Meloidogyne graminicola: a major threat to rice agriculture

Clarifying the Functional Role of Serotonin in Meloidogyne graminicola Host Plant Parasitism by Immunolocalization and RNA Interference

Serotonin (5-hydroxytryptamine) is an essential neurotransmitter involved in regulating various behaviors in plant-parasitic nematodes, including locomotion, egg laying, feeding, and mating. However, the functional role of serotonin in root-knot nematode invasion of host plants and the molecular mechanisms underlying feeding behavior remain poorly understood. In this study, we tested the effects of exogenous serotonin and the pharmacological compounds fluoxetine and methiothepin on the feeding behaviors of Meloidogyne graminicola. Our results suggested that M. graminicola possesses an endogenous serotonin signaling pathway and that serotonin plays a crucial role in modulating feeding behaviors in M. graminicola second-stage juveniles. We also identified and cloned the serotonin synthesis enzyme tryptophan hydroxylase (Mg-tph-1) in M. graminicola and investigated the role of endogenous serotonin by generating RNA interference nematodes in Mg-tph-1. Silencing Mg-tph-1 substantially reduced nematode invasion, development, and reproduction. According to the immunostaining results, we speculated that these serotonin immunoreactive cells near the nerve ring in M. graminicola are likely homologous to Caenorhabditis elegans ADFs, NSMs, and RIH serotonergic neurons. Furthermore, we investigated the impact of phytoserotonin on nematode invasion and development in rice by overexpressing OsTDC-3 or supplementing rice plants with tryptamine and found that an increase in phytoserotonin increases nematode pathogenicity. Overall, our study provides insights into the essential role of serotonin in M. graminicola host plant parasitism and proposes that the serotonergic signaling pathway could be a potential target for controlling plant-parasitic nematodes.

Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand

Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.

Brown planthopper infestation on rice reduces plant susceptibility to Meloidogyne graminicola by reducing root sugar allocation

Plants are simultaneously attacked by different pests that rely on sugars uptake from plants. An understanding of the role of plant sugar allocation in these multipartite interactions is limited. Here, we characterized the expression patterns of sucrose transporter genes and evaluated the impact of targeted transporter gene mutants and brown planthopper (BPH) phloem-feeding and oviposition on root sugar allocation and BPH-reduced rice susceptibility to Meloidogyne graminicola. We found that the sugar transporter genes OsSUT1 and OsSUT2 are induced at BPH oviposition sites. OsSUT2 mutants showed a higher resistance to gravid BPH than to nymph BPH, and this was correlated with callose deposition, as reflected in a different effect on M. graminicola infection. BPH phloem-feeding caused inhibition of callose deposition that was counteracted by BPH oviposition. Meanwhile, this pivotal role of sugar allocation in BPH-reduced rice susceptibility to M. graminicola was validated on rice cultivar RHT harbouring BPH resistance genes Bph3 and Bph17. In conclusion, we demonstrated that rice susceptibility to M. graminicola is regulated by BPH phloem-feeding and oviposition on rice through differences in plant sugar allocation.

Induced knockdown of Mg-odr-1 and Mg-odr-3 perturbed the host seeking behavior of Meloidogyne graminicola in rice

Root-knot nematode Meloidogyne graminicola is one of the most destructive plant parasites in upland as well as direct seeded rice. As an integral part of nematode biology, host finding behavior involves perceiving and responding to different chemical cues originating from the rhizosphere. A sustainable management tactic may include retardation of nematode chemoreception that would impair them to detect and discriminate the host stimuli. Deciphering the molecular basis of nematode chemoreception is vital to identify chokepoints for chemical or genetic interventions. However, compared to the well-characterized chemoreception mechanism in model nematode Caenorhabditis elegans, plant nematode chemoreception is yet underexplored. Herein, the full-length cDNA sequences of two chemotaxis-related genes (Mg-odr-1 and Mg-odr-3) were cloned from M. graminicola. Both the genes were markedly upregulated in the early developmental stages of M. graminicola suggesting their involvement in host finding processes. RNAi-induced independent knockdown of Mg-odr-1 and Mg-odr-3 caused behavioral aberration in second-stage juveniles of M. graminicola which in turn perturbed the nematodes' host finding ability and parasitic success inside rice roots. Additionally, nematodes' chemotactic response to different host root exudates, volatile and nonvolatile compounds was affected. Our results demonstrating the role of specific chemosensory genes in modulating M. graminicola host seeking behavior can enrich the existing knowledge of plant nematode chemoreception mechanism, and these genes can be targeted for novel nematicide development or in planta RNAi screens.

Strigolactone deficiency induces jasmonate, sugar and flavonoid phytoalexin accumulation enhancing rice defense against the blast fungus Pyricularia oryzae

Strigolactones (SLs) are carotenoid-derived phytohormones that regulate plant growth and development. While root-secreted SLs are well-known to facilitate plant symbiosis with beneficial microbes, the role of SLs in plant interactions with pathogenic microbes remains largely unexplored. Using genetic and biochemical approaches, we demonstrate a negative role of SLs in rice (Oryza sativa) defense against the blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae). We found that SL biosynthesis and perception mutants, and wild-type (WT) plants after chemical inhibition of SLs, were less susceptible to P. oryzae. Strigolactone deficiency also resulted in a higher accumulation of jasmonates, soluble sugars and flavonoid phytoalexins in rice leaves. Likewise, in response to P. oryzae infection, SL signaling was downregulated, while jasmonate and sugar content increased markedly. The jar1 mutant unable to synthesize jasmonoyl-l-isoleucine, and the coi1-18 RNAi line perturbed in jasmonate signaling, both accumulated lower levels of sugars. However, when WT seedlings were sprayed with glucose or sucrose, jasmonate accumulation increased, suggesting a reciprocal positive interplay between jasmonates and sugars. Finally, we showed that functional jasmonate signaling is necessary for SL deficiency to induce rice defense against P. oryzae. We conclude that a reduction in rice SL content reduces P. oryzae susceptibility by activating jasmonate and sugar signaling pathways, and flavonoid phytoalexin accumulation.

Molecular and functional characterization of chemosensory genes from the root-knot nematode Meloidogyne graminicola

BACKGROUND

Root-knot nematode Meloidogyne graminicola has emerged as a major threat in rice agroecosystems owing to climate change-induced changes in cultivation practices. Synthetic nematicides are continually being withdrawn from the nematode management toolbox because of their ill effects on the environment. A sustainable strategy would be to develop novel nematicides or resistant plants that would target nematode sensory perception, which is a key step in the host finding biology of plant-parasitic nematodes (PPNs). However, compared to the extensive literature on the free-living nematode Caenorhabditis elegans, negligible research has been performed on PPN chemosensory biology.

RESULTS

The present study characterizes the five chemosensory genes (Mg-odr-7, Mg-tax-4, Mg-tax-4.1, Mg-osm-9, and Mg-ocr-2) from M. graminicola that are putatively associated with nematode host-finding biology. All the genes were highly transcribed in the early life stages, and RNA interference (RNAi)-induced downregulation of each candidate gene perturbed the normal behavioural phenotypes of M. graminicola, as determined by examining the tracking pattern of juveniles on Pluronic gel medium, attraction to and penetration in rice root tip, and developmental progression in rice root. In addition, a detrimental effect on nematode chemotaxis towards different volatile and nonvolatile organic compounds and host root exudates was documented.

CONCLUSION

Our findings enrich the existing literature on PPN chemosensory biology and can supplement future research aimed at identifying a comprehensive chemosensory signal transduction pathway in PPNs.

Dicer-like 3a mediates intergenerational resistance against root-knot nematodes in rice via hormone responses

In a continuously changing and challenging environment, passing down the memory of encountered stress factors to offspring could provide an evolutionary advantage. In this study, we demonstrate the existence of "intergenerational acquired resistance" in the progeny of rice (Oryza sativa) plants attacked by the belowground parasitic nematode Meloidogyne graminicola. Transcriptome analyses revealed that genes involved in defense pathways are generally downregulated in progeny of nematode-infected plants under uninfected conditions but show a stronger induction upon nematode infection. This phenomenon was termed "spring loading" and depends on initial downregulation by the 24-nucleotide (nt) siRNA biogenesis gene dicer-like 3a (dcl3a) involved in the RNA-directed DNA methylation pathway. Knockdown of dcl3a led to increased nematode susceptibility and abolished intergenerational acquired resistance, as well as jasmonic acid/ethylene spring loading in the offspring of infected plants. The importance of ethylene signaling in intergenerational resistance was confirmed by experiments on a knockdown line of ethylene insensitive 2 (ein2b), which lacks intergenerational acquired resistance. Taken together, these data indicate a role for DCL3a in regulating plant defense pathways during both within-generation and intergenerational resistance against nematodes in rice.

Autophagy promotes jasmonate-mediated defense against nematodes

Autophagy, as an intracellular degradation system, plays a critical role in plant immunity. However, the involvement of autophagy in the plant immune system and its function in plant nematode resistance are largely unknown. Here, we show that root-knot nematode (RKN; Meloidogyne incognita) infection induces autophagy in tomato (Solanum lycopersicum) and different atg mutants exhibit high sensitivity to RKNs. The jasmonate (JA) signaling negative regulators JASMONATE-ASSOCIATED MYC2-LIKE 1 (JAM1), JAM2 and JAM3 interact with ATG8s via an ATG8-interacting motif (AIM), and JAM1 is degraded by autophagy during RKN infection. JAM1 impairs the formation of a transcriptional activation complex between ETHYLENE RESPONSE FACTOR 1 (ERF1) and MEDIATOR 25 (MED25) and interferes with transcriptional regulation of JA-mediated defense-related genes by ERF1. Furthermore, ERF1 acts in a positive feedback loop and regulates autophagy activity by transcriptionally activating ATG expression in response to RKN infection. Therefore, autophagy promotes JA-mediated defense against RKNs via forming a positive feedback circuit in the degradation of JAMs and transcriptional activation by ERF1.

Potential of Exogenous Treatment with Dehydroascorbate to Control Root-knot Nematode Infection in Rice

Induced resistance (IR) is a unique physiological state characterized by reduced plant susceptibility to (a)biotic stress. Our previous studies showed that exogenous foliar application of dehydroascorbate (DHA), the oxidized form of ascorbic acid, induces systemic resistance against root-knot nematode Meloidogyne graminicola in rice. In the present study, the potential of DHA in protecting rice plants against M. graminicola was evaluated in lab, pot, and field studies. In an experiment where the interval between foliar treatment and inoculation was varied, 20 mM DHA was found to protect rice plants from M. graminicola for at least 14 days. Pot and field studies confirmed that 10 or 20 mM DHA are highly effective in reducing gall formation and led to a significant increase in rice seed yield. A half dose of DHA (10 mM) combined with another IR-stimulus - piperonylic acid (PA) 300 µM - was at par with DHA 20 mM, leading to reductions in gall formation of more than 80%. In in vitro bioassays, DHA was found to be highly nematicidal to the second-stage juveniles of M. graminicola, with more than 90% mortality within 3 h of exposure to 10 or 20 mM concentrations. While seed treatment had no effect, root drenching or root dipping was also effective in reducing rice susceptibility to M. graminicola, next to foliar treatment. As a dual-action compound with extended protection and ease of application, DHA has great potential for effective nematode management in rice.

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.

Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola

Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.

CRISPR/Cas9-mediated mutagenesis of the susceptibility gene OsHPP04 in rice confers enhanced resistance to rice root-knot nematode

CRISPR crops carrying a mutation in susceptibility (S) genes provide an effective strategy for controlling plant disease, because they could be 'transgene-free' and commonly have more broad-spectrum and durable type of resistance. Despite their importance, CRISPR/Cas9-mediated editing of S genes for engineering resistance to plant-parasitic nematode (PPN) disease has not been reported. In this study, we employed the CRISPR/Cas9 system to specifically induce targeted mutagenesis of the S gene rice copper metallochaperone heavy metal-associated plant protein 04 (OsHPP04), and successfully obtained genetically stable homozygous rice mutants with or without transgenic elements. These mutants confer enhanced resistance to the rice root-knot nematode (Meloidogyne graminicola), a major plant pathogenic nematode in rice agriculture. Moreover, the plant immune responses triggered by flg22, including reactive oxygen species burst, defence-related genes expression and callose deposition, were enhanced in the 'transgene-free' homozygous mutants. Analysis of rice growth and agronomic traits of two independent mutants showed that there are no obvious differences between wild-type plants and mutants. These findings suggest that OsHPP04 may be an S gene as a negative regulator of host immunity and genetic modification of S genes through the CRISPR/Cas9 technology can be used as a powerful tool to generate PPN resistant plant varieties.

Diproline-induced resistance to parasitic nematodes in the same and subsequent rice generations: Roles of iron, nitric oxide and ethylene

Induced resistance (IR) is a plant phenotype characterized by lower susceptibility to biotic challenges upon elicitation by so-called IR stimuli. Earlier, we identified diproline (cyclo(l-Pro-l-Pro)) as IR stimulus that protects rice (Oryza sativa) against the root-knot nematode Meloidogyne graminicola (Mg). In the current study, detailed transcriptome analyses at different time points, and under uninfected and nematode-infected conditions revealed that this rice IR phenotype is correlated with induction of genes related to iron (Fe), ethylene (ET) and reactive oxygen species (ROS)/reactive nitrogen species (RNS) metabolism. An infection experiment under Fe limiting conditions confirmed that diproline-IR is only effective under optimal Fe supply. Although total root Fe levels were not affected in diproline-treated plants, phytosiderophore secretion was found to be induced by this treatment. Experiments on mutant and transgenic rice lines impaired in ET or ROS/RNS metabolism confirmed that these metabolites are involved in diproline-IR. Finally, we provide evidence for transgenerational inheritance of diproline-IR (diproline-TIR), as two successive generations of diproline-treated ancestors exhibited an IR phenotype while themselves never being exposed to diproline. Transcriptome analyses on the offspring plants revealed extensive overlap between the pathways underpinning diproline-IR and diproline-TIR. Although diproline induces significant systemic changes in global DNA methylation levels early after treatment, such changes in DNA methylation were not detected in the descendants of these plants. To our knowledge, this is the first report of TIR in rice and the first transcriptional assessment of TIR in monocots.

A quantitative and qualitative assessment of sugar beet genotype resistance to root-knot nematode, Meloidogyne incognita

Sugar beet productivity is highly constrained by the root-knot nematode (RKN) Meloidogyne incognita. Eight sugar beet genotypes were screened under greenhouse conditions for their susceptibility to M. incognita according to an adapted quantitative scheme for assignment Canto-Saenz's host suitability (resistance) designations (AQSCS). Besides, the degree of susceptibility or tolerance of the examined genotypes was recorded by the modified host-parasite index (MHPI) scale based on yield performance. In addition, single nucleotide polymorphism (SNP) was also determined. Sugar beet genotypes have been classified into four categories for their susceptibility or tolerance according to the AQSCS scale. The first category, the moderately resistant (MR) group implies only one variety named SVH 2015, which did not support nematode reproduction (RF≤1), and had less root damage (GI≈2). Second, the tolerant group (T) involving Lilly and Halawa KWS supported fairly high nematode reproduction (RF>1) with relatively plant damage (GI≤2). Whereas the susceptible (S) category involved four varieties, FARIDA, Lammia KWS, Polat, and Capella, which supported nematode reproduction factor (RF>1) with high plant damage (GI>2). The fourth category refers to the highly susceptible (HYS) varieties such as Natura KWS that showed (RF≤1) and very high plant damage (GI>2). However, the MHPI scale showed that Lammia KWS variety was shifted from the (S) category to the (T) category. Results revealed significant differences among genotypes regarding disease severity, yield production, and quality traits. The SVH 2015 variety exhibited the lowest disease index values concerning population density with 800/250 cm³ soils, RF=2, root damage/gall index (GI=1.8), gall size (GS=2.3), gall area (GA=3.7), damage index (DI=3.4), susceptibility rate (SR=2.4), and MHP index (MHPI=2.5). However, Lammia KWS showed the highest disease index values regarding population density with 8890/250 cm³ soils, RF= 22.2, GI= 4.8, and SR= 14.1. Meanwhile, Natura KWS the highest GS, GA and MHPI with 7.1, 8 and 20.9, respectively. The lowest DI was achieved by Capella (DI= 6) followed by Lammia KWS (DI= 5.9). For yield production, and quality traits, SVH 2015 exhibited the lowest reductions of sugar yields/beet's root with 11.1%. While Natura KWS had the highest reduction with 79.3%, as well as it showed the highest reduction in quality traits; including sucrose, T.S.S, and purity with 65, 27.3, and 51.9%, respectively. The amino acid alignment and prediction of the DNA sequences revealed the presence of five SNPs among all sugar beet verities.

Characterization of Lysobacter enzymogenes B25, a potential biological control agent of plant-parasitic nematodes, and its mode of action

It is certainly difficult to estimate productivity losses due to the action of phytopathogenic nematodes but it might be about 12 % of world agricultural production. Although there are numerous tools to reduce the effect of these nematodes, there is growing concern about their environmental impact. Lysobacter enzymogenes B25 is an effective biological control agent against plant-parasitic nematodes, showing control over root-knot nematodes (RKN) such as Meloidogyne incognita and Meloidogyne javanica. In this paper, the efficacy of B25 to control RKN infestation in tomato plants (Solanum lycopersicum cv. Durinta) is described. The bacterium was applied 4 times at an average of concentration around 10⁸ CFU/mL showing an efficacy of 50-95 % depending on the population and the pressure of the pathogen. Furthermore, the control activity of B25 was comparable to that of the reference chemical used. L. enzymogenes B25 is hereby characterized, and its mode of action studied, focusing on different mechanisms that include motility, the production of lytic enzymes and secondary metabolites and the induction of plant defenses. The presence of M. incognita increased the twitching motility of B25. In addition, cell-free supernatants obtained after growing B25, in both poor and rich media, showed efficacy in inhibiting RKN egg hatching in vitro. This nematicidal activity was sensitive to high temperatures, suggesting that it is mainly due to extracellular lytic enzymes. The secondary metabolites heat-stable antifungal factor and alteramide A/B were identified in the culture filtrate and their contribution to the nematicidal activity of B25 is discussed. This study points out L. enzymogenes B25 as a promising biocontrol microorganism against nematode infestation of plants and a good candidate to develop a sustainable nematicidal product.

Host-delivered RNAi-mediated silencing using fusion cassettes of different functional groups of genes precludes Meloidogyne incognita multiplication in Nicotiana tabacum

This study demonstrates multi-gene silencing approach for simultaneous silencing of several functional genes through a fusion gene strategy for protecting plants against root-knot nematode, Meloidogyne incognita. The ability of root-knot nematode (RKN), Meloidogyne incognita, to cause extensive yield decline in a wide range of cultivated crops is well-documented. Due to the inadequacies of current management approaches, the alternatively employed contemporary RNA interference (RNAi)-based host-delivered gene silencing (HD-RNAi) strategy targeting different functional effectors/genes has shown substantial potential to combat RKNs. In this direction, we have explored the possibility of simultaneous silencing of four esophageal gland genes, six plant cell-wall modifying enzymes (PCWMEs) and a serine protease gene of M. incognita using the fusion approach. In vitro RNAi showed that combinatorial gene silencing is the most effective in affecting nematode behavior in terms of reduced attraction, penetration, development, and reproduction in tomato and adzuki beans. In addition, qRT-PCR analysis of M. incognita J2s soaked in fusion-dsRNA showed perturbed expression of all the genes comprising the fusion construct confirming successful dsRNA processing which is also supported by increased mRNA abundance of five key-RNAi pathway genes. In addition, hairpin RNA expressing constructs of multi-gene fusion cassettes were developed and used for generation of Nicotiana tabacum transgenic plants. The integration of gene constructs and expression of siRNAs in transgenic events were confirmed by Southern and Northern blot analyses. Besides, bio-efficacy analyses of transgenic events, conferred up to 87% reduction in M. incognita multiplication. Correspondingly, reduced transcript accumulation of the target genes in the M. incognita females extracted from transgenic events confirmed successful gene silencing.

Distinct chemical resistance-inducing stimuli result in common transcriptional, metabolic, and nematode community signatures in rice root and rhizosphere

Induced resistance (IR), a phenotypic state induced by an exogenous stimulus and characterized by enhanced resistance to future (a)biotic challenge, is an important component of plant immunity. Numerous IR-inducing stimuli have been described in various plant species, but relatively little is known about 'core' systemic responses shared by these distinct IR stimuli and the effects of IR on plant-associated microbiota. In this study, rice (Oryza sativa) leaves were treated with four distinct IR stimuli (β-aminobutyric acid, acibenzolar-S-methyl, dehydroascorbic acid, and piperonylic acid) capable of inducing systemic IR against the root-knot nematode Meloidogyne graminicola and evaluated their effect on the root transcriptome and exudome, and root-associated nematode communities. Our results reveal shared transcriptional responses-notably induction of jasmonic acid and phenylpropanoid metabolism-and shared alterations to the exudome that include increased amino acid, benzoate, and fatty acid exudation. In rice plants grown in soil from a rice field, IR stimuli significantly affected the composition of rhizosphere nematode communities 3 d after treatment, but by 14 d after treatment these changes had largely reverted. Notably, IR stimuli did not reduce nematode diversity, which suggests that IR might offer a sustainable option for managing plant-parasitic nematodes.

Co-implementation of conservation tillage and herbicides reduces weed and nematode infestation and enhances the productivity of direct-seeded rice in North-western Indo-Gangetic Plains

Direct-seeded rice (DSR) can be a resource-efficient alternative to puddled transplanted rice (PTR), but weeds and nematodes pose severe challenges. Conservation agriculture (CA)-based DSR may inhibit/influence weeds/nematodes, which can be further intensified by adopting better weed control. Hence, this experiment was undertaken. Five CA-based DSR practices involving zero tillage, residue retention, brown manuring, and superimposed with four weed control/herbicide options were compared with PTR in a split-plot design replicated three times. All DSRs encountered more weeds and plant parasitic nematodes (PPNs) than PTR. Root-knot nematodes (RKN) infested five among 14 weeds present in rice and was first time found in Dinebra retroflexa. A CA-based zero till (ZT)DSR+ mungbean residue – ZT wheat + rice residue – ZT mungbean+wheat residue system reduced weeds significantly. It reduced RKN galls in Echinochloa colona, Echinochloa crusgalli, and rice plants by 72, 58, and 56%, respectively. In soil too, RKN and other PPNs, namely, Tylenchorhynchus brevilineatus and Pratylenchus thornei were reduced by 39%, 32%, and 26%, respectively, which gave a 6.3–22.7% higher yield in this CA practice than other DSRs. Pyrazosulfuron-ethyl, cyhalofop-butyl, and bispyribac-Na applied sequentially reduced weeds and PPNs, increased rice yield by 176.1%, and were at below detectable levels in soil, rice grains, and straw, and were safe for rotational crops. The above ZT-based triple cropping with residue supplemented with herbicides through better weed and nematode control would be an alternative to PTR in the North-wester Indo-Gangetic Plains of India and in similar agroecologies of the tropics/sub-tropics. This study would help farmers and policymakers to design integrated weed and nematode management modules using tillage, crop residue, and herbicides/pesticides for higher DSR yield and income.

First Report of Root-knot Nematode, Meloidogyne Graminicola on Brassica Juncea in China

In southern China, the staple food rice (Oryza sativa) field is commonly rotated with brown mustard Brassica juncea. Root-knot nematodes (RKNs) are a major threat to rice production. From 2019 to 2021, B. juncea in 56 fields from 26 counties in Guangxi Province were observed with symptoms of leaf yellowing, stunting, and several hook-shaped galls on the roots. Females and egg masses of Meloidogyne sp. were found within the galls. The females, males, and second-stage juveniles (J2s) were collected, and identified with morphological and molecular characteristics and female perineal patterns. Brassica juncea was transplanted in pots and a pathogenicity test was conducted to confirm the species as Meloidogyne graminicola. In China, this is the first record of a natural infection of mustard with M. graminicola, and this finding has great importance for Chinese mustard production, since this nematode may damage mustard plants and become an additional problem for this crop.

Biocontrol potential of Pseudomonas rhodesiae GC-7 against the root-knot nematode Meloidogyne graminicola through both antagonistic effects and induced plant resistance

Plant-parasitic nematodes (PPNs) cause serious damage to agricultural production worldwide. Currently, because of a lack of effective and environmental-friendly chemical nematicides, the use of microbial nematicides has been proposed as an eco-friendly management strategy to control PPNs. A nematicidal bacterium GC-7 was originally isolated from the rice rhizosphere, and was identified as Pseudomonas rhodesiae. Treatment with the fermentation supernatant of GC-7 in vitro showed a highly lethal effect on second-stage juveniles of Meloidogyne graminicola, with the mortality rate increasing to 95.82% at 24 h and egg hatching significantly inhibited, with a hatch inhibition rate of 60.65% at 96 h. The bacterium significantly reduced the level of damage caused by M. graminicola infestations to rice (Oryza sativa) in greenhouse and field experiments. Under greenhouse conditions, the GC-7 culture efficiently reduced the gall index and nematode population in rice roots and soils, as well as inhibited nematode development compared to the control. Under field conditions, application of the GC-7 consistently showed a high biocontrol efficacy against M. graminicola (with a control efficiency of 58.85%) and promoted plant growth. In addition, the inoculation of GC-7 in M. graminicola-infested rice plant fields significantly suppressed final nematode populations in soil under natural conditions. Furthermore, activities of plant defense-related enzymes, peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase were remarkably increased in plant roots treated with GC-7 compared with roots that were challenge to M. graminicola. Moreover, quantitative real-time PCR analysis showed that GC-7 significantly enhanced the expression of defense genes (PR1a, WRKY45, JaMYB, AOS2, ERF1, and ACS1) related to salicylic acid, jasmonic acid, and ethylene signaling pathways in rice roots after inoculation with GC-7 at different levels. The results indicated that GC-7 could be an effective biological component in the integrated management of M. graminicola infecting rice.

Dehydroascorbate induces plant resistance in rice against root-knot nematode Meloidogyne graminicola

Ascorbic acid (AsA) is an important antioxidant in plants and regulates various physiological processes. In this study, we show that exogenous treatments with the oxidized form of AsA, that is, dehydroascorbate (DHA), activates induced systemic resistance in rice against the root-knot nematode Meloidogyne graminicola, and investigate the molecular and biochemical mechanisms underlying this phenotype. Detailed transcriptome analysis on roots of rice plants showed an early and robust transcriptional response on foliar DHA treatment, with induction of several genes related to plant stress responses, immunity, antioxidant activity, and secondary metabolism already at 1 day after treatment. Quantitative and qualitative evaluation of H₂ O₂ levels confirmed the appearance of a reactive oxygen species (ROS) burst on DHA treatment, both at the site of treatment and systemically. Experiments using chemical ROS inhibitors or scavengers confirmed that H₂ O₂ accumulation contributes to DHA-based induced resistance. Furthermore, hormone measurements in DHA-treated plants showed a significant systemic accumulation of the defence hormone salicylic acid (SA). The role of the SA pathway in DHA-based induced resistance was confirmed by nematode infection experiments using an SA-signalling deficient WRKY45-RNAi line and reverse transcription-quantitative PCR on SA marker genes. Our results collectively reveal that DHA activates induced systemic resistance in rice against the root-knot nematode M. graminicola, mediated through the production of ROS and activation of the SA pathway.

Rice diterpenoid phytoalexins are involved in defence against parasitic nematodes and shape rhizosphere nematode communities

Rice diterpenoid phytoalexins (DPs) are secondary metabolites with a well known role in resistance to foliar pathogens. As DPs are also known to be produced and exuded by rice roots, we hypothesised that they might play an important role in plant-nematode interactions, and particularly in defence against phytoparasitic nematodes. We used transcriptome analysis on rice roots to analyse the effect of infection by the root-knot nematode Meloidogyne graminicola or treatment with resistance-inducing chemical stimuli on DP biosynthesis genes, and assessed the susceptibility of mutant rice lines impaired in DP biosynthesis to M. graminicola. Moreover, we grew these mutants and their wild-type in field soil and used metabarcoding to assess the effect of impairment in DP biosynthesis on rhizosphere and root nematode communities. We show that M. graminicola suppresses DP biosynthesis genes early in its invasion process and, conversely, that resistance-inducing stimuli transiently induce the biosynthesis of DPs. Moreover, we show that loss of DPs increases susceptibility to M. graminicola. Metabarcoding on wild-type and DP-deficient plants grown in field soil reveals that DPs significantly alter the composition of rhizosphere and root nematode communities. Diterpenoid phytoalexins are important players in basal and inducible defence against nematode pathogens of rice and help shape rice-associated nematode communities.

Silencing the conserved small nuclear ribonucleoprotein SmD1 target gene alters susceptibility to root-knot nematodes in plants

Root-knot nematodes (RKNs) are among the most damaging pests of agricultural crops. Meloidogyne is an extremely polyphagous genus of nematodes that can infect thousands of plant species. A few genes for resistance (R-genes) to RKN suitable for use in crop breeding have been identified, but virulent strains and species of RKN have emerged that render these R-genes ineffective. Secretion of RKN effectors targeting plant functions mediates the reprogramming of root cells into specialized feeding cells, the giant cells, essential for RKN development and reproduction. Conserved targets among plant species define the more relevant strategies for controlling nematode infection. The EFFECTOR18 (EFF18) protein from M. incognita interacts with the spliceosomal small nuclear ribonucleoprotein D1 (SmD1) in Arabidopsis (Arabidopsis thaliana), disrupting its function in alternative splicing regulation and modulating the giant cell transcriptome. We show here that EFF18 is a conserved RKN-specific effector that targets this conserved spliceosomal SmD1 protein in Solanaceae. This interaction modulates alternative splicing events produced by tomato (Solanum lycopersicum) in response to M. incognita infection. The alteration of SmD1 expression by virus-induced gene silencing in Solanaceae affects giant cell formation and nematode development. Thus, our work defines a promising conserved SmD1 target gene to develop broad resistance for the control of Meloidogyne spp. in plants.

BSA-seq Identifies a Major Locus on Chromosome 6 for Root-Knot Nematode (Meloidogyne graminicola) Resistance From Oryza glaberrima

Root-knot nematode (Meloidogyne graminicola) is one of the emerging threats to rice production worldwide that causes substantial yield reductions. There is a progressive shift of the cropping system from traditional transplanting to direct-seeded water-saving rice production that favored the development of M. graminicola. Scouting and deploying new resistance genes is an economical approach to managing the root-knot nematodes. Here, we report that the inheritance of root-knot nematode resistance in Oryza glaberrima acc. IRGC102206 is governed by a single dominant gene. Traditional mapping coupled with BSA-seq is used to map nematode resistance gene(s) using the BC₁F₁ population derived from a cross of O. sativa cv. PR121 (S) and O. glaberrima acc. IRGC102206 (R). One major novel genomic region spanning a 3.0-Mb interval on chromosome 6 and two minor QTLs on chromosomes 2 and 4 are the potential genomic regions associated with rice root-knot nematode resistance. Within the QTL regions, 19 putative candidate genes contain 81 non-synonymous variants. The detected major candidate region could be fine mapped to accelerate marker-assisted breeding for root-knot nematode resistance in rice.

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.

Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines

Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238-553,648 unique SNPs and 32,395-65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.

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.

Morphological characterization reveals new insights into giant cell development of Meloidogyne graminicola on rice

Three types of nematode-feeding sites (NFSs) caused by M. graminicola on rice were suggested, and the NFS polarized expansion stops before the full NFS maturation that occurs at adult female stage. Root-knot nematodes, Meloidogyne spp., secrete effectors and recruit host genes to establish their feeding sites giant cells, ensuring their nutrient acquisition. There is still a limited understanding of the mechanism underlying giant cell development. Here, the three-dimensional structures of M. graminicola-caused nematode-feeding sites (NFSs) on rice as well as changes in morphological features and cytoplasm density of the giant cells (GCs) during nematode parasitism were reconstructed and characterized by confocal microscopy and the Fiji software. Characterization of morphological features showed that three types of M. graminicola-caused NFSs, type I-III, were detected during parasitism at the second juvenile (J2), the third juvenile (J3), the fourth juvenile (J4) and adult female stages. Type I is the majority at all stages and type II develops into type I at J3 stage marked by its longitudinal growth. Meanwhile, NFSs underwent polarized expansion, where the lateral and longitudinal expansion ceased at later parasitic J2 stage and the non-feeding J4 stage, respectively. The investigation of giant cell cytoplasm density indicates that it reaches a peak at the midpoint of early parasitic J2 and adult female stages. Our data suggest the formation of three types of NFSs caused by M. graminicola on rice and the NFS polarized expansion stopping before full NFS maturation, which provides unprecedented spatio-temporal characterization of development of giant cells caused by a root-knot nematode.

Cucurbitaceae COld Peeling Extracts (CCOPEs) Protect Plants From Root-Knot Nematode Infections Through Induced Resistance and Nematicidal Effects

With nematicides progressively being banned due to their environmental impact, an urgent need for novel and sustainable control strategies has arisen. Stimulation of plant immunity, a phenomenon referred to as "induced resistance" (IR), is a promising option. In this study, Cucurbitaceae COld Peeling Extracts (CCOPEs) were shown to protect rice (Oryza sativa) and tomato (Solanum lycopersicum) against the root-knot nematodes Meloidogyne graminicola and Meloidogyne incognita, respectively. Focusing on CCOPE derived from peels of melon (Cucumis melo var. cantalupensis; mCOPE), we unveiled that this extract combines an IR-triggering capacity with direct nematicidal effects. Under lab conditions, the observed resistance was comparable to the protection obtained by commercially available IR stimuli or nematicides. Via mRNA sequencing and confirmatory biochemical assays, it was proven that mCOPE-IR in rice is associated with systemic effects on ethylene accumulation, reactive oxygen species (ROS) metabolism and cell wall-related modifications. While no negative trade-offs were detected with respect to plant growth or plant susceptibility to necrotrophic pests or pathogens, additional infection experiments indicated that mCOPE may have a predominant activity toward biotrophs. In summary, the presented data illustrate a propitious potential for these extracts, which can be derived from agro-industrial waste streams.

Meloidogyne graminicola-A Threat to Rice Production: Review Update on Distribution, Biology, Identification, and Management

Simple Summary

New risks to plant health are constantly emerging. Such is the case of the rice root knot nematode Meloidogyne graminicola, adapted to flooded conditions and representing a risk to all types of rice agro-systems. It has been recently detected in Italy and added to the European and Mediterranean Plant Protection Organization (EPPO) Alert List. The presence of this nematode in Europe poses a threat to rice production, as there is a high probability to spread, due to trade activities and climate changes. In view of its importance, an extensive updated review was carried out.

Abstract

Rice (Oryza sativa L.) is one of the main cultivated crops worldwide and represents a staple food for more than half of the world population. Root-knot nematodes (RKNs), Meloidogyne spp., and particularly M. graminicola, are serious pests of rice, being, probably, the most economically important plant-parasitic nematode in this crop. M. graminicola is an obligate sedentary endoparasite adapted to flooded conditions. Until recently, M. graminicola was present mainly in irrigated rice fields in Asia, parts of the Americas, and South Africa. However, in July 2016, it was found in northern Italy in the Piedmont region and in May 2018 in the Lombardy region in the province of Pavia. Following the first detection in the EPPO region, this pest was included in the EPPO Alert List as its wide host range and ability to survive during long periods in environments with low oxygen content, represent a threat for rice production in the European Union. Considering the impact of this nematode on agriculture, a literature review focusing on M. graminicola distribution, biology, identification, and management was conducted.

Systematic Investigation of Plant-Parasitic Nematodes Associated with Main Subtropical Crops in Guangxi Province, China

Plant parasitic nematodes (PPNs) are a pathogenic group that causes momentous crop yield loss by retarding plant growth and development through plant parasitization. In this study, the distribution of PPNs based on the main crops in Guangxi Province of China was investigated. A total of 425 samples of soil or roots from sugarcane, rice, maize, and soybean were collected in 68 counties, and a total of 48 order/family/genera of PPNs were identified, of which some genera were found in more than one crop. A total of 31 order/family/genera of PPNs were found in rice, among which Hirschmanniella was the most abundant, accounting for 79.23%, followed by Tylenchorhynchus (34.43%). Forty order/family/genera were observed in maize, of which the dominant genera were Pratylenchus and Tylenchorhynchus at 45.14% and 32.64%, respectively. In addition, 30 order/family/genera of PPNs were detected from sugarcane, and the percentages of Tylenchorhynchus and Helicotylenchus were 70.42% and 39.44%, respectively. The main crop of Eastern ecological regions was rice, with a high frequency of Hirschmanniella. The greatest frequency of Pratylenchus was found in the Western eco-region, which had a large area of maize. In the Northern eco-region, rice and maize were popular, with abundant Hirschmanniella and Helicotylenchus. In the Central eco-region, Pratylenchus was detected on the main crop of sugarcane. Hirschmanniella (72.94%) was dominant in clay, and Tylenchorhynchus (54.17%) showed the highest frequency in loam. The distribution of PPNs varied with different altitudes. The diversity of this phenomenon was closely related to host plants. These results could improve understanding of the distribution of PPNs and provide important information for controlling PPNs.

The Meloidogyne javanica effector Mj2G02 interferes with jasmonic acid signalling to suppress cell death and promote parasitism in Arabidopsis

Plant-parasitic nematodes can cause devastating damage to crops. These nematodes secrete effectors that suppress the host immune responses to enhance their survival. In this study, Mj2G02, an effector from Meloidogyne javanica, is described. In situ hybridization and transcriptional analysis showed that Mj2G02 was highly expressed in the early infection stages and exclusively expressed in the nematode subventral oesophageal gland cells. In planta RNA interference targeting Mj2G02 impaired M. javanica parasitism, and Mj2G02-transgenic Arabidopsis lines displayed more susceptibility to M. javanica. Using an Agrobacterium-mediated transient expression system and plant immune response assays, we demonstrated that Mj2G02 localized in the plant cell nuclei and could suppress Gpa2/RBP-1-induced cell death. Moreover, by RNA-Seq and quantitative reverse transcription PCR analyses, we showed that Mj2G02 was capable of interfering with the host jasmonic acid (JA) signalling pathway. Multiple jasmonate ZIM-domain (JAZ) genes were significantly upregulated, whereas the JAR1 gene and four JA-responsive genes, MYC3, UPI, THI2.1, and WRKY75, were significantly downregulated. In addition, HPLC analysis showed that the endogenous jasmonoyl-isoleucine (JA-Ile) level in Mj2G02-transgenic Arabidopsis lines was significantly decreased compared to that in wildtype plants. Our results indicate that the M. javanica effector Mj2G02 suppresses the plant immune response, therefore facilitating nematode parasitism. This process is probably mediated by a JA-Ile reduction and JAZ enhancement to repress JA-responsive genes.

The Use of Biochar for Plant Pathogen Control

To support the search for alternative, nonchemical plant disease control strategies, we present a review of the pathogen-suppressive effects of biochar, a product derived from agricultural and other organic wastes, used as a soil amendment. A wide range of biochar effects contribute to the control of root or foliar fungal pathogens through modification of root exudates, soil properties, and nutrient availability, which influence the growth of antagonist microorganisms. The induction of systemic plant defenses by biochar in the roots to reduce foliar pathogenic fungi, the activation of stress-hormone responses, as well as changes in active oxygen species are indicative of a coordinated hormonal signaling within the plant. Although scarce data are available for oomycetes and bacterial pathogens, reports indicate that biochar promotes changes in the soil microbiota influencing pathogen motility and colonization, and the induction of plant systemic defenses, both contributing to disease suppression. Biochar also suppresses nematode and insect pests. For plant-parasitic nematodes, the primary modes of action are changes in soil microbial community diversity, the release of nematicidal compounds, and the induction of plant defenses. Use of biochar-based soil amendments is a promising strategy compatible with a circular economy, based on zero waste, as part of integrated pathogen and pest management. Since biochars exert complex and distinct modes of action for the control of plant pathogens, its nature and application regimes should be designed for particular pathogens and its effects studied locally.

Induced Resistance by Ascorbate Oxidation Involves Potentiating of the Phenylpropanoid Pathway and Improved Rice Tolerance to Parasitic Nematodes

Anticipating an increased ecological awareness, scientists have been exploring new strategies to reduce the use of chemical pesticides to control pests and diseases. Triggering the intrinsic plant defense system is one of the promising strategies to reduce yield loss by pathogenic organisms, such as nematodes. Ascorbate oxidase (AO) enzyme plays an important role in plant defense by regulating the apoplastic ascorbate/dehydroascorbate (DHA) ratio via the ascorbate oxidation process. Ascorbate oxidation is known to induce systemic resistance in rice against parasitic root-knot nematodes (RKN). Here, we sought to evaluate if AO- or DHA-induced resistance (IR) against RKN M. graminicola involves activation of the phenylpropanoid pathway and whether this IR phenotype has potential effects on growth of rice seedlings under stressed and unstressed conditions. Our results show that AO/DHA-IR against these parasitic nematodes is dependent on activation of phenylalanine ammonia lyase (PAL). However, application of reduced ascorbic acid (AA) did not induce this response. Gene expression analysis via qRT-PCR showed that OsPAL2 and OsPAL4 are highly expressed in AO/DHA-sprayed nematode-infected roots and PAL-activity measurements confirmed that AO/DHA spraying triggers the plants for primed activation of this enzyme upon nematode infection. AO/DHA-IR is not effective in plants sprayed with a chemical PAL inhibitor confirming that AO/DHA-induced resistance is dependent on PAL activity. Improved plant growth and low nematode infection in AO/DHA-sprayed plants was found to be correlated with an increase in shoot chlorophyll fluorescence (Fv/Fm), chlorophyll index (ChlIdx), and modified anthocyanin reflection index which were proven to be good above-ground parameters for nematode infestation. A detailed growth analysis confirmed the improved growth of AO/DHA-treated plants under nematode-infected conditions. Taken together, our results indicate that ascorbate oxidation enhances the phenylpropanoid-based response to nematode infection and leads to a tolerance phenotype in treated rice plants.

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.

An improved draft genome assembly of Meloidogyne graminicola IARI strain using long-read sequencing

The rice root-knot nematode Meloidogyne graminicola is a major biotic stress for the rice crop under upland, rain-fed lowland and irrigated cultivation conditions. Here, we present an improved draft genome assembly of M. graminicola IARI strain using the long-read sequencing approach (PacBio Sequel platform). The assembled genome size was 36.86 Mb with 514 contigs and N50 value of 105 kb. BUSCO estimated the genome to be 88.6% complete. Meloidogyne graminicola genome contained 17.83% repeat elements and showed 14,062 protein-coding gene models, 4,974 conserved orthologous genes, 561 putative secreted proteins, 49 RNAi pathway genes, 1,853 proteins involved in pathogen-host interactions, 1,575 carbohydrate-active enzymes, and 32,138 microsatellites. Five of the carbohydrate-active enzymes were found only in M. graminicola genome and were not present in any other analysed root-knot nematode genome. Together with the previous two genome assemblies, this improved genome assembly would facilitate comparative and functional genomics for M. graminicola.

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.

Genome-wide shifts in histone modifications at early stage of rice infection with Meloidogyne graminicola

Epigenetic processes play a crucial role in the regulation of plant stress responses, but their role in plant-pathogen interactions remains poorly understood. Although histone-modifying enzymes have been observed to be deregulated in galls induced by root-knot nematodes (RKN, Meloidogyne graminicola) in rice, their influence on plant defence and their genome-wide impact has not been comprehensively investigated. First, the role of histone modifications in plant-nematode interactions was confirmed by pharmacological inhibition of histone-modifying enzymes, which all significantly affected rice susceptibility to RKN. For a more specific view, three histone marks, H3K9ac, H3K9me2, and H3K27me3, were subsequently studied by chromatin-immunoprecipitation-sequencing on RKN-induced galls at 3 days postinoculation. While levels of H3K9ac and H3K27me3 were strongly enriched, H3K9me2 was generally depleted in galls versus control root tips. Differential histone peaks were generally associated with plant defence-related genes. Transcriptome analysis using RNA-Seq and RT-qPCR-based validation revealed that genes marked with H3K9ac or H3K9me2 showed the expected activation or repression gene expression pattern, but this was not the case for H3K27me3 marks. Our results indicate that histone modifications respond dynamically to RKN infection, and that posttranslational modifications mainly at H3K9 specifically target plant defence-related genes.

Rapid and Sensitive Detection of Meloidogyne graminicola in Soil Using Conventional PCR, Loop-Mediated Isothermal Amplification, and Real-Time PCR Methods

Meloidogyne graminicola is one of the major plant-parasitic nematodes (PPNs) that affect rice agriculture. Rapid identification and quantification of M. graminicola in soil is crucial for early diagnosis so that measures can be taken to reduce the impact of PPN diseases and ensure food security. In this study, M. graminicola species-specific primers for conventional PCR, loop-mediated isothermal amplification (LAMP), and real-time PCR were designed based on the sequence-characterized amplified region. The primers were highly specific and sensitive, and only samples containing M. graminicola DNA showed positive results. The sensitivity of LAMP and real-time PCR (two second-stage juvenile [J2] M. graminicola in 100 g of soil) was higher than that of conventional PCR (200 J2s in 100 g of soil). A standard curve (correlation coefficient R² = 0.970, P < 0.001) was generated by amplifying DNA extracted from 0.5 g of soil, and a significant correlation was observed between the number of M. graminicola determined by microscopic examination and that predicted from the standard curve (R² = 0.477, P = 0.0160). In quantification analyses of M. graminicola isolated from 31 naturally infested soils, the sensitivity of LAMP and real-time PCR (22 M. graminicola in 100 g of soil) was higher than that of conventional PCR (211 M. graminicola in 100 g of soil). The conventional PCR, LAMP, and real-time PCR methods have the potential to provide a useful platform for rapid species identification according to the experimental conditions. The real-time PCR assay and standard curve can be used for quantification of M. graminicola. These newly developed assays will help to facilitate the control of these economically important PPNs.

Occurrence and molecular characterization of Meloidogyne graminicola on rice in Central Punjab, Pakistan

Meloidogyne graminicola threatens global rice production, yet is understudied for many areas where it is cultivated. To better understand the prevalence and incidence of M. graminicola in central Punjab, Pakistan, we carried out field surveys of rice fields in the districts of Faisalabad and Chiniot. M. graminicola isolates were recovered from soil and root samples and identified on the basis of perineal patterns and rDNA ITS-based sequencing. The severity of nematode attack on rice roots and infested fields at various locations was based on galling index, root-knot nematode juveniles per root system, juveniles per 100 ml of soil, and prevalence of stylet-bearing nematodes and non-stylet-bearing nematodes. Maximum prevalence (22.5 and 27.5%) and minimum prevalence (17.5 and 20%) of M. graminicola was observed in Chiniot and Faisalabad, respectively. Eleven alternate host-plant species were examined in this study revealing varying degrees of M. graminicola infestation. ITS sequencing and phylogenetic analysis indicated that isolates from this study form a well-resolved clade with others from Asia, while another isolate falls outside of this clade in an unresolved polytomy with those from Europe and South America. Though monophyletic with the other M. graminicola, the isolates from Pakistan are distinguished by their high genetic variability and long branch lengths relative to the other isolates of M. graminicola, suggesting Pakistan as a possible ancestral area. Our results indicate that rice is severely attacked by a genetically diverse and aggressive M. graminicola, necessitating the development of appropriate control measures for its management in rice and other graminaceous crops.

In-vitro and In-vivo management of Meloidogyne incognita (Kofoid and White) Chitwood and Rhizoctonia bataticola (Taub.) Butler in cotton using organic's

Root-knot nematodes Meloidogyne incognita (Kofoid and White) Chitwood and Rhizoctonia bataticola (Taub.) Butler, fungus, are very dangerous root damaging pathogens. Present study was planned to establish a chemical control of these root deteriorating pathogens under lab conditions as well as in field. Maximum death rate of nematode juveniles and minimum numbers of nematode eggs hatched were recorded in plates treated with Cadusafos (Rugby® 100G) @12 g/100 ml and Cartap® (4% G) @9g/100 ml. Chemical treatment of Rhizoctonia bataticola with Trifloxystrobin + Tebuconazole (Nativo®) @0.2 g/100 ml and Mancozeb + Matalaxyl (Axiom) @0.25 g/100 ml significantly controlled the mycelial growth in plates. The best treatments tested in laboratory were applied in field as protective and curative treatments. Results proved that chemical control of root-knot nematode and root rot fungi by tested chemicals at recommended time and dose is a significant management technique under field conditions.

Identification and Characterization of a Novel Protein Disulfide Isomerase Gene (MgPDI2) from Meloidogyne graminicola

Protein disulfide isomerase (PDI) is a multifunctional enzyme that catalyzes rate-limiting reactions such as disulfide bond formation, isomerization, and reduction. There is some evidence that indicates that PDI is also involved in host-pathogen interactions in plants. In this study, we show that the rice root-knot nematode, Meloidogyne graminicola, has evolved a secreted effector, MgPDI2, which is expressed in the subventral esophageal glands and up-regulated during the early parasitic stage of M. graminicola. Purified recombinant MgPDI2 functions as an insulin disulfide reductase and protects plasmid DNA from nicking. As an effector, MgPDI2 contributes to nematode parasitism. Silencing of MgPDI2 by RNA interference in the pre-parasitic second-stage juveniles (J2s) reduced M. graminicola multiplication and also increased M. graminicola mortality under H2O2 stress. In addition, an Agrobacterium-mediated transient expression assay found that MgPDI2 caused noticeable cell death in Nicotiana benthamiana. An intact C-terminal region containing the first catalytic domain (a) with an active motif (Cys-Gly-His-Cys, CGHC) and the two non-active domains (b and b') is required for cell death induction in N. benthamiana. This research may provide a promising target for the development of new strategies to combat M. graminicola infections.

Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam

Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilborne parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we discovered that M. graminicola infection caused modifications of the root bacterial community composition and network structure. Interestingly, we observed in infected roots a higher diversity and species richness (+24% observed ESVs) as well as a denser and more complex co-occurrence network (+44% nodes and +136% links). We identified enriched taxa that include several hubs, which could serve as potential indicators or biocontrol agents of the nematode infection. Moreover, the community of infected roots is more specific suggesting changes in the functional capabilities to survive in the gall environment. We thus describe the signature of the gall microbiome (the 'gallobiome') with shifting abundances and enrichments that lead to a strong restructuration of the root microbiome.

Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola)

Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294 kb, totaling 41.5 Mb). The completeness scores of our assembly are among the highest currently published for Meloidogyne genomes. We predicted 10,284 protein-coding genes spanning 75.5% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of M. graminicola parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of Meloidogyne species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of M. graminicola and its closest relatives.

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice.

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.