Meloidogyne incognita - rice (Oryza sativa) interaction: a new model system to study plant-root-knot nematode interactions in monocotyledons

Unraveling the involvement of WRKY TFs in regulating plant disease defense signaling

MAIN CONCLUSION

This review article explores the intricate role, regulation, and signaling mechanisms of WRKY TFs in response to biotic stress, particularly emphasizing their pivotal role in the trophism of plant-pathogen interactions. Transcription factors (TFs) play a vital role in governing both plant defense and development by controlling the expression of various downstream target genes. Early studies have shown the differential expression of certain WRKY transcription factors by microbial infections. Several transcriptome-wide studies later demonstrated that diverse sets of WRKYs are significantly activated in the early stages of viral, bacterial, and fungal infections. Furthermore, functional investigations indicated that overexpression or silencing of certain WRKY genes in plants can drastically alter disease symptoms as well as pathogen multiplication rates. Hence the new aspects of pathogen-triggered WRKY TFs mediated regulation of plant defense can be explored. The already recognized roles of WRKYs include transcriptional regulation of defense-related genes, modulation of hormonal signaling, and participation in signal transduction pathways. Some WRKYs have been shown to directly bind to pathogen effectors, acting as decoys or resistance proteins. Notably, the signaling molecules like salicylic acid, jasmonic acid, and ethylene which are associated with plant defense significantly increase the expression of several WRKYs. Moreover, induction of WRKY genes or heightened WRKY activities is also observed during ISR triggered by the beneficial microbes which protect the plants from subsequent pathogen infection. To understand the contribution of WRKY TFs towards disease resistance and their exact metabolic functions in infected plants, further studies are required. This review article explores the intrinsic transcriptional regulation, signaling mechanisms, and hormonal crosstalk governed by WRKY TFs in plant disease defense response, particularly emphasizing their specific role against different biotrophic, hemibiotrophic, and necrotrophic pathogen infections.

Symbiotic compatibility between rice cultivars and arbuscular mycorrhizal fungi genotypes affects rice growth and mycorrhiza-induced resistance

Introduction

Arbuscular mycorrhizal fungi (AMF) belong to the Glomeromycota clade and can form root symbioses with 80% of Angiosperms, including crops species such as wheat, maize and rice. By increasing nutrient availability, uptake and soil anchoring of plants, AMF can improve plant's growth and tolerance to abiotic stresses. AMF can also reduce symptoms and pathogen load on infected plants, both locally and systemically, through a phenomenon called mycorrhiza induced resistance (MIR). There is scarce information on rice mycorrhization, despite the high potential of this symbiosis in a context of sustainable water management in rice production systems.

Methods

We studied the symbiotic compatibility (global mycorrhization & arbuscules intensity) and MIR phenotypes between six rice cultivars from two subspecies (indica: IR64 & Phka Rumduol; japonica: Nipponbare, Kitaake, Azucena & Zhonghua 11) and three AMF genotypes (Funneliformis mosseae FR140 (FM), Rhizophagus irregularis DAOM197198 (RIR) & R. intraradices FR121 (RIN)). The impact of mycorrhization on rice growth and defence response to Xanthomonas oryzae pv oryzae (Xoo) infection was recorded via both phenotypic indexes and rice marker gene expression studies.

Results

All three AMF genotypes colonise the roots of all rice varieties, with clear differences in efficiency depending on the combination under study (from 27% to 84% for Phka Rumduol-RIN and Nipponbare-RIR combinations, respectively). Mycorrhization significantly (α=0.05) induced negative to beneficial effects on rice growth (impact on dry weight ranging from -21% to 227% on Azucena-FM and Kitaake-RIN combinations, respectively), and neutral to beneficial effects on the extent of Xoo symptoms on leaves (except for Azucena-RIN combination which showed a 68% increase of chlorosis). R. irregularis DAOM197198 was the most compatible AMF partner of rice, with high root colonisation intensity (84% of Nipponbare's roots hyphal colonisation), beneficial effects on rice growth (dry weight +28% (IR64) to +178% (Kitaake)) and decrease of Xoo-induced symptoms (-6% (Nipponbare) to -27% (IR64)). Transcriptomic analyses by RT-qPCR on leaves of two rice cultivars contrasting in their association with AMF show two different patterns of response on several physiological marker genes.

Discussion

Overall, the symbiotic compatibility between rice cultivars and AMF demonstrates adequate colonization, effectively restricting the nutrient starvation response and mitigating symptoms of phytopathogenic infection.

MG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode

The rice root-knot nematode (Meloidogyne graminicola) is one of the most destructive pests threatening rice (Oryza sativa L.) production in Asia; however, no rice resistance genes have been cloned. Here, we demonstrate that M. GRAMINICOLA-RESISTANCE GENE 1 (MG1), an R gene highly expressed at the site of nematode invasion, determines resistance against the nematode in several rice varieties. Introgressing MG1 into susceptible varieties increases resistance comparable to resistant varieties, for which the leucine-rich repeat domain is critical for recognizing root-knot nematode invasion. We also report transcriptome and cytological changes that are correlated with a rapid and robust response during the incompatible interaction that occurs in resistant rice upon nematode invasion. Furthermore, we identified a putative protease inhibitor that directly interacts with MG1 during MG1-mediated resistance. Our findings provide insight into the molecular basis of nematode resistance as well as valuable resources for developing rice varieties with improved nematode resistance.

Arbuscular mycorrhizal fungi-mediated activation of plant defense responses in direct seeded rice (Oryza sativa L.) against root-knot nematode Meloidogyne graminicola

Rhizosphere is the battlefield of beneficial and harmful (so called phytopathogens) microorganisms. Moreover, these microbial communities are struggling for their existence in the soil and playing key roles in plant growth, mineralization, nutrient cycling and ecosystem functioning. In the last few decades, some consistent pattern have been detected so far that link soil community composition and functions with plant growth and development; however, it has not been studied in detail. AM fungi are model organisms, besides potential role in nutrient cycling; they modulate biochemical pathways directly or indirectly which lead to better plant growth under biotic and abiotic stress conditions. In the present investigations, we have elucidated the AM fungi-mediated activation of plant defense responses against Meloidogyne graminicola causing root-knot disease in direct seeded rice (Oryza sativa L.). The study describes the multifarious effects of Funneliformis mosseae, Rhizophagus fasciculatus, and Rhizophagus intraradices inoculated individually or in combination under glasshouse conditions in rice plants. It was found that F. mosseae, R. fasciculatus and R. intraradices when applied individually or in combination modulated the biochemical and molecular mechanisms in the susceptible and resistant inbred lines of rice. AM inoculation significantly increased various plant growth attributes in plants with simultaneous decrease in the root-knot intensity. Among these, the combined application of F. mosseae, R. fasciculatus, and R. intraradices was found to enhance the accumulation and activities of biomolecules and enzymes related to defense priming as well as antioxidation in the susceptible and resistant inbred lines of rice pre-challenged with M. graminicola. The application of F. mosseae, R. fasciculatus and R. intraradices, induced the key genes involved in plant defense and signaling and it has been demonstrated for the first time. Results of the present investigation advocated that the application of F. mosseae, R. fasciculatus and R. intraradices, particularly a combination of all three, not only helped in the control of root-knot nematodes but also increased plant growth as well as enhances the gene expression in rice. Thus, it proved to be an excellent biocontrol as well as plant growth-promoting agent in rice even when the crop is under biotic stress of the root-knot nematode, M. graminicola.

Effect of Pochonia chlamydosporia Endophytism and Meloidogyne incognita Parasitism on WRKYs and Defense Gene Expression in Tomato Roots

The expression of WRKY transcription factors and plant defense-related genes was studied in the roots of Apulian tomato (Solanum lycopersicum) cv Regina di Fasano (accessions MRT and PLZ) endophytically colonized by Pochonia chlamydosporia and parasitized or not by the root-knot nematode (RKN) Meloidogyne incognita. The effect on plant growth, nematode parasitism and histological aspect of the interaction were considered. The association of P. chlamydosporia with RKN-parasitized MRT plants increased the total biomass and shoot fresh weight in comparison with healthy plants and with those only parasitized by RKN, without the endophyte. However, the PLZ accession showed no significant difference in the observed biometric parameters. The number of RKN-induced galls per plant was not affected by endophytism eight days after inoculation. No histological changes were observed in the nematode feeding sites in the presence of the fungus. Gene expression analysis showed an accession-specific response to P. chlamydosporia with differential activation of WRKY-related genes. No significant change was found for WRKY76 expression in nematode-parasitized plants compared with control roots, confirming cultivar susceptibility. Data indicate genotype-specific responses of the WRKY genes to parasitism examined in roots with nematodes and/or endophytic P. chlamydosporia. At 25 days post-inoculation with P. chlamydosporia, no significant difference was observed in the expression of defense-related genes in both accessions, suggesting that salicylic acid (SA) (PAL and PR1) and jasmonate (JA) related genes (Pin II) are not active during endophytism.

Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice

Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F₂ hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.

Changes in the expression level of genes encoding transcription factors and cell wall-related proteins during Meloidogyne arenaria infection of maize (Zea mays)

BACKGROUND

Meloidogyne arenaria is an economically important root-knot nematode (RKN) species whose hosts include maize (Zea mays). The plant response to RKN infection activates many cellular mechanisms, among others, changes in the expression level of genes encoding transcription and elongation factors as well as proteins related to cell wall organization.

METHODS AND RESULTS

This study is aimed at characterization of expression of selected transcription and elongation factors encoding the genes WRKY53, EF1a, and EF1b as well as the ones encoding two proteins associated with cell wall functioning (glycine-rich RNA-binding protein, GRP and polygalacturonase, PG) during the maize response to M. arenaria infection. The changes in the relative level of expression of genes encoding these proteins were assessed using the reverse transcription-quantitative real-time PCR. The material studied were leaves and root samples collected from four maize varieties showing different susceptibilities toward M. arenaria infection, harvested at three different time points. Significant changes in the expression level of GRP between susceptible and tolerant varieties were observed.

CONCLUSIONS

Results obtained in the study suggest pronounced involvement of glycine-rich RNA-binding protein and EF1b in the maize response and resistance to RKN.

Impact of Meloidogyne incognita (nematode) infection on root tissues and cell wall composition of okra (Abelmoschus esculentus L. Moench, Malvaceae)

Root-knot nematodes are endoparasites whose mature females lodge and grow inside the root of some cultivated plants, leading to losses in productivity. Herein, we investigated if the infection of okra, Abelmoschus esculentus (Malvaceae), promoted by the root-knot nematode Meloidogyne incognita (Meloidogynidae) changes some agronomic traits of the host plant, as well as the cell wall composition of the root tissues. The okra Santa Cruz 47® cultivar was infected with a suspension of 5000 M. incognita juveniles. The inoculated and non-inoculated okra plants were then submitted to morphological analysis at the end of experiment, as well as histological (at 4, 11, 18, 39, ad 66 days after inoculation) and immunocytochemical analysis (control and 66 days after inoculation). Root-knot nematode infection reduced the dry weight of the stem system but, unexpectedly, the number and weight of fruits increased. At 11 days after inoculation, we detected the presence of giant cells that increased in number and size until the end of the experiment, at 66 days after inoculation. These cells came from the xylem parenchyma and showed intense and moderate labeling for epitopes recognized by JIM5 and JIM7. The presence of homogalacturonans (HGs) with different degrees of methyl esterification seems to be related to the injuries caused by the nematode feeding activity and to the processes of giant cell hypertrophy. In addition, the presence of HGs with high methyl-esterified groups can increase the cell wall porosity and facilitate the flux of nutrients for the root-knot nematode.

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola

Background

Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues.

Results

We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data.

Conclusions

To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07735-7.

A rice root-knot nematode Meloidogyne graminicola-resistant mutant rice line shows early expression of plant-defence genes

Resistance to rice root-knot nematode Meloidogyne graminicola in a mutant rice line is suggested to be conferred by higher expression of several genes putatively involved in damage-associated molecular pattern recognition, secondary metabolite biosynthesis including phytoalexins, and defence-related genes. Meloidogyne graminicola has emerged as the most destructive plant-parasitic nematode disease of rice (Oryza sativa L.). Genetic resistance to M. graminicola is one of the most effective methods for its management. A M. graminicola-resistant O. sativa ssp. indica mutant line-9 was previously identified through a forward genetic screen (Hatzade et al. Biologia 74:1197-1217, 2019). In the present study, we used RNA-Sequencing to investigate the molecular mechanisms conferring nematode resistance to the mutant line-9 compared to the susceptible parent JBT 36/14 at 24 h post-infection. A total of 674 transcripts were differentially expressed in line-9. Early regulation of genes putatively related to nematode damage-associated molecular pattern recognition (e.g., wall-associated receptor kinases), signalling [Nucleotide-binding, Leucine-Rich Repeat (NLRs)], pathogenesis-related (PR) genes (PR1, PR10a), defence-related genes (NB-ARC domain-containing genes), as well as a large number of genes involved in secondary metabolites including diterpenoid biosynthesis (CPS2, OsKSL4, OsKSL10, Oscyp71Z2, oryzalexin synthase, and momilactone A synthase) was observed in M. graminicola-resistant mutant line-9. It may be suggested that after the nematode juveniles penetrate the roots of line-9, early recognition of invading nematodes triggers plant immune responses mediated by phytoalexins, and other defence proteins such as PR proteins inhibit nematode growth and reproduction. Our study provides the first transcriptomic comparison of nematode-resistant and susceptible rice plants in the same genetic background and adds to the understanding of mechanisms underlying plant-nematode resistance in rice.

A method for evaluating root-knot nematode infection in rice using a transparent paper pouch

The root-knot nematode (RKN) Meloidogyne incognita is one of the most economically damaging plant-parasitic nematodes. Molecular studies of the plant-RKN interaction have been vigorously carried out in dicotyledonous model plants, while the host range of M. incognita is wide including monocotyledonous plants. As M. incognita causes quality and yield losses in rice (Oryza sativa L.) cultivated in both upland and irrigated systems, we developed a method to examine the plant-RKN interaction in this model monocotyledonous crop plant. Here, we show that a transparent paper pouch could be used to evaluate nematode infection rates in rice with similar results to that of the traditional soil method. The system using a transparent paper pouch can be used to observe the spatial and temporal distribution of developing galls and can save the space of growth chamber.

Analyses of the Root-Knot Nematode (Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection were previously characterized but no information is available about the molecular dialogue established with a resistant plant. We compared the M. graminicola transcriptomes of stage-two juveniles (J2s) before and during infection of susceptible or resistant rice. Among 36,121 M. graminicola genes surveyed, 367 were differentially expressed during infection of resistant or susceptible plants. Genes encoding cell wall-degrading enzymes, peptidases and neuropeptides were expressed for a longer time in resistant plants compared to susceptible plants. Conversely, genes related to nematode development were not activated in the resistant host. The majority of M. graminicola effector genes had similar expression patterns, whatever the host genotype. However, two venom allergen-like protein (VAP)-encoding genes were specifically induced in resistant plants and Mg-VAP1 silencing in J2s reduced their ability to colonize roots. This study highlighted that M. graminicola adapts its gene expression to the host susceptibility. Further investigation is required to assess the role of Mg-VAPs in the rice-nematode interaction.

Proteome-Wide Analyses Provide New Insights into the Compatible Interaction of Rice with the Root-Knot Nematode Meloidogyne graminicola

The root-knot nematode Meloidogyne graminicola is an important pathogen in rice, causing huge yield losses annually worldwide. Details of the interaction between rice and M. graminicola and the resistance genes in rice still remain unclear. In this study, proteome-wide analyses of the compatible interaction of the japonica rice cultivar “Nipponbare” (NPB) with M. graminicola were performed. In total, 6072 proteins were identified in NPB roots with and without infection of M. graminicola by label-free quantitative mass spectrometry. Of these, 513 specifically or significantly differentially expressed proteins were identified to be uniquely caused by nematode infection. Among these unique proteins, 99 proteins were enriched on seven Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. By comparison of protein expression and gene transcription, LOC_Os01g06600 (ACX, a glutaryl-CoA dehydrogenase), LOC_Os09g23560 (CAD, a cinnamyl-alcohol dehydrogenase), LOC_Os03g39850 (GST, a glutathione S-transferase) and LOC_Os11g11960 (RPM1, a disease resistance protein) on the alpha-linolenic acid metabolism, phenylpropanoid biosynthesis, glutathione metabolism and plant–pathogen interaction pathways, respectively, were all associated with disease defense and identified to be significantly down-regulated in the compatible interaction of NPB with nematodes, while the corresponding genes were remarkably up-regulated in the roots of a resistant rice accession “Khao Pahk Maw” with infection of nematodes. These four genes likely played important roles in the compatible interaction of rice with M. graminicola. Conversely, these disease defense-related genes were hypothesized to be likely involved in the resistance of resistant rice lines to this nematode. The proteome-wide analyses provided many new insights into the interaction of rice with M. graminicola.

Transcriptomic changes in the pre-parasitic juveniles of Meloidogyne incognita induced by silencing of effectors Mi-msp-1 and Mi-msp-20

Plant-parasitic root-knot nematode Meloidogyne incognita uses an array of effector proteins to establish successful plant infections. Mi-msp-1 and Mi-msp-20 are two known effectors secreted from nematode subventral oesophageal glands; Mi-msp-1 being a putative secretory venom allergen AG5-like protein, whereas Mi-msp-20 is a pioneer gene with a coiled-coil motif. Expression of specific effector is known to cause disturbances in the expression of other effectors. Here, we used RNA-Seq to investigate the pleiotropic effects of silencing Mi-msp-1 and Mi-msp-20. A total of 25.1-51.9 million HQ reads generated from Mi-msp-1 and Mi-msp-20 silenced second-stage juveniles (J2s) along with freshly hatched J2s were mapped to an already annotated M. incognita proteome to understand the impact on various nematode pathways. As compared to control, silencing of Mi-msp-1 caused differential expression of 29 transcripts, while Mi-msp-20 silencing resulted in differential expression of a broader set of 409 transcripts. In the Mi-msp-1 silenced J2s, cytoplasm (GO:0005737) was the most enriched gene ontology (GO) term, whereas in the Mi-msp-20 silenced worms, embryo development (GO:0009792), reproduction (GO:0000003) and nematode larval development (GO:0002119) were the most enriched terms. Limited crosstalk was observed between these two effectors as a sheer 5.9% of the up-regulated transcripts were common between Mi-msp-1 and Mi-msp-20 silenced nematodes. Our results suggest that in addition to the direct knock-down caused by silencing of Mi-msp-1 and Mi-msp-20, the cascading effect on other genes might also be contributing to a reduction in nematode's parasitic abilities.

Transcriptomic profiling of Solanum peruvianum LA3858 revealed a Mi-3-mediated hypersensitive response to Meloidogyne incognita

Background

The Mi-1 gene was the first identified and cloned gene that provides resistance to root-knot nematodes (RKNs) in cultivated tomato. However, owing to its temperature sensitivity, this gene does not meet the need for breeding disease-resistant plants that grow under high temperature. In this study, Mi-3 was isolated from the wild species PI 126443 (LA3858) and was shown to display heat-stable resistance to RKNs. However, the mechanism that regulates this resistance remains unknown.

Results

In this study, 4760, 1024 and 137 differentially expressed genes (DEGs) were enriched on the basis of pairwise comparisons (34 °C vs. 25 °C) at 0 (before inoculation), 3 and 6 days post-inoculation (dpi), respectively. A total of 7035 DEGs were identified from line LA3858 in the respective groups under the different soil temperature treatments. At 3 dpi, most DEGs were enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to plant biotic responses, such as “plant-pathogen interaction” and “plant hormone signal transduction”. Significantly enriched DEGs were found to encode key proteins such as R proteins and heat-shock proteins (HSPs). Moreover, other DEGs were found to participate in Ca²⁺ signal transduction; the production of ROS; DEGs encoding transcription factors (TFs) from the bHLH, TGA, ERF, heat-shock transcription factor (HSF) and WRKY families were highly expressed, which contribute to be involved into the formation of phytohormones, such as salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), the expression of most was upregulated at 3 dpi at the 25 °C soil temperature compared with the 34 °C soil temperature.

Conclusion

Taken together, the results of our study revealed reliable candidate genes from wild materials LA3858, that are related to Mi-3-mediate resistance to Meloidogyne incognita. A large number of vital pathways and DEGs were expressed specifically in accession LA3858 grown at 34 °C and 25 °C soil temperatures at 3 dpi. Upon infection by RKNs, pattern-recognition receptors (PRRs) specifically recognized conserved pathogen-associated molecular patterns (PAMPs) as a result of pathogen-triggered immunity (PTI), and the downstream defensive signal transduction pathway was likely activated through Ca²⁺ signal channels. The expression of various TFs was induced to synthesize phytohormones and activate R proteins related to resistance, resulting in the development of effector-triggered immunity (ETI). Last, a hypersensitive response in the roots occurred, which was probably induced by the accumulation of ROS.

Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection

Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.

A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants

Root-knot nematodes (RKN), from the Meloidogyne genus, have a worldwide distribution and cause severe economic damage to many life-sustaining crops. Because of their lack of specificity and danger to the environment, most chemical nematicides have been banned from use. Thus, there is a great need for new and safe compounds to control RKN. Such research involves identifying beforehand the nematode proteins essential to the invasion. Since G protein-coupled receptors GPCRs are the target of a large number of drugs, we have focused our research on the identification of putative nematode GPCRs such as those capable of controlling the movement of the parasite towards (or within) its host. A datamining procedure applied to the genome of Meloidogyne incognita allowed us to identify a GPCR, belonging to the neuropeptide GPCR family that can serve as a target to carry out a virtual screening campaign. We reconstructed a 3D model of this receptor by homology modeling and validated it through extensive molecular dynamics simulations. This model was used for large scale molecular dockings which produced a filtered limited set of putative antagonists for this GPCR. Preliminary experiments using these selected molecules allowed the identification of an active compound, namely C260-2124, from the ChemDiv provider, which can serve as a starting point for further investigations.

Rice susceptibility to root-knot nematodes is enhanced by the Meloidogyne incognita MSP18 effector gene

MAIN CONCLUSION

This study revealed novel insights into the function of MSP18 effector during root-knot nematode parasitism in rice roots. MSP18 may modulate host immunity and enhance plant susceptibility to Meloidogyne spp. Rice (Oryza sativa) production is seriously impacted by root-knot nematodes (RKN), including Meloidogyne graminicola, Meloidogyne incognita, and Meloidogyne javanica, in upland and irrigated culture systems. Successful plant infection by RKN is likely achieved by releasing into the host cells some effector proteins to suppress the activation of immune responses. Here, we conducted a series of functional analyses to assess the role of the Meloidogyne-secreted protein (MSP) 18 from M. incognita (Mi-MSP18) during rice infection by RKN. Developmental expression profiles of M. javanica and M. graminicola showed that the MSP18 gene is up-regulated throughout nematode parasitic stages in rice. Reproduction of M. javanica and M. graminicola is enhanced in rice plants overexpressing Mi-MSP18, indicating that the Mi-MSP18 protein facilitates RKN parasitism. Transient expression assays in onion cells suggested that Mi-MSP18 is localized to the cytoplasm of the host cells. In tobacco, Mi-MSP18 suppressed the cell death induced by the INF1 elicitin, suggesting that Mi-MSP18 can interfere with the plant defense pathways. The data obtained in this study highlight Mi-MSP18 as a novel RKN effector able to enhance plant susceptibility and modulate host immunity.

Tomato SlWRKY3 acts as a positive regulator for resistance against the root-knot nematode Meloidogyne javanica by activating lipids and hormone-mediated defense-signaling pathways

Diseases caused by plant-parasitic nematodes in vegetables, among them Meloidogyne spp. root-knot nematodes (RKNs), lead to extensive yield decline. A molecular understanding of the mechanisms underlying plants' innate resistance may enable developing safe alternatives to harmful chemical nematicides in controlling RKNs. A tight relationship has been revealed between the WRKY transcription factors and RKN parasitism on tomato roots. We investigated the function role of tomato SlWRK3 and SlWRKY35 in regulating nematode disease development. Using promoter-GUS reporter gene fusions, we show that both SlWRKY3 and SlWRKY35 are induced within 5 days of infection and through feeding-site development and gall maturation, with a much stronger response of the former vs. the latter to nematode infection. Histological analysis of nematode-feeding sites indicated a high expression of SlWRKY3 in developing and mature feeding cells and associated vasculature cells, whereas SlWRKY35 expression was only observed in mature feeding sites. Both SlWRKY3 and SlWRKY35 promoters were induced by the defense phytohormones salicylic acid and indole-3-butyric acid, with no response to either jasmonic acid or methyl jasmonate. SlWRKY3 overexpression resulted in lower infection of the RKN Meloidogyne javanica, whereas knocking down SlWRKY3 resulted in increased infection. Phytohormone and oxylipin profiles determined by LC-MS/MS showed that the enhanced resistance in the former is coupled with an increased accumulation of defense molecules from the shikimate and oxylipin pathways. Our results pinpoint SlWRKY3 as a positive regulator of induced resistance in response to nematode invasion and infection, mostly during the early stages of nematode infection.

Host-mediated RNAi of a Notch-like receptor gene in Meloidogyne incognita induces nematode resistance

GLP-1 (abnormal germline proliferation) is a Notch-like receptor protein that plays an essential role in pharyngeal development. In this study, an orthologue of Caenorhabditis elegans glp-1 was identified in Meloidogyne incognita. A computational analysis revealed that the orthologue contained almost all the domains present in the C. elegans gene: specifically, the LIN-12/Notch repeat, the ankyrin repeat, a transmembrane domain and different ligand-binding motifs were present in orthologue, but the epidermal growth factor-like motif was not observed. An expression analysis showed differential expression of glp-1 throughout the life cycle of M. incognita, with relatively higher expression in the egg stage. To evaluate the silencing efficacy of Mi-glp-1, transgenic Arabidopsis plants carrying double-stranded RNA constructs of glp-1 were generated, and infection of these plants with M. incognita resulted in a 47-50% reduction in the numbers of galls, females and egg masses. Females obtained from the transgenic RNAi lines exhibited 40-60% reductions in the transcript levels of the targeted glp-1 gene compared with females isolated from the control plants. Second-generation juveniles (J2s), which were descendants of the infected females from the transgenic lines, showed aberrant phenotypes. These J2s exhibited a significant decrease in the overall distance from the stylet to the metacorpus region, and this effect was accompanied by disruption around the metacorporeal bulb of the pharynx. The present study suggests a role for this gene in organ (pharynx) development during embryogenesis in M. incognita and its potential use as a target in the management of nematode infestations in plants.

Nicotiana benthamiana as model plant for Meloidogyne graminicola infection

Nicotiana benthamiana is widely used as a model plant to analyse cell biology and to obtain insight into the molecular host-pathogen interaction because it is susceptible to many pathogens. Since N. benthamiana can be transformed easily, it is also used to study pathogens for which it is not a known host. Meloidogyne graminicola has a fairly broad host range of mainly monocots and some dicots but no data were available on the ability of M. graminicola to infect N. benthamiana. In this study, we show that M. graminicola is able to infect and complete its life cycle in N. benthamiana, although our experiments demonstrate a lower susceptibility compared to rice. In addition, M. graminicola was also able to develop in N. tabacum but the reproduction was very low. Therefore, we conclude that N. benthamiana can be considered as a host, while this is not the case for N. tabacum.

A novel Meloidogyne graminicola effector, MgGPP, is secreted into host cells and undergoes glycosylation in concert with proteolysis to suppress plant defenses and promote parasitism

Plant pathogen effectors can recruit the host post-translational machinery to mediate their post-translational modification (PTM) and regulate their activity to facilitate parasitism, but few studies have focused on this phenomenon in the field of plant-parasitic nematodes. In this study, we show that the plant-parasitic nematode Meloidogyne graminicola has evolved a novel effector, MgGPP, that is exclusively expressed within the nematode subventral esophageal gland cells and up-regulated in the early parasitic stage of M. graminicola. The effector MgGPP plays a role in nematode parasitism. Transgenic rice lines expressing MgGPP become significantly more susceptible to M. graminicola infection than wild-type control plants, and conversely, in planta, the silencing of MgGPP through RNAi technology substantially increases the resistance of rice to M. graminicola. Significantly, we show that MgGPP is secreted into host plants and targeted to the ER, where the N-glycosylation and C-terminal proteolysis of MgGPP occur. C-terminal proteolysis promotes MgGPP to leave the ER, after which it is transported to the nucleus. In addition, N-glycosylation of MgGPP is required for suppressing the host response. The research data provide an intriguing example of in planta glycosylation in concert with proteolysis of a pathogen effector, which depict a novel mechanism by which parasitic nematodes could subjugate plant immunity and promote parasitism and may present a promising target for developing new strategies against nematode infections.

Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots

BACKGROUND AND AIMS

The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice ( Oryza sativa ) in Asia and Latin America. The accession TOG5681 of African rice, O. glaberrima , presents improved resistance to several biotic and abiotic factors, including nematodes. The aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession.

METHODS

Penetration and development in M. graminicola in TOG5681 and the susceptible O. sativa genotype 'Nipponbare' were compared by microscopic observation of infected roots and histological analysis of galls. In parallel, host molecular responses to M. graminicola were assessed by root transcriptome profiling at 2, 4 and 8 d post-infection (dpi). Specific treatments with hormone inhibitors were conducted in TOG5681 to assess the impact of the jasmonic acid and salicylic acid pathways on nematode penetration and reproduction.

KEY RESULTS

Penetration and development of M. graminicola juveniles were reduced in the resistant TOG5681 in comparison with the susceptible accession, with degeneration of giant cells observed in the resistant genotype from 15 dpi onwards. Transcriptome changes were observed as early as 2 dpi, with genes predicted to be involved in defence responses, phenylpropanoid and hormone pathways strongly induced in TOG5681, in contrast to 'Nipponbare'. No specific hormonal pathway could be identified as the major determinant of resistance in the rice-nematode incompatible interaction. Candidate genes proposed as involved in resistance to M. graminicola in TOG5681 were identified based on their expression pattern and quantitative trait locus (QTL) position, including chalcone synthase, isoflavone reductase, phenylalanine ammonia lyase, WRKY62 transcription factor, thionin, stripe rust resistance protein, thaumatins and ATPase3.

CONCLUSIONS

This study provides a novel set of candidate genes for O. glaberrima resistance to nematodes and highlights the rice- M. graminicola pathosystem as a model to study plant-nematode incompatible interactions.

Gene expression analysis in Musa acuminata during compatible interactions with Meloidogyne incognita

BACKGROUND AND AIMS

Endoparasitic root-knot nematodes (RKNs) ( Meloidogyne spp.) cause considerable losses in banana ( Musa spp.), with Meloidogyne incognita a predominant species in Cavendish sub-group bananas. This study investigates the root transcriptome in Musa acuminata genotypes 4297-06 (AA) and Cavendish Grande Naine (CAV; AAA) during early compatible interactions with M. incognita .

METHODS

Roots were analysed by brightfield light microscopy over a 35 d period to examine nematode penetration and morphological cell transformation. RNA samples were extracted 3, 7 and 10 days after inoculation (DAI) with nematode J2 juveniles, and cDNA libraries were sequenced using lllumina HiSeq technology. Sequences were mapped to the M. acuminata ssp. malaccensis var. Pahang genome sequence, differentially expressed genes (DEGs) identified and transcript representation determined by gene set enrichment and pathway mapping.

KEY RESULTS

Microscopic analysis revealed a life cycle of M. incognita completing in 24 d in CAV and 27 d in 4279-06. Comparable numbers of DEGs were up- and downregulated in each genotype, with potential involvement of many in early host defence responses involving reactive oxygen species and jasmonate/ethylene signalling. DEGs revealed concomitant auxin metabolism and cell wall modification processes likely to be involved in giant cell formation. Notable transcripts related to host defence included those coding for leucine-rich repeat receptor-like serine/threonine-protein kinases, peroxidases, thaumatin-like pathogenesis-related proteins, and DREB, ERF, MYB, NAC and WRKY transcription factors. Transcripts related to giant cell development included indole acetic acid-amido synthetase GH3.8 genes, involved in auxin metabolism, as well as genes encoding expansins and hydrolases, involved in cell wall modification.

CONCLUSIONS

Expression analysis in M. acuminata during compatible interactions with RKNs provides insights into genes modulated during infection and giant cell formation. Increased understanding of both defence responses to limit parasitism during compatible interactions and effector-targeted host genes in this complex interaction will facilitate the development of genetic improvement measures for RKNs.

Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants

Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.

Molecular evidence for biochemical diversification of phenolamide biosynthesis in rice plants

Two phenolamides (PAs), p-coumaroylputrescine and feruloylputrescine strongly accumulate in rice (Oryza sativa cv. Nipponbare) leaves subjected to attack of chewing and sucking herbivores. Here we identified and characterized in vitro three novel rice genes that mediated coumaroyl-CoA/feruloyl-CoA conjugation to polyamines, putrescine and agmatine. Interestingly, two genes were highly specific for their polyamine substrates, encoding putrescine N-hydroxycinnamoyltransferase and agmatine N-hydroxycinnamoyltransferase, while the third enzyme could use both polyamines and it was therefore annotated as putrescine/agmatine N-hydroxycinnamoyltransferase. All genes were preferentially expressed in rice roots and developing flowers, and in addition, the putrescine/agmatine N-hydroxycinnamoyltransferase transcripts were strongly induced by wounding in the young rice leaves. Because the wound response of this gene was only partially suppressed in the jasmonoyl-L-isoleucine deficient plants (Osjar1), it suggests that its upregulation (as well as inducible PAs in rice) may be largely independent of jasmonoyl-L-isoleucine signaling pathway. The finding of three closely related genes with a similar and/or overlapping activity in PA biosynthesis provides another striking example of rapid diversification of plant metabolism in response to environmental stresses in nature.

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae

The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a defense pathway. Overall, this preliminary study in Musa provides the basis for understanding the evolution and regulatory mechanism of MusaWRKY during nematode stress.

Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground

Plants are important mediators of interactions between aboveground (AG) and belowground (BG) pathogens, arthropod herbivores, and nematodes (phytophages). We highlight recent progress in our understanding of within- and cross-compartment plant responses to these groups of phytophages in terms of altered resource dynamics and defense signaling and activation. We review studies documenting the outcome of cross-compartment interactions between these phytophage groups and show patterns of cross-compartment facilitation as well as cross-compartment induced resistance. Studies involving soilborne pathogens and foliar nematodes are scant. We further highlight the important role of defense signaling loops between shoots and roots to activate a full resistance complement. Moreover, manipulation of such loops by phytophages affects systemic interactions with other plant feeders. Finally, cross-compartment-induced changes in root defenses and root exudates extend systemic defense loops into the rhizosphere, enhancing or reducing recruitment of microbes that induce systemic resistance but also affecting interactions with root-feeding phytophages.

Dual RNA-seq reveals Meloidogyne graminicola transcriptome and candidate effectors during the interaction with rice plants

Root-knot nematodes secrete proteinaceous effectors into plant tissues to facilitate infection by suppressing host defences and reprogramming the host metabolism to their benefit. Meloidogyne graminicola is a major pest of rice (Oryza sativa) in Asia and Latin America, causing important crop losses. The goal of this study was to identify M. graminicola pathogenicity genes expressed during the plant-nematode interaction. Using the dual RNA-sequencing (RNA-seq) strategy, we generated transcriptomic data of M. graminicola samples covering the pre-parasitic J2 stage and five parasitic stages in rice plants, from the parasitic J2 to the adult female. In the absence of a reference genome, a de novo M. graminicola transcriptome of 66 396 contigs was obtained from those reads that were not mapped on the rice genome. Gene expression profiling across the M. graminicola life cycle revealed key genes involved in nematode development and provided insights into the genes putatively associated with parasitism. The development of a 'secreted protein prediction' pipeline revealed a typical set of proteins secreted by nematodes, as well as a large number of cysteine-rich proteins and putative nuclear proteins. Combined with expression data, this pipeline enabled the identification of 15 putative effector genes, including two homologues of well-characterized effectors from cyst nematodes (CLE-like and VAP1) and a metallothionein. The localization of gene expression was assessed by in situ hybridization for a subset of candidates. All of these data represent important molecular resources for the elucidation of M. graminicola biology and for the selection of potential targets for the development of novel control strategies for this nematode species.

Comparing the defence-related gene expression changes upon root-knot nematode attack in susceptible versus resistant cultivars of rice

Rice is one of the major staple food crops in the world and an excellent model system for studying monocotyledonous plants. Diseases caused by nematodes in rice are well documented and among them, root-knot nematode (RKN), Meloidogyne graminicola, causes extensive yield decline. It is therefore necessary to identify novel sources of natural resistance to RKN in rice and to investigate the rice-RKN interaction in detail to understand the basal plant defence mechanisms and nematode manipulation of the host physiology. To this end, six different cultivars of rice were initially screened for RKN infection and development; Pusa 1121 and Vandana were found to be most susceptible and resistant to RKN infection, respectively. In order to investigate the role of major hormone-regulated plant defence pathways in compatible/incompatible rice-RKN interaction, some well-identified marker genes involved in salicylate/jasmonate/ethylene pathway were evaluated for their differential expression through qRT-PCR. In general, our study shows a remarkable discrepancy in the expression pattern of those genes between compatible and incompatible rice-RKN interaction. As most information on the molecular interplay between plants and nematodes were generated on dicotyledonous plants, the current study will strengthen our basic understanding of plant-nematode interaction in the monocot crops, which will aid in defining future strategies for best plant health measures.

Plant-parasitic nematode infections in rice: molecular and cellular insights

Being one of the major staple foods in the world, and an interesting model monocot plant, rice (Oryza sativa L.) has recently received attention from molecular nematologists studying the cellular and molecular aspects of the interaction between this crop and plant-parasitic nematodes. In this review, we highlight recent advances in this field, with a focus on the best-studied root-knot nematodes. Histological studies have revealed the cellular changes inside root-knot nematode-induced feeding sites, both in the compatible interaction with Oryza sativa and the incompatible interaction with the related species Oryza glaberrima. After comparing the published data from transcriptome analyses, mutant studies, and exogenous hormone applications, we provide a comprehensive model showing the role and interaction of plant hormone pathways in defense of this monocot crop against root nematodes, where jasmonate seems to play a key role. Finally, recent evidence indicates that effectors secreted from rice-infecting nematodes can suppress plant defense.