Host-delivered RNAi: an effective strategy to silence genes in plant parasitic nematodes

Biochemical and nanotechnological approaches to combat phytoparasitic nematodes

The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.

Host-induced RNA interference targeting the neuromotor gene FMRFamide-like peptide-14 (Mi-flp14) perturbs Meloidogyne incognita parasitic success in eggplant

KEY MESSAGE

The study demonstrates the successful management of Meloidogyne incognita in eggplant using Mi-flp14 RNA interference, showing reduced nematode penetration and reproduction without off-target effects across multiple generations. Root-knot nematode, Meloidogyne incognita, causes huge yield losses worldwide. Neuromotor function in M. incognita governed by 19 neuropeptides is vital for parasitism and parasite biology. The present study establishes the utility of Mi-flp14 for managing M. incognita in eggplant in continuation of our earlier proof of concept in tobacco (US patent US2015/0361445A1). Mi-flp14 hairpin RNA construct was used for generating 19 independent transgenic eggplant events. PCR and Southern hybridization analysis confirmed transgene integration and its orientation, while RT-qPCR and Northern hybridization established the generation of dsRNA and siRNA of Mi-flp14. In vitro and in vivo bio-efficacy analysis of single-copy events against M. incognita showed reduced nematode penetration and development at various intervals that negatively impacted reproduction. Interestingly, M. incognita preferred wild-type plants over the transgenics even when unbiased equal opportunity was provided for the infection. A significant reduction in disease parameters was observed in transgenic plants viz., galls (40-48%), females (40-50%), egg masses (35-40%), eggs/egg mass (50-55%), and derived multiplication factor (60-65%) compared to wild type. A unique demonstration of perturbed expression of Mi-flp14 in partially penetrated juveniles and female nematodes established successful host-mediated RNAi both at the time of penetration even before the nematodes started withdrawing plant nutrients and later stage, respectively. The absence of off-target effects in transgenic plants was supported by the normal growth phenotype of the plants and T-DNA integration loci. Stability in the bio-efficacy against M. incognita across T1- to T4-generation transgenic plants established the utility of silencing Mi-flp14 for nematode management. This study demonstrates the significance of targeting Mi-flp14 in eggplant for nematode management, particularly to address global agricultural challenges posed by M. incognita.

A nematode-inducible promoter can effectively drives RNAi construct to confer Meloidogyne incognita resistance in tomato

KEY MESSAGE

Heterologous expression of a nematode-responsive promoter in tomato successfully driven the RNAi constructs to impart root-knot nematode resistance. The root-knot nematode Meloidogyne incognita seriously afflicts the global productivity of tomatoes. Nematode management options are extremely reliant on chemical methods, however, only a handful of nematicides are commercially available. Additionally, nematodes have developed resistance-breaking phenotypes against the commercially available Mi gene-expressing tomatoes. Nematode resistance in crop plants can be enhanced using the bio-safe RNAi technology, in which plants are genetically modified to express nematode gene-specific dsRNA/siRNA molecules. However, the majority of the RNAi crops conferring nematode tolerance have used constitutive promoters, which have many limitations. In the present study, using promoter-GUS fusion, we functionally validated two nematode-inducible root-specific promoters (pAt1g74770 and pAt2g18140, identified from Arabidopsis thaliana) in the Solanum lycopersicum-M. incognita pathosystem. pAt2g18140 was found to be nematode-responsive during 10-21 days post-inoculation (dpi) and became non-responsive during the late infection stage (28 dpi). In contrast, pAt1g74770 remained nematode-responsive for a longer duration (10-28 dpi). Next, a number of transgenic lines were developed that expressed RNAi constructs (independently targeting the M. incognita integrase and splicing factor genes) driven by the pAt1g74770 promoter. M. incognita parasitic success (measured by multiplication factor ratio) in pAt1g74770:integrase and pAt1g74770:splicing factor RNAi lines were significantly reduced by 60.83-74.93% and 69.34-75.31%, respectively, compared to the control. These data were comparable with the RNAi lines having CaMV35S as the promoter. Further, a long-term RNAi effect was evident, because females extracted from transgenic lines were of deformed shape with depleted transcripts of integrase and splicing factor genes. We conclude that pAt1g74770 can be an attractive alternative to drive localized expression of RNAi constructs rather than using a constitutive promoter. The pAt1g74770-driven gene silencing system can be expanded into different plant-nematode interaction models.

Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions

Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.

Recent trends and advances of RNA interference (RNAi) to improve agricultural crops and enhance their resilience to biotic and abiotic stresses

Over the last two decades, significant advances have been made using genetic engineering technology to modify genes from various exotic origins and introduce them into plants to induce favorable traits. RNA interference (RNAi) was discovered earlier as a natural process for controlling the expression of genes across all higher species. It aims to enhance precision and accuracy in pest/pathogen resistance, quality improvement, and manipulating the architecture of plants. However, it existed as a widely used technique recently. RNAi technologies could well be used to down-regulate any genes' expression without disrupting the expression of other genes. The use of RNA interference to silence genes in various organisms has become the preferred method for studying gene functions. The establishment of new approaches and applications for enhancing desirable characters is essential in crops by gene suppression and the refinement of knowledge of endogenous RNAi mechanisms in plants. RNAi technology in recent years has become an important and choicest method for controlling insects, pests, pathogens, and abiotic stresses like drought, salinity, and temperature. Although there are certain drawbacks in efficiency of this technology such as gene candidate selection, stability of trigger molecule, choice of target species and crops. Nevertheless, from past decade several target genes has been identified in numerous crops for their improvement towards biotic and abiotic stresses. The current review is aimed to emphasize the research done on crops under biotic and abiotic stress using RNAi technology. The review also highlights the gene regulatory pathways/gene silencing, RNA interference, RNAi knockdown, RNAi induced biotic and abiotic resistance and advancements in the understanding of RNAi technology and the functionality of various components of the RNAi machinery in crops for their improvement.

Strategies for Controlling the Sporulation in Fusarium spp

Fusarium species are the most destructive phytopathogenic and toxin-producing fungi, causing serious diseases in almost all economically important plants. Sporulation is an essential part of the life cycle of Fusarium. Fusarium most frequently produces three different types of asexual spores, i.e., macroconidia, chlamydospores, and microconidia. It also produces meiotic spores, but fewer than 20% of Fusaria have a known sexual cycle. Therefore, the asexual spores of the Fusarium species play an important role in their propagation and infection. This review places special emphasis on current developments in artificial anti-sporulation techniques as well as features of Fusarium's asexual sporulation regulation, such as temperature, light, pH, host tissue, and nutrients. This description of sporulation regulation aspects and artificial anti-sporulation strategies will help to shed light on the ways to effectively control Fusarium diseases by inhibiting the production of spores, which eventually improves the production of food plants.

RNA Interference for Improving Disease Resistance in Plants and Its Relevance in This Clustered Regularly Interspaced Short Palindromic Repeats-Dominated Era in Terms of dsRNA-Based Biopesticides

RNA interference (RNAi) has been exploited by scientists worldwide to make a significant contribution in the arena of sustainable agriculture and integrated pest management. These strategies are of an imperative need to guarantee food security for the teeming millions globally. The already established deleterious effects of chemical pesticides on human and livestock health have led researchers to exploit RNAi as a potential agri-biotechnology tool to solve the burning issue of agricultural wastage caused by pests and pathogens. On the other hand, CRISPR/Cas9, the latest genome-editing tool, also has a notable potential in this domain of biotic stress resistance, and a constant endeavor by various laboratories is in progress for making pathogen-resistant plants using this technique. Considerable outcry regarding the ill effects of genetically modified (GM) crops on the environment paved the way for the research of RNAi-induced double-stranded RNAs (dsRNA) and their application to biotic stresses. Here, we mainly focus on the application of RNAi technology to improve disease resistance in plants and its relevance in today's CRISPR-dominated world in terms of exogenous application of dsRNAs. We also focused on the ongoing research, public awareness, and subsequent commercialization of dsRNA-based biocontrol products.

Feasibility of Systemically Applied dsRNAs for Pest-Specific RNAi-Induced Gene Silencing in White Oak

The efficacy of double-stranded RNA (dsRNA) in inducing host specific gene knockdown and mortality has been demonstrated in a multitude of insects and dsRNAs are being integrated for pest suppression in a variety of agricultural and horticultural crops. However, less attention has been applied to their use in forest settings, despite the demonstrated susceptibility of multiple forest pests to RNAi. Prior to implementation for forest pest suppression, characterization of the specificity, efficacy, and behavior of dsRNAs in the environment is essential. Therefore, we investigated the translocation and retention of exogenously applied dsRNA in an economically and ecologically significant hardwood tree when applied hydroponically. White oak (Quercus alba, L.) seedlings were exposed to dsRNAs as a root soak, and at 1, 3, 5, and 7 days post-exposure were destructively sampled, divided into stem and leaf tissue, and the RNA extracted. Gel electrophoresis was used to visualize the presence of exogenous dsRNA in treated seedling material and Sanger sequencing was used to further verify recovery of treatment dsRNAs. Both techniques confirmed the presence of the exogenously applied dsRNAs in each tissue type at each sample interval, demonstrating successful uptake and translocation of dsRNAs through white oak tissues. Our findings support root uptake as a viable delivery method for dsRNAs in hardwood seedlings, which could provide single tree protection from selected tree feeding pests or pathogens.

Meloidogyne-SP4 effector gene silencing reduces reproduction of root-knot nematodes in rice (Oryza sativa)

The root-knot nematodes (RKN) Meloidogyne graminicola and M. incognita are responsible for rice yield losses worldwide, particularly in Asia and Africa. Previous studies demonstrated that nematode-secreted proteins are crucial for root invasion and establishment in the host. We present some characteristics of a pioneer effector, M. incognita-secreted protein 4 (Mi-SP4), which is conserved in RKN and required for infection in compatible rice-RKN interactions. In situ hybridisation assays revealed Mi-SP4 expression in the dorsal pharyngeal gland of M. incognita second-stage juveniles (J2). Meloidogyne-SP4 transcripts strongly accumulated in pre-parasitic J2 and decreased in later parasitic stages of M. incognita and M. graminicola. Transient expression of the nematode effector gene in Nicotiana benthamiana leaves and onion cells indicated that GFP-tagged Mi-SP4 was present in the cytoplasm and accumulated in the nucleus of the plant cells. In vitro RNA interference (RNAi) gene silencing, obtained by soaking J2 with small-interfering (si)RNA si4-1, decreased Mi -SP4 expression in J2 by 35% and significantly reduced M. incognita reproduction in rice by at least 30%. Similarly, host-mediated gene silencing of the nematode SP4 effector candidate gene in transgenic rice plants significantly reduced M. graminicola reproduction by 26% to 47%. The data obtained demonstrate that Mi -SP4 is a pioneer virulence effector, which plays an essential role in both M. incognita and M. graminicola pathogenicity on rice.

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.

A new fungus-mediated RNAi method established and used to study the fatty acid and retinol binding protein function of the plant-parasitic nematode Aphelenchoides besseyi

RNA interference (RNAi) is a powerful tool for gene functional analysis of plant-parasitic nematodes (PPNs). RNAi involving soaking in a dsRNA solution and in planta methods is commonly applied in the study of gene function in PPNs. However, certain problems restrict the application of these methods. Therefore, more convenient and effective RNAi methods need to be established for different PPNs according to their biological characteristics. In this study, the fatty acid and retinoid binding protein genes (Ab-far-1, Ab-far-4, and combinatorial Ab-far-1 and Ab-far-4) of the rice white tip nematode (RWTN), Aphelenchoides besseyi, were used as target genes to construct a fungal RNAi vector, and the Ab-far-n dsRNA transgenic Botrytis cinerea (ARTBn) were generated using Agrobacterium-mediated transformation technology. After RWTN feeding on ARTBn, the expression of Ab-far-1 and Ab-far-4 in the nematodes was efficiently silenced, and the reproduction and pathogenicity of the nematodes were clearly inhibited. The Ab-far-1 and Ab-far-4 co-RNAi effects were better than the effects when each gene was individually targeted with RNAi. Additionally, the RNAi induced when RWTNs fed on ARTB1 were persistent and heritable. Thus, a new method of fungus-mediated RNAi was established for fungivorous PPNs and was verified as effective and applicable to the study of nematode gene function. This technique will remove the technological bottlenecks and provide a new method to studying the multiple genes with polygene co-RNAi in fungivorous PPNs. This study also provides a theoretical basis and new thought for further study of the gene function in PPNs.Abbreviations: FAR(Fatty acid and retinol-binding proteins); RWTN (The rice white tip nematode, Aphelenchoides besseyi); Ab-far-n (Fatty acid and retinol binding protein gene of A. besseyi); ARTB1 (Ab-far-1 hpRNA transgenic Botrytis cinerea); ARTB4 (Ab-far-4 hpRNA transgenic Botrytis cinerea); ARTB1/4 (combinatorial Ab-far-1 and Ab-far-4 hpRNA transgenic B. cinerea); EVTB (Empty vector transgenic B. cinerea); GRTB (eGFP hpRNA transgenic B. cinerea); WTB (Wild-type B. cinerea).

RNA interference and crop protection against biotic stresses

RNA interference (RNAi) is a universal phenomenon of RNA silencing or gene silencing with broader implications in important physiological and developmental processes of most eukaryotes, including plants. Small RNA (sRNA) are the critical drivers of the RNAi machinery that ensures down-regulation of the target genes in a homology-dependent manner and includes small-interfering RNAs (siRNAs) and micro RNAs (miRNAs). Plant researchers across the globe have exploited the powerful technique of RNAi to execute targeted suppression of desired genes in important crop plants, with an intent to improve crop protection against pathogens and pests for sustainable crop production. Biotic stresses cause severe losses to the agricultural productivity leading to food insecurity for future generations. RNAi has majorly contributed towards the development of designer crops that are resilient towards the various biotic stresses such as viruses, bacteria, fungi, insect pests, and nematodes. This review summarizes the recent progress made in the RNAi-mediated strategies against these biotic stresses, along with new insights on the future directions in research involving RNAi for crop protection.

Simultaneous RNAi Knockdown of Three FMRFamide-Like Peptide Genes, Mi-flp1, Mi-flp12, and Mi-flp18 Provides Resistance to Root-Knot Nematode, Meloidogyne incognita

Root-knot nematode, Meloidogyne incognita, is a devastating sedentary endoparasite that causes considerable damage to agricultural crops worldwide. Modern approaches targeting the physiological processes have confirmed the potential of FMRFamide like peptide (FLPs) family of neuromotor genes for nematode management. Here, we assessed the knock down effect of Mi-flp1, Mi-flp12, and Mi-flp18 of M. incognita and their combinatorial fusion cassette on infection and reproduction. Comparative developmental profiling revealed higher expression of all three FLPs in the infective 2nd stage juveniles (J2s). Further, Mi-flp1 expression in J2s could be localized in the ventral pharyngeal nerves near to metacarpal bulb of the central nervous system. In vitro RNAi silencing of three FLPs and their fusion cassette in M. incognita J2s showed that combinatorial silencing is the most effective and affected nematode host recognition followed by reduced penetration ability and subsequent infection into tomato and adzuki bean roots. Northern blot analysis of J2s soaked in fusion dsRNA revealed the presence of siRNA of all three target FLPs establishing successful processing of fusion gene dsRNA in the J2s. Further, evaluation of the fusion gene cassette is done through host-delivered RNAi in tobacco. Transgenic plants with fusion gene RNA-expressing vector were generated in which transgene integration was confirmed by PCR, qRT-PCR, and Southern blot analysis. Transcript accumulation of three FLPs constituting the fusion gene was reduced in the M. incognita females collected from the transgenic plants that provided additional evidence for successful gene silencing. Evaluation of positive T₁ transgenic lines against M. incognita brought down the disease burden as indicated by various disease parameters that ultimately reduced the nematode multiplication factor (MF) by 85% compared to the wild-type plants. The study establishes the possibility of simultaneous silencing of more than one FLPs gene for effective management of M. incognita.

Chitin Biosynthesis Inhibition of Meloidogyne incognita by RNAi-Mediated Gene Silencing Increases Resistance to Transgenic Tobacco Plants

Meloidogyne incognita is a devastating plant parasitic nematode that causes root knot disease in a wide range of plants. In the present study, we investigated host-induced RNA interference (RNAi) gene silencing of chitin biosynthesis pathway genes (chitin synthase, glucose-6-phosphate isomerase, and trehalase) in transgenic tobacco plants. To develop an RNAi vector, ubiquitin (UBQ1) promoter was directly cloned, and to generate an RNAi construct, expression of three genes was suppressed using the GATEWAY system. Further, transgenic Nicotiana benthamiana lines expressing dsRNA for chitin synthase (CS), glucose-6-phosphate isomerase (GPI), and trehalase 1 (TH1) were generated. Quantitative PCR analysis confirmed endogenous mRNA expression of root knot nematode (RKN) and revealed that all three genes were more highly expressed in the female stage than in eggs and in the parasitic stage. In vivo, transformed roots were challenged with M. incognita. The number of eggs and root knots were significantly decreased by 60-90% in RNAi transgenic lines. As evident, root galls obtained from transgenic RNAi lines exhibited 0.01- to 0.70-fold downregulation of transcript levels of targeted genes compared with galls isolated from control plants. Furthermore, phenotypic characteristics such as female size and width were also marginally altered, while effect of egg mass per egg number in RNAi transgenic lines was reduced. These results indicate the relevance and significance of targeting chitin biosynthesis genes during the nematode lifespan. Overall, our results suggest that further developments in RNAi efficiency in commercially valued crops can be applied to employ RNAi against other plant parasitic nematodes.

Host-Induced Silencing of FMRFamide-Like Peptide Genes, flp-1 and flp-12, in Rice Impairs Reproductive Fitness of the Root-Knot Nematode Meloidogyne graminicola

Rice (Oryza sativa L.) is one of the major staple food crops of the world. The productivity of rice is considerably affected by the root-knot nematode, Meloidogyne graminicola. Modern nematode management strategies targeting the physiological processes have established the potency of use of neuromotor genes for their management. Here, we explored the utility of two FMRFamide like peptide coding genes, Mg-flp-1 and Mg-flp-12 of M. graminicola for its management through host-induced gene silencing (HIGS) using Agrobacterium-mediated transformation of rice. The presence and integration of hairpin RNA (hpRNA) constructs in transgenic lines were confirmed by PCR, qRT-PCR, and Southern and Northern hybridization. Transgenic plants were evaluated against M. graminicola, where phenotypic effect of HIGS was pronounced with reduction in galling by 20-48% in the transgenic plants. This also led to significant decrease in total number of endoparasites by 31-50% for Mg-flp-1 and 34-51% for Mg-flp-12 transgenics. Likewise, number of egg masses per plant and eggs per egg mass also declined significantly in the transgenics, ultimately affecting the multiplication factor, when compared to the wild type plants. This study establishes the effectiveness of the two M. graminicola flp genes for its management and also for gene pyramiding.

Development of nematode resistance in Arabidopsis by HD-RNAi-mediated silencing of the effector gene Mi-msp2

Root-knot nematodes (RKNs) are devastating parasites that infect thousands of plants. As RKN infection is facilitated by oesophageal gland effector genes, one such effector gene, Mi-msp2, was selected for a detailed characterization. Based on domain analysis, the Mi-MSP2 protein contains an ShKT domain, which is likely involved in blocking K⁺ channels and may help in evading the plant defence response. Expression of the Mi-msp2 gene was higher in juveniles (parasitic stage of RKNs) than in eggs and adults. Stable homozygous transgenic Arabidopsis lines expressing Mi-msp2 dsRNA were generated, and the numbers of galls, females and egg masses were reduced by 52-54%, 60-66% and 84-95%, respectively, in two independent RNAi lines compared with control plants. Furthermore, expression analysis revealed a significant reduction in Mi-msp2 mRNA abundance (up to 88%) in female nematodes feeding on transgenic plants expressing dsRNA, and northern blot analysis confirmed expression of the Mi-msp2 siRNA in the transgenic plants. Interestingly, a significant reduction in the reproduction factor was observed (nearly 40-fold). These data suggest that the Mi-msp2 gene can be used as a potential target for RKN management in crops of economic importance.

Host-derived gene silencing of parasite fitness genes improves resistance to soybean cyst nematodes in stable transgenic soybean

KEY MESSAGE

Soybean expressing small interfering RNA of SCN improved plant resistance to SCN consistently, and small RNA-seq analysis revealed a threshold of siRNA expression required for resistance ability. Soybean cyst nematode (SCN), Heterodera glycines, is one of the most destructive pests limiting soybean production worldwide, with estimated losses of $1 billion dollars annually in the USA alone. RNA interference (RNAi) has become a powerful tool for silencing gene expression. We report here that the expression of hairpin RNAi constructs, derived from two SCN genes related to reproduction and fitness, HgY25 and HgPrp17, enhances resistance to SCN in stably transformed soybean plants. The analyses of T3 to T5 generations of stable transgenic soybeans by molecular strategies and next-generation sequencing confirmed the presence of specific short interfering RNAs complementary to the target SCN genes. Bioassays performed on transgenic soybean lines targeting SCN HgY25 and HgPrp17 fitness genes showed significant reductions (up to 73%) for eggs/g root in the T3 and T4 homozygous transgenic lines. Targeted mRNAs of SCN eggs collected from the transgenic soybean lines were efficiently down-regulated, as confirmed by quantitative RT-PCR. Based on the small RNA-seq data and bioassays, it is our hypothesis that a threshold of small interfering RNA molecules is required to significantly reduce SCN populations feeding on the host plants. Our results demonstrated that host-derived gene silencing of essential SCN fitness genes could be an effective strategy for enhancing resistance in crop plants.

In Vitro Acquisition of Specific Small Interfering RNAs Inhibits the Expression of Some Target Genes in the Plant Ectoparasite Xiphinema index

Xiphinema index is an important plant parasitic nematode that induces direct damages and specifically transmits the Grapevine fanleaf virus, which is particularly harmful for grapevines. Genomic resources of this nematode species are still limited and no functional gene validation technology is available. RNA interference (RNAi) is a powerful technology to study gene function and here we describe the application of RNAi on several genes in X. index. Soaking the nematodes for 48 h in a suspension containing specific small interfering RNAs resulted in a partial inhibition of the accumulation of some targeted mRNA. However, low reproducible silencing efficiency was observed which could arise from X. index silencing pathway deficiencies. Indeed, essential accustomed proteins for these pathways were not found in the X. index proteome predicted from transcriptomic data. The most reproducible silencing effect was obtained when targeting the piccolo gene potentially involved in endo-exocytosis of synaptic molecules. This represents the first report of gene silencing in a nematode belonging to the Longidoridae family.

RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants

With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.

RNAi for Resistance Against Biotic Stresses in Crop Plants

RNA interference (RNAi)-based gene silencing has become one of the most successful strategies in not only identifying gene function but also in improving agronomical traits of crops by silencing genes of different pathogens/pests and also plant genes for improvement of desired trait. The conserved nature of RNAi pathway across different organisms increases its applicability in various basic and applied fields. Here we attempt to summarize the knowledge generated on the fundamental mechanisms of RNAi over the years, with emphasis on insects and plant-parasitic nematodes (PPNs). This chapter also reviews the rich history of RNAi research, gene regulation by small RNAs across different organisms, and application potential of RNAi for generating transgenic plants resistant to major pests_. But, there are some limitations too which restrict wider applications of this technology to its full potential. Further refinement of this technology in terms of resolving these shortcomings constitutes one of the thrust areas in present RNAi research. Nevertheless, its application especially in breeding agricultural crops resistant against biotic stresses will certainly offer the possible solutions for some of the breeding objectives which are otherwise unattainable.

The Elusive Search for Reniform Nematode Resistance in Cotton

The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) has emerged as the most important plant-parasitic nematode of cotton in the United States cotton belt. Success in the development of reniform nematode-resistant upland cotton cultivars (Gossypium hirsutum L.) has not been realized despite over three decades of breeding efforts. Research approaches ranging from conventional breeding to triple species hybrids to marker-assisted selection have been employed to introgress reniform nematode resistance from other species of cotton into upland cultivars. Reniform nematode-resistant breeding lines derived from G. longicalyx were developed in 2007. However, these breeding lines displayed stunting symptoms and a hypersensitive response to reniform nematode infection. Subsequent breeding efforts focused on G. barbadense, G. aridum, G. armoreanum, and other species that have a high level of resistance to reniform nematode. Marker-assisted selection has greatly improved screening of reniform nematode-resistant lines. The use of advanced molecular techniques such as CRISPER-Cas9 systems and alternative ways such as delivery of suitable "cry" proteins and specific double-stranded RNA to nematodes will assist in developing resistant cultivars of cotton. In spite of the efforts of cotton breeders and nematologists, successes are limited only to the development of reniform nematode-resistant breeding lines. In this article, we provide an overview of the approaches employed to develop reniform nematode-resistant upland cotton cultivars in the past, progress to date, major obstacles, and some promising future research activity.

Cross-kingdom RNA trafficking and environmental RNAi-nature's blueprint for modern crop protection strategies

In plants, small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating host immunity against bacteria, fungi, oomycetes, viruses, and pests. Similarly, sRNAs from pathogens and pests also play an important role in modulating their virulence. Strikingly, recent evidence supports that some sRNAs can travel between interacting organisms and induce gene silencing in the counter party, a mechanism termed cross-kingdom RNAi. Exploiting this new knowledge, host-induced gene silencing (HIGS) by transgenic expression of pathogen gene-targeting double-stranded (ds)RNA has the potential to become an important disease-control method. To circumvent transgenic approaches, direct application of dsRNAs or sRNAs (environmental RNAi) onto host plants or post-harvest products leads to silencing of the target microbe/pest gene (referred to spray-induced gene silencing, SIGS) and confers efficient disease control. This review summarizes the current understanding of cross-kingdom RNA trafficking and environmental RNAi and how these findings can be developed into novel effective strategies to fight diseases caused by microbial pathogens and pests.

Host Delivered RNAi of Two Cuticle Collagen Genes, Mi-col-1 and Lemmi-5 Hampers Structure and Fecundity in Meloidogyne incognita

Root-knot nematodes have emerged as devastating parasites causing substantial losses to agricultural economy worldwide. Tomato is the most favored host for major species of root-knot nematodes. Control strategies like use of nematicides have proved to be harmful to the environment. Other control methods like development of resistant cultivars and crop rotation have serious limitations. This study deals with the application of host generated RNA interference toward development of resistance against root-knot nematode Meloidogyne incognita in tomato. Two cuticle collagen genes viz. Mi-col-1 and Lemmi-5 involved in the synthesis and maintenance of the cuticle in M. incognita were targeted through host generated RNA interference. Expression of both Mi-col-1 and Lemmi-5 was found to be higher in adult females followed by egg masses and J2s. Tomato var. Pusa Ruby was transformed with the RNAi constructs of these genes to develop transgenic lines expressing the target dsRNAs. 30.80-35.00% reduction in the number of adult females, 50.06-65.73% reduction in the number of egg mass per plant and 76.47-82.59% reduction in the number of eggs per egg mass were observed for the T₁ events expressing Mi-col-1 dsRNA. Similarly, 34.14-38.54% reduction in the number of adult females, 62.34-66.71% reduction in number of egg mass per plant and 67.13-79.76% reduction in the number of eggs per egg mass were observed for the T₁ generation expressing Lemmi-5 dsRNA. The multiplication factor of M. incognita reduced significantly in both the cases and the structure of adult females isolated from transgenic plants were heavily distorted. This study demonstrates the role of the cuticle collagen genes Mi-col-1 and Lemmi-5 in the structure and development of M. incognita cuticle inside the host and reinforces the potential of host generated RNA interference for management of plant parasitic nematodes (PPNs).

Identification, Validation and Utilization of Novel Nematode-Responsive Root-Specific Promoters in Arabidopsis for Inducing Host-Delivered RNAi Mediated Root-Knot Nematode Resistance

The root-knot nematode (RKN), Meloidogyne incognita, is an obligate, sedentary endoparasite that infects a large number of crops and severely affects productivity. The commonly used nematode control strategies have their own limitations. Of late, RNA interference (RNAi) has become a popular approach for the development of nematode resistance in plants. Transgenic crops capable of expressing dsRNAs, specifically in roots for disrupting the parasitic process, offer an effective and efficient means of producing resistant crops. We identified nematode-responsive and root-specific (NRRS) promoters by using microarray data from the public domain and known conserved cis-elements. A set of 51 NRRS genes was identified which was narrowed down further on the basis of presence of cis-elements combined with minimal expression in the absence of nematode infection. The comparative analysis of promoters from the enriched NRRS set, along with earlier reported nematode-responsive genes, led to the identification of specific cis-elements. The promoters of two candidate genes were used to generate transgenic plants harboring promoter GUS constructs and tested in planta against nematodes. Both promoters showed preferential expression upon nematode infection, exclusively in the root in one and galls in the other. One of these NRRS promoters was used to drive the expression of splicing factor, a nematode-specific gene, for generating host-delivered RNAi-mediated nematode-resistant plants. Transgenic lines expressing dsRNA of splicing factor under the NRRS promoter exhibited upto a 32% reduction in number of galls compared to control plants.

Host Delivered RNAi, an efficient approach to increase rice resistance to sheath blight pathogen (Rhizoctonia solani)

Rhizoctonia solani, the causal agent of rice sheath blight disease, causes significant losses worldwide as there are no cultivars providing absolute resistance to this fungal pathogen. We have used Host Delivered RNA Interference (HD-RNAi) technology to target two PATHOGENICITY MAP KINASE 1 (PMK1) homologues, RPMK1-1 and RPMK1-2, from R. solani using a hybrid RNAi construct. PMK1 homologues in other fungal pathogens are essential for the formation of appressorium, the fungal infection structures required for penetration of the plant cuticle, as well as invasive growth once inside the plant tissues and overall viability of the pathogen within the plant. Evaluation of transgenic rice lines revealed a significant decrease in fungal infection levels compared to non-transformed controls and the observed delay in disease symptoms was further confirmed through microscopic studies. Relative expression levels of the targeted genes, RPMK1-1 and RPMK1-2, were determined in R. solani infecting either transgenic or control lines with significantly lower levels observed in R. solani infecting transgenic lines carrying the HD-RNAi constructs. This is the first report demonstrating the effectiveness of HD-RNAi against sheath blight and offers new opportunities for durable control of the disease as it does not rely on resistance conferred by major resistance genes.

RNA Interference: A Novel Source of Resistance to Combat Plant Parasitic Nematodes

Plant parasitic nematodes cause severe damage and yield loss in major crops all over the world. Available control strategies include use of insecticides/nematicides but these have proved detrimental to the environment, while other strategies like crop rotation and resistant cultivars have serious limitations. This scenario provides an opportunity for the utilization of technological advances like RNA interference (RNAi) to engineer resistance against these devastating parasites. First demonstrated in the model free living nematode, Caenorhabtidis elegans; the phenomenon of RNAi has been successfully used to suppress essential genes of plant parasitic nematodes involved in parasitism, nematode development and mRNA metabolism. Synthetic neurotransmitants mixed with dsRNA solutions are used for in vitro RNAi in plant parasitic nematodes with significant success. However, host delivered in planta RNAi has proved to be a pioneering phenomenon to deliver dsRNAs to feeding nematodes and silence the target genes to achieve resistance. Highly enriched genomic databases are exploited to limit off target effects and ensure sequence specific silencing. Technological advances like gene stacking and use of nematode inducible and tissue specific promoters can further enhance the utility of RNAi based transgenics against plant parasitic nematodes.

Aflatoxin-free transgenic maize using host-induced gene silencing

Aflatoxins, toxic secondary metabolites produced by some Aspergillus species, are a universal agricultural economic problem and a critical health issue. Despite decades of control efforts, aflatoxin contamination is responsible for a global loss of millions of tons of crops each year. We show that host-induced gene silencing is an effective method for eliminating this toxin in transgenic maize. We transformed maize plants with a kernel-specific RNA interference (RNAi) gene cassette targeting the aflC gene, which encodes an enzyme in the Aspergillus aflatoxin biosynthetic pathway. After pathogen infection, aflatoxin could not be detected in kernels from these RNAi transgenic maize plants, while toxin loads reached thousands of parts per billion in nontransgenic control kernels. A comparison of transcripts in developing aflatoxin-free transgenic kernels with those from nontransgenic kernels showed no significant differences between these two groups. These results demonstrate that small interfering RNA molecules can be used to silence aflatoxin biosynthesis in maize, providing an attractive and precise engineering strategy that could also be extended to other crops to improve food security.

Using Vital Dyes to Trace Uptake of dsRNA by Green Peach Aphid Allows Effective Assessment of Target Gene Knockdown

RNA interference (RNAi) is an effective tool to study gene function. For in vitro studies of RNAi in insects, microinjection of double-stranded (ds)RNA may cause stress. Non-persuasive oral delivery of dsRNA to trigger RNAi is a better mode of delivery for delicate insects such as aphids because it mimics natural feeding. However, when insects feed ad libitum, some individuals may not feed. For accurate measurement of gene knockdown, analysis should only include insects that have ingested dsRNA. The suitability of eleven dyes was assessed to trace ingestion of dsRNA in an artificial feeding system for green peach aphids (GPA, Myzus persicae). Non-toxic levels of neutral red and acridine orange were suitable tracers: they were visible in the stylet and gut after feeding for 24 h, and may also attract aphids to feed. Nymphs stained with neutral red (0.02%) were analysed for target gene expression after feeding on sucrose with dsRNA (V-ATPase, vha-8). There was a greater reduction in vha-8 expression and reproduction compared to nymphs fed the diet without dye. The results confirm the importance of identifying aphids that have ingested dsRNA, and also provide evidence that the vha-8 gene is a potential target for control of GPAs.

Host-Derived Artificial MicroRNA as an Alternative Method to Improve Soybean Resistance to Soybean Cyst Nematode

The soybean cyst nematode (SCN), Heterodera glycines, is one of the most important pests limiting soybean production worldwide. Novel approaches to managing this pest have focused on gene silencing of target nematode sequences using RNA interference (RNAi). With the discovery of endogenous microRNAs as a mode of gene regulation in plants, artificial microRNA (amiRNA) methods have become an alternative method for gene silencing, with the advantage that they can lead to more specific silencing of target genes than traditional RNAi vectors. To explore the application of amiRNAs for improving soybean resistance to SCN, three nematode genes (designated as J15, J20, and J23) were targeted using amiRNA vectors. The transgenic soybean hairy roots, transformed independently with these three amiRNA vectors, showed significant reductions in SCN population densities in bioassays. Expression of the targeted genes within SCN eggs were downregulated in populations feeding on transgenic hairy roots. Our results provide evidence that host-derived amiRNA methods have great potential to improve soybean resistance to SCN. This approach should also limit undesirable phenotypes associated with off-target effects, which is an important consideration for commercialization of transgenic crops.

RNA Silencing in Plants: Mechanisms, Technologies and Applications in Horticultural Crops

Understanding the fundamental nature of a molecular process or a biological pathway is often a catalyst for the development of new technologies in biology. Indeed, studies from late 1990s to early 2000s have uncovered multiple overlapping but functionally distinct RNA silencing pathways in plants, including the posttranscriptional microRNA and small interfering RNA pathways and the transcriptional RNA-directed DNA methylation pathway. These findings have in turn been exploited for developing artificial RNA silencing technologies such as hairpin RNA, artificial microRNA, intrinsic direct repeat, 3' UTR inverted repeat, artificial trans-acting siRNA, and virus-induced gene silencing technologies. Some of these RNA silencing technologies, such as the hairpin RNA technology, have already been widely used for genetic improvement of crop plants in agriculture. For horticultural plants, RNA silencing technologies have been used to increase disease and pest resistance, alter plant architecture and flowering time, improve commercial traits of fruits and flowers, enhance nutritional values, remove toxic compounds and allergens, and develop high-value industrial products. In this article we aim to provide an overview of the RNA silencing pathways in plants, summarize the existing RNA silencing technologies, and review the current progress in applying these technologies for the improvement of agricultural crops particularly horticultural crops.

Identification and functional analysis of secreted effectors from phytoparasitic nematodes

BACKGROUND

Plant parasitic nematodes develop an intimate and long-term feeding relationship with their host plants. They induce a multi-nucleate feeding site close to the vascular bundle in the roots of their host plant and remain sessile for the rest of their life. Nematode secretions, produced in the oesophageal glands and secreted through a hollow stylet into the host plant cytoplasm, are believed to play key role in pathogenesis. To combat these persistent pathogens, the identity and functional analysis of secreted effectors can serve as a key to devise durable control measures. In this review, we will recapitulate the knowledge over the identification and functional characterization of secreted nematode effector repertoire from phytoparasitic nematodes.

RESEARCH

Despite considerable efforts, the identity of genes encoding nematode secreted proteins has long been severely hampered because of their microscopic size, long generation time and obligate biotrophic nature. The methodologies such as bioinformatics, protein structure modeling, in situ hybridization microscopy, and protein-protein interaction have been used to identify and to attribute functions to the effectors. In addition, RNA interference (RNAi) has been instrumental to decipher the role of the genes encoding secreted effectors necessary for parasitism and genes attributed to normal development. Recent comparative and functional genomic approaches have accelerated the identification of effectors from phytoparasitic nematodes and offers opportunities to control these pathogens.

CONCLUSION

Plant parasitic nematodes pose a serious threat to global food security of various economically important crops. There is a wealth of genomic and transcriptomic information available on plant parasitic nematodes and comparative genomics has identified many effectors. Bioengineering crops with dsRNA of phytonematode genes can disrupt the life cycle of parasitic nematodes and therefore holds great promise to develop resistant crops against plant-parasitic nematodes.

Resistance to Ditylenchus destructor Infection in Sweet Potato by the Expression of Small Interfering RNAs Targeting unc-15, a Movement-Related Gene

Stem nematode (Ditylenchus destructor) is one of most serious diseases that limit the productivity and quality of sweet potato (Ipomoea batatas), a root crop with worldwide importance for food security and nutrition improvement. Hence, there is a global demand for developing sweet potato varieties that are resistant to the disease. In this study, we have investigated the interference of stem nematode infectivity by the expression of small interfering RNAs (siRNAs) in transgenic sweet potato that are homologous to the unc-15 gene, which affects the muscle protein paramyosin of the pathogen. The production of double-stranded RNAs and siRNAs in transgenic lines with a single transgene integration event was verified by Northern blot analysis. The expression of unc-15 was reduced dramatically in stem nematodes collected from the inoculated storage roots of transgenic plants, and the infection areas of their storage roots were dramatically smaller than that of wild-type (WT). Compared with the WT, the transgenic plants showed increased yield in the stem nematode-infested field. Our results demonstrate that the expression of siRNAs targeting the unc-15 gene of D. destructor is an effective approach in improving stem nematode resistance in sweet potato, in adjunct with the global integrated pest management programs.

Host-induced gene silencing inhibits the biotrophic pathogen causing downy mildew of lettuce

Host-induced gene silencing (HIGS) is an RNA interference-based approach in which small interfering RNAs (siRNAs) are produced in the host plant and subsequently move into the pathogen to silence pathogen genes. As a proof-of-concept, we generated stable transgenic lettuce plants expressing siRNAs targeting potentially vital genes of Bremia lactucae, a biotrophic oomycete that causes downy mildew, the most important disease of lettuce worldwide. Transgenic plants, expressing inverted repeats of fragments of either the Highly Abundant Message #34 (HAM34) or Cellulose Synthase (CES1) genes of B. lactucae, specifically suppressed expression of these genes, resulting in greatly reduced growth and inhibition of sporulation of B. lactucae. This demonstrates that HIGS can provide effective control of B. lactucae in lettuce; such control does not rely on ephemeral resistance conferred by major resistance genes and therefore offers new opportunities for durable control of diverse diseases in numerous crops.

A Nematode Calreticulin, Rs-CRT, Is a Key Effector in Reproduction and Pathogenicity of Radopholus similis

Radopholus similis is a migratory plant-parasitic nematode that causes severe damage to many agricultural and horticultural crops. Calreticulin (CRT) is a Ca2+-binding multifunctional protein that plays key roles in the parasitism, immune evasion, reproduction and pathogenesis of many animal parasites and plant nematodes. Therefore, CRT is a promising target for controlling R. similis. In this study, we obtained the full-length sequence of the CRT gene from R. similis (Rs-crt), which is 1,527-bp long and includes a 1,206-bp ORF that encodes 401 amino acids. Rs-CRT and Mi-CRT from Meloidogyne incognita showed the highest similarity and were grouped on the same branch of the phylogenetic tree. Rs-crt is a multi-copy gene that is expressed in the oesophageal glands and gonads of females, the gonads of males, the intestines of juveniles and the eggs of R. similis. The highest Rs-crt expression was detected in females, followed by juveniles, eggs and males. The reproductive capability and pathogenicity of R. similis were significantly reduced after treatment with Rs-crt dsRNA for 36 h. Using plant-mediated RNAi, we confirmed that Rs-crt expression was significantly inhibited in the nematodes, and resistance to R. similis was significantly improved in transgenic tomato plants. Plant-mediated RNAi-induced silencing of Rs-crt could be effectively transmitted to the F2 generation of R. similis; however, the silencing effect of Rs-crt induced by in vitro RNAi was no longer detectable in F1 and F2 nematodes. Thus, Rs-crt is essential for the reproduction and pathogenicity of R. similis.

Tomato transgenic plants expressing hairpin construct of a nematode protease gene conferred enhanced resistance to root-knot nematodes

Root-knot nematodes (Meloidogyne incognita) cause substantial yield losses in vegetables worldwide, and are difficult to manage. Continuous withdrawal of environmentally-harmful nematicides from the global market warrants the need for novel nematode management strategies. Utility of host-delivered RNAi has been demonstrated in several plants (Arabidopsis, tobacco, and soybean) that exhibited resistance against root-knot and cyst nematodes. Herein, a M. incognita-specific protease gene, cathepsin L cysteine proteinase (Mi-cpl-1), was targeted to generate tomato transgenic lines to evaluate the genetically modified nematode resistance. In vitro knockdown of Mi-cpl-1 gene led to the reduced attraction and penetration of M. incognita in tomato, suggesting the involvement of Mi-cpl-1 in nematode parasitism. Transgenic expression of the RNAi construct of Mi-cpl-1 gene resulted in 60-80% reduction in infection and multiplication of M. incognita in tomato. Evidence for in vitro and in vivo silencing of Mi-cpl-1 was confirmed by expression analysis using quantitative PCR. Our study demonstrates that Mi-cpl-1 plays crucial role during plant-nematode interaction and plant-mediated downregulation of this gene elicits detrimental effect on M. incognita development, reinforcing the potential of RNAi technology for management of phytonematodes in crop plants.

Molecular identification and functional characterization of the fatty acid- and retinoid-binding protein gene Rs-far-1 in the burrowing nematode Radopholus similis (Tylenchida: Pratylenchidae)

Fatty acid- and retinoid-binding protein (FAR) is a nematode-specific protein expressed in the nematode hypodermis. It is involved in nematode development, reproduction, and infection and can disrupt the plant defense reaction. In this study, we obtained the full-length sequence of the far gene from Radopholus similis (Rs-far-1), which is 828 bp long and includes a 558 bp ORF encoding 186 amino acids. A protein homology analysis revealed that Rs-FAR-1 is 75% similar to Mj-FAR-1 from Meloidogyne javanica. A neighbor-joining phylogenetic tree was inferred and showed that Rs-FAR-1 is most similar to Pv-FAR-1 from Pratylenchus vulnus. A fluorescence-based ligand-binding analysis confirmed that Rs-FAR-1 can combine with fatty acids and retinol. qPCR was used to assess Rs-far-1 expression levels at different developmental stages in different R. similis populations, and its expression was 2.5 times greater in the highly pathogenic Rs-C population than in the less pathogenic Rs-P population. The highest expression was found in females, followed by eggs, juveniles and males. When R. similis was treated with Rs-far-1 dsRNA for 36 h, the reproduction and pathogenicity decreased significantly. In situ hybridization revealed Rs-far-1 transcripts in the R. similis hypodermis. Additionally, R. similis treated with Rs-far-1 dsRNA or water were inoculated into Arabidopsis thaliana. Allene oxide synthase (AOS) expression in A. thaliana was upregulated during early infection in both treatments and then returned to the expression levels of the control plant. Compared with the control plant, AOS expression significantly decreased in A. thaliana inoculated with water-treated R. similis but significantly increased in A. thaliana inoculated with Rs-far-1 dsRNA-treated R. similis. This finding indicates that Rs-far-1 regulates AOS expression in A. thaliana. Rs-FAR-1 plays a critical role in R. similis development, reproduction, and infection and can disturb the plant defense reaction. Therefore, Rs-far-1 is an important target gene to control R. similis.

Disruption of prefoldin-2 protein synthesis in root-knot nematodes via host-mediated gene silencing efficiently reduces nematode numbers and thus protects plants

MAIN CONCLUSION

The aim of this study is to demonstrate the feasibility of down-regulating endogeneous prefoldin-2 root-knot nematode transcripts by expressing dsRNA with sequence identity to the nematode gene in tobacco roots under the influence of strong Arabidopsis ubiquitin (UBQ1) promoter. Root-knot nematodes (RKNs) are sedentary endoparasites infecting a wide range of plant species. They parasitise the root system, thereby disrupting water and nutrient uptake and causing major reductions in crop yields. The most reliable means of controlling RKNs is via the use of soil fumigants such as methyl bromide. With the emergence of RNA interference (RNAi) technology, which permits host-mediated nematode gene silencing, a new strategy to control plant pathogens has become available. In the present study, we investigated host-induced RNAi gene silencing of prefoldin-2 in transgenic Nicotiana benthamiana. Reductions in prefoldin-2 mRNA transcript levels were observed when nematodes were soaked in a dsRNA solution in vitro. Furthermore, nematode reproduction was suppressed in RNAi transgenic lines, as evident by reductions in the numbers of root knots (by 34-60 % in independent RNAi lines) and egg masses (by 33-58 %). Endogenous expression of prefoldin-2, analysed via real-time polymerase chain reaction and Western blotting, revealed that the gene was strongly expressed in the pre-parasitic J2 stage. Our observations demonstrate the relevance and potential importance of targeting the prefoldin gene during the nematode life cycle. The work also suggests that further improvements in silencing efficiency in economically important crops can be accomplished using RNAi directed against plant-parasitic nematodes.

Down-regulation of Fusarium oxysporum endogenous genes by Host-Delivered RNA interference enhances disease resistance

Fusarium oxysporum is a devastating pathogen causing extensive yield losses in a variety of crops and development of sustainable, environmentally friendly methods to improve crop resistance is crucial. We have used Host-Delivered RNA interference (HD-RNAi) technology to partially silence three different genes (FOW2, FRP1, and OPR) in the hemi-biotrophic fungus F. oxysporum f. sp. conglutinans. Expression of double stranded RNA (dsRNA) molecules targeting fungal pathogen genes was achieved in a number of transgenic Arabidopsis lines. F. oxysporum infecting the transgenic lines displayed substantially reduced mRNA levels on all three targeted genes, with an average of 75, 83, and 72% reduction for FOW2, FRP1, and OPR, respectively. The silencing of pathogen genes had a clear positive effect on the ability of the transgenic lines to fight infection. All transgenic lines displayed enhanced resistance to F. oxysporum with delayed disease symptom development, especially FRP1 and OPR lines. Survival rates after fungal infection were higher in the transgenic lines compared to control wild type plants which consistently showed survival rates of 10%, with FOW2 lines showing 25% survival; FRP1 lines 30-50% survival and OPR between 45 and 70% survival. The down-regulation effect was specific for the targeted genes without unintended effects in related genes. In addition to producing resistant crops, HD-RNAi can provide a useful tool to rapidly screen candidate fungal pathogenicity genes without the need to produce fungal knockout mutants.

The status of RNAi-based transgenic research in plant nematology

With the understanding of nematode-plant interactions at the molecular level, new avenues for engineering resistance have opened up, with RNA interference being one of them. Induction of RNAi by delivering double-stranded RNA (dsRNA) has been very successful in the model non-parasitic nematode, Caenorhabditis elegans, while in plant nematodes, dsRNA delivery has been accomplished by soaking nematodes with dsRNA solution mixed with synthetic neurostimulants. The success of in vitro RNAi of target genes has inspired the use of in planta delivery of dsRNA to feeding nematodes. The most convincing success of host-delivered RNAi has been achieved against root-knot nematodes. Plant-mediated RNAi has been shown to lead to the specific down-regulation of target genes in invading nematodes, which had a profound effect on nematode development. RNAi-based transgenics are advantageous as they do not produce any functional foreign proteins and target organisms in a sequence-specific manner. Although the development of RNAi-based transgenics against plant nematodes is still in the preliminary stage, they offer novel management strategy for the future.

Integrated signaling networks in plant responses to sedentary endoparasitic nematodes: a perspective

Sedentary plant endoparasitic nematodes can cause detrimental yield losses in crop plants making the study of detailed cellular, molecular, and whole plant responses to them a subject of importance. In response to invading nematodes and nematode-secreted effectors, plant susceptibility/resistance is mainly determined by the coordination of different signaling pathways including specific plant resistance genes or proteins, plant hormone synthesis and signaling pathways, as well as reactive oxygen signals that are generated in response to nematode attack. Crosstalk between various nematode resistance-related elements can be seen as an integrated signaling network regulated by transcription factors and small RNAs at the transcriptional, posttranscriptional, and/or translational levels. Ultimately, the outcome of this highly controlled signaling network determines the host plant susceptibility/resistance to nematodes.

RNA Interference of Effector Gene Mc16D10L Confers Resistance Against Meloidogyne chitwoodi in Arabidopsis and Potato

Meloidogyne chitwoodi, a quarantine pathogen, is a significant problem in potato-producing areas worldwide. In spite of considerable genetic diversity in wild potato species, no commercial potato cultivars with resistance to M. chitwoodi are available. Nematode effector genes are essential for the molecular interactions between root-knot nematodes and their hosts. Stable transgenic lines of Arabidopsis and potato (Solanum tuberosum) with resistance against M. chitwoodi were developed. RNA interference (RNAi) construct pART27(16D10i-2) was introduced into Arabidopsis thaliana and potato to express double-stranded RNA complementary to the putative M. chitwoodi effector gene Mc16D10L. Plant-mediated RNAi led to a significant level of resistance against M. chitwoodi in Arabidopsis and potato. In transgenic Arabidopsis lines, the number of M. chitwoodi egg masses and eggs was reduced by up to 57 and 67% compared with empty vector controls, respectively. Similarly, in stable transgenic lines of potato, the number of M. chitwoodi egg masses and eggs was reduced by up to 71 and 63% compared with empty vector controls, respectively. The relative transcript level of Mc16D10L was reduced by up to 76% in M. chitwoodi eggs and infective second-stage juveniles that developed on transgenic pART27(16D10i-2) potato, suggesting that the RNAi effect is systemic and heritable in M. chitwoodi.

New wind in the sails: improving the agronomic value of crop plants through RNAi-mediated gene silencing

RNA interference (RNAi) has emerged as a powerful genetic tool for scientific research over the past several years. It has been utilized not only in fundamental research for the assessment of gene function, but also in various fields of applied research, such as human and veterinary medicine and agriculture. In plants, RNAi strategies have the potential to allow manipulation of various aspects of food quality and nutritional content. In addition, the demonstration that agricultural pests, such as insects and nematodes, can be killed by exogenously supplied RNAi targeting their essential genes has raised the possibility that plant predation can be controlled by lethal RNAi signals generated in planta. Indeed, recent evidence argues that this strategy, called host-induced gene silencing (HIGS), is effective against sucking insects and nematodes; it also has been shown to compromise the growth and development of pathogenic fungi, as well as bacteria and viruses, on their plant hosts. Here, we review recent studies that reveal the enormous potential RNAi strategies hold not only for improving the nutritive value and safety of the food supply, but also for providing an environmentally friendly mechanism for plant protection.

RNA interference: concept to reality in crop improvement

The phenomenon of RNA interference (RNAi) is involved in sequence-specific gene regulation driven by the introduction of dsRNA resulting in inhibition of translation or transcriptional repression. Since the discovery of RNAi and its regulatory potentials, it has become evident that RNAi has immense potential in opening a new vista for crop improvement. RNAi technology is precise, efficient, stable and better than antisense technology. It has been employed successfully to alter the gene expression in plants for better quality traits. The impact of RNAi to improve the crop plants has proved to be a novel approach in combating the biotic and abiotic stresses and the nutritional improvement in terms of bio-fortification and bio-elimination. It has been employed successfully to bring about modifications of several desired traits in different plants. These modifications include nutritional improvements, reduced content of food allergens and toxic compounds, enhanced defence against biotic and abiotic stresses, alteration in morphology, crafting male sterility, enhanced secondary metabolite synthesis and seedless plant varieties. However, crop plants developed by RNAi strategy may create biosafety risks. So, there is a need for risk assessment of GM crops in order to make RNAi a better tool to develop crops with biosafety measures. This article is an attempt to review the RNAi, its biochemistry, and the achievements attributed to the application of RNAi in crop improvement.

Plant-mediated RNAi of a gap gene-enhanced tobacco tolerance against the Myzus persicae

Plant-mediated RNAi has been developed as a powerful weapon in the fight against agricultural insect pests. The gap gene hunchback (hb) is of crucial importance in insect axial patterning and knockdown of hb is deforming and lethal to the next generation. The peach potato aphid, Myzus persicae (Sulzer), has many host plants and can be found throughout the world. To investigate the effect of plant-mediated RNAi on control of this insect, the hb gene in M. persicae was cloned, plant RNAi vector was constructed, and transgenic tobacco expressing Mphb dsRNA was developed. Transgenic tobacco had a different integration pattern of the transgene. Bioassays were performed by applying neonate aphids to homozygous transgenic plants in the T2 generation. Results revealed that continuous feeding of transgenic diet reduced Mphb mRNA level in the fed aphids and inhibited insect reproduction, indicating successful knockdown of the target gene in M. persicae by plant-mediated RNAi.

Functional characterization of nematode effectors in plants

Secreted effectors represent the molecular interface between the nematode and its host plant. Studies that aimed at deciphering molecular plant-nematode interactions are hampered by technical hurdles that prevent the generation of transgenic nematodes. However, RNA interference (RNAi) has proven to be a valuable tool to specifically knock-down nematode effector genes, both ex planta and in planta. Plant-mediated RNAi of nematode genes not only facilitates functional characterization of effectors but also lends itself to a novel control strategy against plant-parasitic nematodes. Here, we describe currently used methods to silence genes in plant-parasitic cyst and root-knot nematodes.

Plant-mediated RNA interference of effector gene Mc16D10L confers resistance against Meloidogyne chitwoodi in diverse genetic backgrounds of potato and reduces pathogenicity of nematode offspring

Meloidogyne chitwoodi is a major problem for potato production in the Pacific Northwest of the USA. In spite of long-term breeding efforts no commercial potato cultivars with resistance to M. chitwoodi exist to date. The resistance gene against M. chitwoodi has been introgressed from Solanum bulbocastanum into cultivated potato (S. tuberosum), but M. chitwoodi pathotypes are able to overcome this resistance. In this study, an RNA interference (RNAi) transgene targeting the M. chitwoodi effector gene Mc16D10L was introduced into potato cvs Russet Burbank and Désirée, and the advanced breeding line PA99N82-4, which carries the gene. Stable transgenic lines were generated for glasshouse infection assays. At 35 days after inoculation (DAI) with M. chitwoodi race 1 the number of egg masses (g root)−1 formed on RNAi lines of cvs Russet Burbank and Désirée was reduced significantly by up to 68% compared to empty vector control plants. At 55 DAI, the number of eggs was reduced significantly by up to 65%. In addition, RNAi of Mc16D10L significantly reduced the development of egg masses and eggs formed by the resistance-breaking M. chitwoodi pathotype Roza on PA99N82-4 by up to 47 and 44%, respectively. Importantly, the plant-mediated silencing effect of Mc16D10L was transmitted to M. chitwoodi offspring and significantly reduced pathogenicity in the absence of selection pressure on empty vector control plants. This finding suggests that the RNAi effect is stable and nematode infection decreases regardless of the genotype of the host once the RNAi process has been initiated in the nematode through a transgenic plant. In summary, plant-mediated down-regulation of effector gene Mc16D10L provides a promising new tool for molecular breeding against M. chitwoodi.

Utility of host delivered RNAi of two FMRF amide like peptides, flp-14 and flp-18, for the management of root knot nematode, Meloidogyne incognita

Root knot nematode, Meloidogyne incognita, is an obligate sedentary endoparasite that infects a large number of crop species and causes substantial yield losses. Non-chemical based control strategies for these nematodes are gaining importance. In the present study, we have demonstrated the significance of two FMRFamide like peptide genes (flp-14 and flp-18) for infection and development of resistance to M. incognita through host-derived RNAi. The study demonstrated both in vitro and in planta validation of RNAi-induced silencing of the two genes cloned from J2 stage of M. incognita. In vitro silencing of both the genes interfered with nematode migration towards the host roots and subsequent invasion into the roots. Transgenic tobacco lines were developed with RNAi constructs of flp-14 and flp-18 and evaluated against M. incognita. The transformed plants did not show any visible phenotypic variations suggesting the absence of any off-target effects. Bioefficacy studies with deliberate challenging of M. incognita resulted in 50-80% reduction in infection and multiplication confirming the silencing effect. We have provided evidence for in vitro and in planta silencing of the genes by expression analysis using qRT-PCR. Thus the identified genes and the strategy can be used as a potential tool for the control of M. incognita. This is the first ever report that has revealed the utility of host delivered RNAi of flps to control M. incognita. The strategy can also be extended to other crops and nematodes.

Stacking resistance to crown gall and nematodes in walnut rootstocks

Background

Crown gall (CG) (Agrobacterium tumefaciens) and the root lesion nematodes (RLNs) (Pratylenchus vulnus) are major challenges faced by the California walnut industry, reducing productivity and increasing the cost of establishing and maintaining orchards. Current nematode control strategies include nematicides, crop rotation, and tolerant cultivars, but these methods have limits. Developing genetic resistance through novel approaches like RNA interference (RNAi) can address these problems. RNAi-mediated silencing of CG disease in walnut (Juglans regia L.) has been achieved previously. We sought to place both CG and nematode resistance into a single walnut rootstock genotype using co-transformation to stack the resistance genes. A. tumefaciens, carrying self-complimentary iaaM and ipt transgenes, and Agrobacterium rhizogenes, carrying a self-complimentary Pv010 gene from P. vulnus, were used as co-transformation vectors. RolABC genes were introduced by the resident T-DNA in the A. rhizogenes Ri-plasmid used as a vector for plant transformation. Pv010 and Pv194 (transgenic control) genes were also transferred separately using A. tumefaciens. To test for resistance, transformed walnut roots were challenged with P. vulnus and microshoots were challenged with a virulent strain of A. tumefaciens.

Results

Combining the two bacterial strains at a 1:1 rather than 1:3 ratio increased the co-transformation efficiency. Although complete immunity to nematode infection was not observed, transgenic lines yielded up to 79% fewer nematodes per root following in vitro co-culture than untransformed controls. Transgenic line 33-3-1 exhibited complete crown gall control and 32% fewer nematodes. The transgenic plants had thicker, longer roots than untransformed controls possibly due to insertion of rolABC genes. When the Pv010 gene was present in roots with or without rolABC genes there was partial or complete control of RLNs. Transformation using only one vector showed 100% control in some lines.

Conclusions

CG and nematode resistance gene stacking controlled CG and RLNs simultaneously in walnuts. Silencing genes encoding iaaM, ipt, and Pv010 decrease CG formation and RLNs populations in walnut. Beneficial plant genotype and phenotype changes are caused by co-transformation using A. tumefaciens and A. rhizogenes strains. Viable resistance against root lesion nematodes in walnut plants may be accomplished in the future using this gene stacking technology.