viral genomes and host factors. In-depth knowledge of the molecular mechanisms underlying the development of disease would further expand the applicability of these recent methods. Advances in next-generation/high-throughput sequencing have made possible more intensive studies into host-virus interactions. Utilizing the omics data and its application has the potential to expedite fast-tracking traditional plant breeding methods, as well as applying modern molecular tools for trait enhancement, including virus resistance. Here, we summarize the recent developments in the CRISPR/Cas system, transcriptomics, endogenous RNA interference, and exogenous application of dsRNA in virus disease management.

RNA-Based Control of Fungal Pathogens in Plants

Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.

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.

Exogenously Induced Silencing of Four MYB Transcription Repressor Genes and Activation of Anthocyanin Accumulation in Solanum lycopersicum

RNA interference (RNAi) is a natural post-transcriptional regulatory mechanism that can be artificially induced by exogenous application of double-stranded RNAs (dsRNAs) to the plant surfaces. Recent studies show that it is possible to silence plant genes and change plant properties using plant RNA spraying and other approaches for dsRNA delivery. In this study, we investigated the effect of exogenous gene-specific dsRNAs on the silencing of four tomato genes encoding MYB-family transcription repressors of anthocyanin biosynthesis in the leaves of tomato Solanum lycopersicum L. We found that the exogenous application of dsRNAs encoding for the SlMYBATV1, SlMYB32, SlMYB76, and SlTRY genes downregulated mRNA levels of these endogenous repressors of anthocyanin production, upregulated the expression of anthocyanin biosynthesis-related genes, and enhanced anthocyanin content in the leaves of S. lycopersicum. The data demonstrated that exogenous gene-specific dsRNAs can induce post-transcriptional gene silencing in tomato leaves by direct foliar application of dsRNAs. This approach may be used for plant secondary metabolism induction and as a silencing tool for gene function studies without the need to produce genetically modified plants.

Putative target sites in synganglion for novel ixodid tick control strategies

Acaricide resistance is a global problem that has impacts worldwide. Tick populations with broad resistance to all commercially available acaricides have been reported. Since resistance selection in ticks and their role in pathogen transmission to animals and humans result in important economic and public health burden, it is essential to develop new strategies for their control (i.e., novel chemical compounds, vaccines, biological control). The synganglion is the tick central nervous system and it is responsible for synthesizing and releasing signaling molecules with different physiological functions. Synganglion proteins are the targets of the majority of available acaricides. In this review we provide an overview of the mode-of-action and resistance mechanisms against neurotoxic acaricides in ticks, as well as putative target sites in synganglion, as a supporting tool to identify new target proteins and to develop new strategies for tick control.

Eco-friendly deacetylated chitosan base siRNA biological-nanopesticide loading cyromazine for efficiently controlling Spodoptera frugiperda

Spodoptera frugiperda is a serious threat to various crops, such as corn and rice, and results in severe economic losses. Herein, a chitin synthase sfCHS highly expressed in the epidermis of S. frugiperda was screened, and when interfered by an sfCHS-siRNA nanocomplex, most individuals could not ecdysis (mortality rate 53.3 %) or pupate (abnormal pupation 80.6 %). Based on the results of structure-based virtual screening, cyromazine (CYR, binding free energy -57.285 kcal/mol) could inhibit ecdysis (LC₅₀, 19.599 μg/g). CYR-CS/siRNA nanoparticles encapsulating CYR and SfCHS-siRNA with chitosan (CS) were successfully prepared, as confirmed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and 74.9 mg/g CYR was characterized in the core of CYR-CS/siRNA by high-performance liquid chromatography and Fourier transform infrared spectroscopy. Small amounts of prepared CYR-CS/siRNA containing only 1.5 μg/g CYR could better inhibit chitin synthesis in the cuticle and peritrophic membrane (mortality rate 84.4 %). Therefore, chitosan/siRNA nanoparticle-loaded pesticides were useful for pesticide reduction and comprehensive control of S. frugiperda.

A call to arms: novel strategies for thrips and tospovirus control

Thrips and the tospoviruses they transmit are some of the most significant threats to food and ornamental crop production globally. Control of the insect and virus is challenging and new strategies are needed. Characterizing the thrips-virus interactome provides new targets for disrupting the transmission cycle. Viral and insect determinants of vector competence are being defined, including the viral attachment protein and its structure as well as thrips proteins that interact with and respond to tospovirus infection. Additional thrips control strategies such as RNA interference need further refinement and field-applicable delivery systems, but they show promise for the knockdown of essential genes for thrips survival and virus transmission. The identification of a toxin that acts to deter thrips oviposition on cotton also presents new opportunities for control of this important pest.

Recent Advances in Nanoparticle-Mediated Co-Delivery System: A Promising Strategy in Medical and Agricultural Field

Drug and gene delivery systems mediated by nanoparticles have been widely studied for life science in the past decade. The application of nano-delivery systems can dramatically improve the stability and delivery efficiency of carried ingredients, overcoming the defects of administration routes in cancer therapy, and possibly maintaining the sustainability of agricultural systems. However, delivery of a drug or gene alone sometimes cannot achieve a satisfactory effect. The nanoparticle-mediated co-delivery system can load multiple drugs and genes simultaneously, and improve the effectiveness of each component, thus amplifying efficacy and exhibiting synergistic effects in cancer therapy and pest management. The co-delivery system has been widely reported in the medical field, and studies on its application in the agricultural field have recently begun to emerge. In this progress report, we summarize recent progress in the preparation and application of drug and gene co-delivery systems and discuss the remaining challenges and future perspectives in the design and fabrication.

Current Scenario of Exogenously Induced RNAi for Lepidopteran Agricultural Pest Control: From dsRNA Design to Topical Application

Invasive insects cost the global economy around USD 70 billion per year. Moreover, increasing agricultural insect pests raise concerns about global food security constraining and infestation rising after climate changes. Current agricultural pest management largely relies on plant breeding-with or without transgenes-and chemical pesticides. Both approaches face serious technological obsolescence in the field due to plant resistance breakdown or development of insecticide resistance. The need for new modes of action (MoA) for managing crop health is growing each year, driven by market demands to reduce economic losses and by consumer demand for phytosanitary measures. The disabling of pest genes through sequence-specific expression silencing is a promising tool in the development of environmentally-friendly and safe biopesticides. The specificity conferred by long dsRNA-base solutions helps minimize effects on off-target genes in the insect pest genome and the target gene in non-target organisms (NTOs). In this review, we summarize the status of gene silencing by RNA interference (RNAi) for agricultural control. More specifically, we focus on the engineering, development and application of gene silencing to control Lepidoptera through non-transforming dsRNA technologies. Despite some delivery and stability drawbacks of topical applications, we reviewed works showing convincing proof-of-concept results that point to innovative solutions. Considerations about the regulation of the ongoing research on dsRNA-based pesticides to produce commercialized products for exogenous application are discussed. Academic and industry initiatives have revealed a worthy effort to control Lepidoptera pests with this new mode of action, which provides more sustainable and reliable technologies for field management. New data on the genomics of this taxon may contribute to a future customized target gene portfolio. As a case study, we illustrate how dsRNA and associated methodologies could be applied to control an important lepidopteran coffee pest.

Clay nanoparticles efficiently deliver small interfering RNA to intact plant leaf cells

RNA interference is triggered in plants by the exogenous application of double-stranded RNA or small interfering RNA (siRNA) to silence the expression of target genes. This approach can potentially provide insights into metabolic pathways and gene function and afford plant protection against viruses and other plant pathogens. However, the effective delivery of biomolecules such as siRNA into plant cells is difficult because of the unique barrier imposed by the plant cell wall. Here, we demonstrate that 40-nm layered double hydroxide (LDH) nanoparticles are rapidly taken up by intact Nicotiana benthamiana leaf cells and by chloroplasts, following their application via infiltration. We also describe the distribution of infiltrated LDH nanoparticles in leaves and demonstrate their translocation through the apoplast and vasculature system. Furthermore, we show that 40-nm LDH nanoparticles can greatly enhance the internalization of nucleic acids by N. benthamiana leaf cells to facilitate siRNA-mediated downregulation of targeted transgene mRNA by >70% within 1 day of exogenous application. Together, our results show that 40-nm LDH nanoparticle is an effective platform for delivery of siRNA into intact plant leaf cells.

New insights into transmission pathways and possible off-target effects of insecticidal dsRNA released by treated plants

RNAi has shown great potential in controlling pests and pathogens, and dsRNA-based pesticides have been used in different ways. Due to off-target effects, the transmission pathways and possible impacts of dsRNA on non-target organisms after release should be researched. Here, we tested pathways of dsRNA transmission through the rice-hopper-spider food chain and their efficiency for triggering RNAi. The results revealed five new pathways by which plants transfer dsRNA into the environment through the food chain. We found that ingestion of the tissues or guttation droplets of treated plant could trigger both targeted and off-target RNAi both in consumers and predators. Ingestion of consumer hoppers could also result in localized RNAi in the midguts of the predator spiders. Trace amounts of dsRNA were detected in plant root excretions and in hopper honeydew. Cutting the root tips dramatically increased the levels of dsRNA in root excretions. Host shifting experiments proved that hoppers could transfer a trace amount of dsRNA via vomit. With specially designed dsRNAs, we showed that dsRNA sharing matching sequences of 29 bp or 32 bp in length with non-target genes could trigger off-target RNAi, but that dsRNA sharing 13 bp matching sequences could not. We conclude that field-released pesticidal dsRNA could be transmitted via the hydrophilic transport system in plants, and that this may pose a safety risk to non-target animal consumers that are closely related to target pests. Rational use of pesticidal dsRNAs should involve careful consideration of dsRNA design to manage the biosafety risk.

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.