Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens

Biocontrol activity and potential mechanism of Bacillus cereus G5 against Meloidogyne graminicola

Root-knot nematodes (Meloidogyne spp.) are highly destructive pests that cause significant yield losses annually. Biological control of nematodes has emerged as a potential alternative in sustainable agriculture. In this study, we originally isolated Bacillus cereus G5 from the rhizosphere soil of rice (Oryza sativa). Treatment with the fermentation supernatant of G5 in vitro demonstrated high toxicity to second-stage juveniles (J2) of Meloidogyne graminicola and remarkably inhibited egg hatching. Moreover, G5 steadily colonized rhizosphere soil and rice seedlings, and exhibited excellent biocontrol efficacy against M. graminicola under greenhouse conditions. Notably, the volatile organic compounds (VOCs) produced by G5 displayed high fumigant activity against M. graminicola. The G5 VOCs efficiently reduced the gall index and nematode population in rice roots, while also promoting rice growth in double-layered pot tests. Additionally, the expression of defense genes involved in the salicylic acid (OsNPR1, OsWRKY45, OsPAL1), jasmonic acid (OsJaMYB, OsAOS2) and ethylene (OsACS1) signalling pathways was significantly upregulated in rice seedlings treated with G5 VOCs. This suggests that G5 VOCs contribute to eliciting plant defense responses. Furthermore, we identified 14 major VOCs produced by G5 using solid-phase micro-extraction gas chromatography and mass spectrometry (SPEM-GC-MS). Notably, allomatrine, morantel, 1-octen-3-ol and 3-methyl-2-butanol displayed strong contact nematicidal activity. Among these, only 1-octen-3-ol demonstrated fumigant activity against J2s of M. graminicola, with an LC50 value of 758.95 mg/L at 24 h. Overall, these results indicated that the B. cereus G5 and its synthetic VOCs possess high potential as biocontrol agents for managing root-knot nematodes.

Design, Synthesis, and Nematocidal Evaluation of Waltherione A Derivatives: Leveraging a Structural Simplification Strategy

Southern root-knot nematodes are among the most pernicious phytoparasites; they are responsible for substantial yield losses in agricultural crops worldwide. The limited availability of nematicides for the prevention and control of plant-parasitic nematodes necessitates the urgent development of novel nematicides. Natural products have always been a key source for the discovery of pesticides. Waltherione A, an alkaloid, exhibits potent nematocidal activity. In this study, we designed and synthesized a series of quinoline and quinolone derivatives from Waltherione A, leveraging a strategy of structural simplification. Bioassays have revealed that the quinoline derivatives exhibit better activity than quinolone derivatives in terms of both nematocidal and fungicidal activities. Notably, compound D1 demonstrated strong nematocidal activity, with a 72 h LC50 of 23.06 μg/mL, and it effectively controlled the infection of root-knot nematodes on cucumbers. The structure-activity relationship suggests that the quinoline moiety is essential for the nematocidal efficacy of Waltherione A. Additionally, compound D1 exhibited broad-spectrum fungicidal activity, with an EC50 of 2.98 μg/mL against Botrytis cinerea. At a concentration of 200 μg/mL, it significantly inhibited the occurrence of B. cinerea on tomato fruits, with an inhibitory effect of 96.65%, which is slightly better than the positive control (90.30%).

Overexpression of NtEXPA7 promotes seedling growth and resistance to root-knot nematode in tobacco

Root-knot nematode (RKN) is one of the most damaging plant pathogen in the world. They exhibit a wide host range and cause serious crop losses. The cell wall, encasing every plant cell, plays a crucial role in defending of RKN invasion. Expansins are a group of cell wall proteins inducing cell wall loosening and extensibility. They are widely involved in the regulation of plant growth and the response to biotic and abiotic stresses. In this study, we have characterized the biological function of tobacco (Nicotiana tabacum) NtEXPA7, the homologue of Solyc08g080060.2 (SlEXPA18), of which the transcription level was significantly reduced in susceptible tomato upon RKN infection. The expression of NtEXPA7 was up-regulated after inoculation of RKNs. The NtEXPA7 protein resided in the cell wall. Overexpression of NtEXPA7 promoted the seedling growth of transgenic tobacco. Meanwhile the increased expression of NtEXPA7 was beneficial to enhance the resistance against RKNs. This study expands the understanding of biological role of expansin in coordinate plant growth and disease resistance.

Light signaling regulates root-knot nematode infection and development via HY5-SWEET signaling

BACKGROUND

Meloidogyne incognita is one of the most important plant-parasitic nematodes and causes tremendous losses to the agricultural economy. Light is an important living factor for plants and pathogenic organisms, and sufficient light promotes root-knot nematode infection, but the underlying mechanism is still unclear.

RESULTS

Expression level and genetic analyses revealed that the photoreceptor genes PHY, CRY, and PHOT have a negative impact on nematode infection. Interestingly, ELONGATED HYPOCOTYL5 (HY5), a downstream gene involved in the regulation of light signaling, is associated with photoreceptor-mediated negative regulation of root-knot nematode resistance. ChIP and yeast one-hybrid assays supported that HY5 participates in plant-to-root-knot nematode responses by directly binding to the SWEET negative regulatory factors involved in root-knot nematode resistance.

CONCLUSIONS

This study elucidates the important role of light signaling pathways in plant resistance to nematodes, providing a new perspective for RKN resistance research.

Resistance to both aphids and nematodes in tobacco plants expressing a Bacillus thuringiensis crystal protein

BACKGROUND

Bacillus thuringiensis (Bt) and its crystal toxin or δ-endotoxins (Cry) offer great potential for the efficient control of crop pests. A vast number of pests can potentially infect the same host plant, either simultaneously or sequentially. However, no effective Bt-Cry protein has been reported to control both aphids and plant parasitic nematodes due to its highly specific activity.

RESULTS

Our study indicated that the Cry5Ba2 protein was toxic to the green peach aphid Myzus persicae, which had a median lethal concentration (LC50) of 9.7 ng μL-1 and fiducial limits of 3.1-34.6 ng μL-1. Immunohistochemical localization of Cry5Ba2 revealed that it could bind to the apical tip of microvilli in midgut regions. Moreover, transgenic tobacco plants expressing Cry5Ba2 exhibited significant resistance to Myzus persicae, as evidenced by reduced insect survival and impaired fecundity, and also intoxicated the Meloidogyne incognita as indicated by a decrease in galls and progeny reproduction.

CONCLUSION

In sum, we identified a new aphicidal Bt toxin resource that could simultaneously control both aboveground and belowground pests, thus extending the application range of Bt-based strategy for crop protection. © 2024 Society of Chemical Industry.

Unraveling the enigma of root-knot nematodes: from origins to advanced management strategies in agriculture

MAIN CONCLUSION

Integrated management strategies, including novel nematicides and resilient cultivars, offer sustainable solutions to combat root-knot nematodes, crucial for safeguarding global agriculture against persistent threats. Root-knot nematodes (RKN) pose a significant threat to a diverse range of host plants, with their obligatory endoparasitic nature leading to substantial agricultural losses. RKN spend much of their lives inside or in contact by secreting plant cell wall-modifying enzymes resulting in the giant cell development for establishing host-parasite relationships. Additionally, inflicting physical harm to host plants, RKN also contributes to disease complexes creation with fungi and bacteria. This review comprehensively explores the origin, history, distribution, and physiological races of RKN, emphasizing their economic impact on plants through gall formation. Management strategies, ranging from cultural and physical to biological and chemical controls, along with resistance mechanisms and marker-assisted selection, are explored. While recognizing the limitations of traditional nematicides, recent breakthroughs in non-fumigant alternatives like fluensulfone, spirotetramat, and fluopyram offer promising avenues for sustainable RKN management. Despite the success of resistance mechanisms like the Mi gene, challenges persist, prompting the need for integrative approaches to tackle Mi-virulent isolates. In conclusion, the review stresses the importance of innovative and resilient control measures for sustainable agriculture, emphasizing ongoing research to address evolving challenges posed by RKN. The integration of botanicals, resistant cultivars, and biological controls, alongside advancements in non-fumigant nematicides, contributes novel insights to the field, laying the ground work for future research directions to ensure the long-term sustainability of agriculture in the face of persistent RKN threats.

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

We present the chromosome-scale genome assembly of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly was annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes were phased using ancestral k-mer spectral analysis. Subgenome B appears to show fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identified regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens.

Flooding soil with biogas slurry suppresses root-knot nematodes and alters soil nematode communities

Root-knot nematodes (RKNs) pose a serious threat to crop production. Flooding soil with biogas slurry, combined with soil heating before crop planting, has the potential for RKN disease suppression. However, the actual effect of this method has not been verified under field conditions. Here, we present the results of a two-year field experiment in a greenhouse demonstrating the control effect on RKN disease and plant growth using this method, as well as its influence on the soil nematode community. Four treatments were set: untreated control (CK), local control method for RKN (CC), soil flooded with 70 % biogas slurry (BS70), and soil flooded with undiluted biogas slurry (BS100). In the first year, all three RKN control treatments significantly reduced the root-knot index (p < 0.05). In the next year, only BS70 and BS100 still presented significantly suppressed effects (p < 0.05), and it was more obvious under BS70 with a relative control effect of 74.6 %. In the first year, BS70 and BS100 significantly inhibited the plant height of watermelon (p < 0.05). In the next year, however, all three RKN control treatments promoted the growth of watermelon, and their stem diameter was significantly greater than that of CK. The application of biogas slurry (BS70 and BS100) significantly increased nematode richness and the Shannon index in the second year (p < 0.05). However, the structure index showed no significant difference among treatments (p > 0.05), indicating that biogas slurry application did not increase the soil food web complex. Principal component analysis showed that the application of biogas slurry changed the nematode community, especially under BS70, which presented a more lasting influence. The high-level input of biogas slurry also caused soil NH4+-N and heavy-metal and arsenic accumulation in the first year, but these soil-pollution risks disappeared in the second year.

Biological Control of a Root-Knot Nematode Meloidogyne incognita Infection of Tomato (Solanum lycopersicum L.) by the Oomycete Biocontrol Agent Pythium oligandrum

The biocontrol agent Pythium oligandrum, which is a member of the phylum Oomycota, can control diseases caused by a taxonomically wide range of plant pathogens, including fungi, bacteria, and oomycetes. However, whether P. oligandrum could control diseases caused by plant root-knot nematodes (RKNs) was unknown. We investigated a recently isolated P. oligandrum strain GAQ1, and the P. oligandrum strain CBS530.74, for the control of an RKN Meloidogyne incognita infection of tomato (Solanum lycopersicum L.). Initially, P. oligandrum culture filtrates were found to be lethal to M. incognita second-stage juveniles (J2s) with up to 84% mortality 24 h after treatment compared to 14% in the control group. Consistent with the lethality to M. incognita J2s, tomato roots treated with P. oligandrum culture filtrates reduced their attraction of nematodes, and the number of nematodes penetrating the roots was reduced by up to 78%. In a greenhouse pot trial, the P. oligandrum GAQ1 inoculation of tomato plants significantly reduced the gall number by 58% in plants infected with M. incognita. Notably, the P. oligandrum GAQ1 mycelial treatment significantly increased tomato plant height (by 36%), weight (by 27%), and root weight (by 48%). A transcriptome analysis of tomato seedling roots inoculated with the P. oligandrum GAQ1 strain identified ~2500 differentially expressed genes. The enriched GO terms and annotations in the up-regulated genes suggested a modulation of the plant hormone-signaling and defense-related pathways in response to P. oligandrum. In conclusion, our results support that P. oligandrum GAQ1 can serve as a potential biocontrol agent for M. incognita control in tomato. Multiple mechanisms appear to contribute to the biocontrol effect, including the direct inhibition of M. incognita, the potential priming of tomato plant defenses, and plant growth promotion.

Morphological and Molecular Characterization of a New Root-Knot Nematode, Meloidogyne limonae n. sp. (Nematoda: Meloidogynidae), Parasitizing Lemon in China

Root-knot nematodes of the genus Meloidogyne parasitize the roots of thousands of plants and can cause severe damage and yield losses. Here, we report a new root-knot nematode, Meloidogyne limonae n. sp., parasitizing "lemon" (Citrus limon) in Hainan Province, South China. Lemon trees infected by the root-knot nematode showed poor-quality lemons, chlorosis of foliage, weak growth, and numerous root galls with white females and egg masses protruding outside. Phylogenetic trees of sequences within the ribosomal and mitochondrial DNA demonstrated that this species differs clearly from other previously described root-knot nematodes. Morphologically, the new species is characterized by an oval-shaped perineal pattern and the lateral field marked by a ridge of cuticle on one or both sides; the dorsal arch is low, with fine to coarse, smooth cuticle striae; the vulva slit is centrally located at the unstriated area; the spicules of males are arcuate and curved ventrally; the gubernaculum is distinct and curved; the labial disc of second-stage juveniles is prominent and dumbbell shaped; stylet knobs are oval and sloping backwardly; pharyngeal glands are not filling the body cavity and overlapping the intestine ventrally; and the conical tail is gradually tapering. Phylogenetic trees based on the ITS1-5.8S-ITS2, D2-D3 of the 28S rDNA, and COI and COII-16S rRNA genes of the mtDNA showed that M. limonae n. sp. belongs to an undescribed root-knot nematode lineage that is separated from other species with the resemblance in morphology, such as M. floridensis, M. hispanica, M. acronea, and M. paranaensis.

A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield

Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.

Morphologic, Morphometric, and Molecular Characterization of Vietnamese Populations of Meloidogyne incognita

Meloidogyne incognita is considered the most damaging and common root-knot nematode to numerous host plants worldwide. During a survey of nematodes in Vietnam, 1,106 samples from 22 different plant species were collected. M. incognita was recorded on 13 of the 22 host plants. Four populations of M. incognita from four host plants were chosen for comparison and confirmation of their morphologic, morphometric, and molecular characteristics. Genetically based phylogenetic trees were constructed to show relationships among root-knot nematodes. Molecular barcodes of four gene regions, ITS, D2-D3 of 28S rRNA, COI, and Nad5 mtDNA, integrated with morphologic and morphometric data were used as reliable references for molecular identification of M. incognita. Our analyses indicated that tropical root-knot nematodes are very similar in characterization of ITS, D2-D3 of 28S rRNA, and COI regions. However, these gene regions can be used to separate the tropical root-knot nematode group from other groups. On the other hand, the analysis of Nad5 mtDNA and multiplex-PCR with specific primers can be used to distinguish tropical species.

A Deep Learning-Based Decision Support Tool for Plant-Parasitic Nematode Management

Plant-parasitic nematodes (PPN), especially sedentary endoparasitic nematodes like root-knot nematodes (RKN), pose a significant threat to major crops and vegetables. They are responsible for causing substantial yield losses, leading to economic consequences, and impacting the global food supply. The identification of PPNs and the assessment of their population is a tedious and time-consuming task. This study developed a state-of-the-art deep learning model-based decision support tool to detect and estimate the nematode population. The decision support tool is integrated with the fast inferencing YOLOv5 model and used pretrained nematode weight to detect plant-parasitic nematodes (juveniles) and eggs. The performance of the YOLOv5-640 model at detecting RKN eggs was as follows: precision = 0.992; recall = 0.959; F1-score = 0.975; and mAP = 0.979. YOLOv5-640 was able to detect RKN eggs with an inference time of 3.9 milliseconds, which is faster compared to other detection methods. The deep learning framework was integrated into a user-friendly web application system to build a fast and reliable prototype nematode decision support tool (NemDST). The NemDST facilitates farmers/growers to input image data, assess the nematode population, track the population growths, and recommend immediate actions necessary to control nematode infestation. This tool has the potential for rapid assessment of the nematode population to minimise crop yield losses and enhance financial outcomes.

Secondary Metabolites from the Nematode-Trapping Fungus Dactylellina haptotyla YMF1.03409

As a representative nematode-trapping fungus, Dactylellina haptotyla can capture and kill nematodes by producing traps, known as adhesive knobs. In this paper, the strain of D. haptotyla YMF1.03409 was studied by means of medium screening, fermentation, and purification and identification of crude extracts. Eighteen compounds were obtained from D. haptotyla YMF1.03409, including two new metabolites, nosporins C (1) and D (2). The known metabolites were identified to be 3-chloro-4-methoxybenzaldehyde (3), 3-chloro-4-methoxybenzoic acid (4), 2-chloro-1-methoxy-4-(methoxymethyl)benzene (5), 3-hydroxy-3-methyloxindole (6), nicotinic acid (7), succinic acid (8), 3,4-dihydroxybutanoic acid (9), 5'-O-methyladenosine (10), uridine (11), 2'-deoxyuridine (12), thymidine (13), 3-(phenylmethyl)-2,5-morpholinedione (14), methyl-β-D-glucopyranoside (15), 1,2-benzenedicarboxylic acid bis(2-methyl heptyl) ester (16), β-sitosterol (17), and 3β,6α-diol-stigmastane (18). The bioactive assay showed that these compounds had no obvious nematicidal activity against the nematodes Meloidogyne incognita and Panagrellus redivivus.

Volatile Organic Compounds of Bacillus pumilus Strain S1-10 Exhibit Fumigant Activity Against Meloidogyne incognita

Root-knot nematodes (RKNs) are highly specialized parasites that cause significant yield losses worldwide. In this study, we isolated Bacillus pumilus strain S1-10 from the rhizosphere soil of Zingiber officinale Rosc. plants and evaluated its fumigant activity against Meloidogyne incognita. S1-10 exhibited a strong repellent effect on second-stage juveniles (J2s) of M. incognita, and in vitro assays indicated that S1-10 volatile organic compounds (VOCs) suppressed J2 activity and egg hatching. Under greenhouse conditions, 71 and 79% reductions of nematodes and eggs were detected on plants treated with S-10 VOCs compared with controls. Ten VOCs were identified through gas chromatography and mass spectrometry (GC-MS), of which 2-(methylamino)-ethanol (2-ME) had strong fumigant activity against J2s of M. incognita, with an LC50 value of 1.5 mM at 12 h. These results indicate that S1-10 represents a potential novel biocontrol agent for RKNs.

ROS-responsive modified chitosan oligosaccharide nanocapsules for improving pesticide efficiency and intelligent release

BACKGROUND

Some traditional pesticide formulations are inefficient, leading to excessive use and abuse of pesticides, which in turn effects environment. Intelligent release pesticide formulations are ideal for improving pesticide utilization and persistence while reducing environmental pollution.

RESULTS

We designed a benzil-modified chitosan oligosaccharide (CO-BZ) to encapsulate avermectin (Ave). Ave@CO-BZ nanocapsules are prepared based on a simple interfacial method via cross-linking of CO-BZ with diphenylmethane diisocyanate (MDI). The Ave@CO-BZ nanocapsules have an average particle size of 100 nm and exhibited a responsive release performance for ROS. The cumulative release rate of nanocapsules at 24 h with ROS increased by about 11.4% compared to that without ROS. The Ave@CO-BZ nanocapsules displayed good photostability. Ave@CO-BZ nanocapsules can penetrate root-knot nematodes more easily and exhibited better nematicidal activity against root-knot nematodes. The pot experiment showed that the control effect of Ave CS at low concentration was 53.31% at the initial stage of application (15 d), while Ave@CO-BZ nanocapsules was 63.54%. Under the same conditions, the control effect of Ave@CO-BZ nanocapsules on root-knot nematodes was 60.00% after 45 days of application, while Ave EC was only 13.33%. The acute toxicity experiments of earthworms showed that the toxicity of nanocapsules was significantly lower than that of EC.

CONCLUSION

The ROS-responsive nanocapsules can improve the utilization of pesticides and non-target biosafety. This modified chitosan oligosaccharide has great potential as a bio stimuli-responsive material, and this simple and convenient method for preparing Ave@CO-BZ nanocapsules provides a direction for the effective utilization of pesticides. © 2023 Society of Chemical Industry.

The marksman: Bioactivated nematicides selectively kill plant-parasitic nematodes

Plant-parasitic nematodes destroy crops and have a major impact on the food supply, but using chemicals to control them poses a risk to other animals and people. Selectivins kill nematodes but have little effect on other organisms.

A Novel Robust Screening Assay Identifies Pseudomonas Strains as Reliable Antagonists of the Root-Knot Nematode Meloidogyne incognita

Forty-four bacterial strains isolated from greenhouse soil and beetroots were tested for their antagonistic activity against the plant-parasitic root-knot nematode (RKN) Meloidogyne incognita, which causes significant yield losses in a number of important crops worldwide. Through a novel combination of in vitro and on planta screening assays, Pseudomonas spp. 105 and 108 were identified as the most promising bacterial isolates. Both strains were evaluated for their potential to control different RKN population densities and as root protectants against nematode infestation. Regardless of the application method, both strains significantly reduced root galling caused by M. incognita. These two strains were subjected to whole genome sequencing and de novo genome assembly as a basis for phylogenetic and future functional characterization. Phylogenetic analysis revealed that both Pseudomonas strains cluster within the Pseudomonas fluorescens clade among previously characterized RKN antagonists and Pseudomonas-based biocontrol agents of plant diseases.

Root-knot nematodes produce functional mimics of tyrosine-sulfated plant peptides

Root-knot nematodes (Meloidogyne spp.) are highly evolved obligate parasites threatening global food security. These parasites have a remarkable ability to establish elaborate feeding sites in roots, which are their only source of nutrients throughout their life cycle. A wide range of nematode effectors have been implicated in modulation of host pathways for defense suppression and/or feeding site development. Plants produce a diverse array of peptide hormones including PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY)-family peptides, which promote root growth via cell expansion and proliferation. A sulfated PSY-like peptide RaxX (required for activation of XA21 mediated immunity X) produced by the biotrophic bacterial pathogen (Xanthomonas oryzae pv. oryzae) has been previously shown to contribute to bacterial virulence. Here, we report the identification of genes from root-knot nematodes predicted to encode PSY-like peptides (MigPSYs) with high sequence similarity to both bacterial RaxX and plant PSYs. Synthetic sulfated peptides corresponding to predicted MigPSYs stimulate root growth in Arabidopsis. MigPSY transcript levels are highest early in the infection cycle. Downregulation of MigPSY gene expression reduces root galling and egg production, suggesting that the MigPSYs serve as nematode virulence factors. Together, these results indicate that nematodes and bacteria exploit similar sulfated peptides to hijack plant developmental signaling pathways to facilitate parasitism.

Selective control of parasitic nematodes using bioactivated nematicides

Parasitic nematodes are a major threat to global food security, particularly as the world amasses 10 billion people amid limited arable land^1-4. Most traditional nematicides have been banned owing to poor nematode selectivity, leaving farmers with inadequate means of pest control^4-12. Here we use the model nematode Caenorhabditis elegans to identify a family of selective imidazothiazole nematicides, called selectivins, that undergo cytochrome-p450-mediated bioactivation in nematodes. At low parts-per-million concentrations, selectivins perform comparably well with commercial nematicides to control root infection by Meloidogyne incognita, a highly destructive plant-parasitic nematode. Tests against numerous phylogenetically diverse non-target systems demonstrate that selectivins are more nematode-selective than most marketed nematicides. Selectivins are first-in-class bioactivated nematode controls that provide efficacy and nematode selectivity.

Advances in omics research on peanut response to biotic stresses

Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.

Chromosome-scale genome assembly-assisted identification of Mi-9 gene in Solanum arcanum accession LA2157, conferring heat-stable resistance to Meloidogyne incognita

Root-knot nematodes (RKNs) are infamous plant pathogens in tomato production, causing considerable losses in agriculture worldwide. Mi-1 is the only commercially available RKN-resistance gene; however, the resistance is inactivated when the soil temperature is over 28 °C. Mi-9 in wild tomato (Solanum arcanum LA2157) has stable resistance to RKNs under high temperature but has not been cloned and applied. In this study, a chromosome-scale genome assembly of S. arcanum LA2157 was constructed through Nanopore and Hi-C sequencing. Based on molecular markers of Mi-9 and comparative genomic analysis, the localization region and candidate Mi-9 genes cluster consisting of seven nucleotide-binding sites and leucine-rich repeat (NBS-LRR) genes were located. Transcriptional expression profiles confirmed that five of the seven candidate genes were expressed in root tissue. Moreover, virus-induced gene silencing of the Sarc_034200 gene resulted in increased susceptibility of S. arcanum LA2157 to Meloidogyne incognita, and genetic transformation of the Sarc_034200 gene in susceptible Solanum pimpinellifolium conferred significant resistance to M. incognita at 25 °C and 30 °C and showed hypersensitive responses at nematode infection sites. This suggested that Sarc_034200 is the Mi-9 gene. In summary, we cloned, confirmed and applied the heat-stable RKN-resistance gene Mi-9, which is of great significance to tomato breeding for nematode resistance.

A cytological revisit on parthenogenetic Artemia and the deficiency of a meiosis-specific recombinase DMC1 in the possible transition from bisexuality to parthenogenesis

Although parthenogenesis is widespread in nature and known to have close relationships with bisexuality, the transitional mechanism is poorly understood. Artemia is an ideal model to address this issue because bisexuality and "contagious" obligate parthenogenesis independently exist in its congeneric members. In the present study, we first performed chromosome spreading and immunofluorescence to compare meiotic processes of Artemia adopting two distinct reproductive ways. The results showed that, unlike conventional meiosis in bisexual Artemia, meiosis II in parthenogenic Artemia is entirely absent and anaphase I is followed by a single mitosis-like equational division. Interspecific comparative transcriptomics showed that two central molecules in homologous recombination (HR), Dmc1 and Rad51, exhibited significantly higher expression in bisexual versus parthenogenetic Artemia. qRT-PCR indicated that the expression of both genes peaked at the early oogenesis and gradually decreased afterward. Knocking-down by RNAi of Dmc1 in unfertilized females of bisexual Artemia resulted in a severe deficiency of homologous chromosome pairing and produced univalents at the middle oogenesis stage, which was similar to that of parthenogenic Artemia, while in contrast, silencing Rad51 led to no significant chromosome morphological change. Our results indicated that Dmc1 is vital for HR in bisexual Artemia, and the deficiency of Dmc1 may be correlated with or even possibly one of core factors in the transition from bisexuality to parthenogenesis.

Nematicidal lipopeptides from Bacillus paralicheniformis and Bacillus subtilis: A comparative study

The aim of this work was to develop a comparative study between Bacillus paralicheniformis TB197 and B. subtilis ATCC 21332 strains in terms of growth, cyclic lipopeptide production, nematicidal activity, and active lipopeptide characteristics. Crude lipopeptide extracts (CLEs) from their fermentation broths were obtained, and their nematicidal activity (NA) was estimated as the mean lethal dose (LD₅₀), employing Caenorhabditis elegans. Using a bioguided approach, CLE components were fractionated by semipreparative thin layer chromatography, and active lipopeptides were characterized by mass spectrometry. Both strains produced similar concentrations of CLEs (p ≥ 0.05) (0.99 ± 0.11 and 1.14 ± 0.15 mg/mL by TB197 and ATCC 21332, respectively). The estimated LD₅₀ values of CLEs from the TB197 and ATCC 21332 strains were 3.88 and 8.15 mg/mL, respectively, showing that the NA of the TB197 strain CLE was 2.1-fold higher (p ≤ 0.05). Mass spectrometry revealed that strain TB197 synthesizes several families of lipopeptides, namely, fengycin A (C₁₄-C₁₇), fengycin B (C₁₆-C₁₇), surfactin (C₁₅-C₁₇), and lichenysin (C₁₂, C₁₃, C₁₄, and C₁₆), from which fengycins and lichenysins possess the highest NA (100 and 60% mortality in C. elegans larvae, respectively), while the ATCC 21332 strain produces mainly surfactin (C₁₃-C₁₇) (NA 63% mortality). The main differences found in this study were that the TB197 strain has a higher tolerance to inhibition by the product, and the lipopeptides they synthesize have a higher nematicidal activity due to the diversity of families compared to ATCC 21332. Likewise, it was shown that more polar lipopeptides (fengycins) are more effective at causing mortality in C. elegans larvae. KEY POINTS: • The nematicidal activity of lipopeptides from TB197 is higher than from ATCC 21332 • TB197 produces surfactin, lichenysin, and fengycin, while ATCC 21332 mainly produces surfactin • The most polar lipopeptides (fengycins) cause more mortality in C. elegans L2.

Two Candidate Meloidogyne javanica Effector Genes, MjShKT and MjPUT3: A Functional Investigation of Their Roles in Regulating Nematode Parasitism

During parasitism, root-knot nematode Meloidogyne spp. inject molecules termed effectors that have multifunctional roles in construction and maintenance of nematode feeding sites. As an outcome of transcriptomic analysis of Meloidogyne javanica, we identified and characterized two differentially expressed genes encoding the predicted proteins MjShKT, carrying a Stichodactyla toxin (ShKT) domain, and MjPUT3, carrying a ground-like domain, both expressed during nematode parasitism of the tomato plant. Fluorescence in-situ hybridization revealed expression of MjShKT and MjPUT3 in the dorsal esophageal glands, suggesting their injection into host cells. MjShKT expression was upregulated during the parasitic life stages, to a maximum at the mature female stage, whereas MjPUT3 expression increased in third- to fourth-stage juveniles. Subcellular in-planta localization of MjShKT and MjPUT3 using a fused fluorescence marker indicated MjShKT co-occurrence with the endoplasmic reticulum, the perinuclear endoplasmatic reticulum, and the Golgi organelle markers, while MjPUT3 localized, to some extent, within the endoplasmatic reticulum and was clearly observed within the nucleoplasm. MjShKT inhibited programmed cell death induced by overexpression of MAPKKKα and Gpa2/RBP-1. Overexpression of MjShKT in tomato hairy roots allowed an increase in nematode reproduction, as indicated by the high number of eggs produced on roots overexpressing MjShKT. Roots overexpressing MjPUT3 were characterized by enhanced root growth, with no effect on nematode development on those roots. Investigation of the two candidate effectors suggested that MjShKT is mainly involved in manipulating the plant effector-triggered immune response toward establishment and maintenance of active feeding sites, whereas MjPUT3 might modulate roots morphology in favor of nematode fitness in the host roots. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Sublethal concentrations of conventional nematicides alter the physiological activities of Meloidogyne incognita and suppress parasitism

Reducing nematicide dose rates could be a useful strategy for mitigating their negative effects on health and the environment. In this study, enzymatic activities and the parasitic ability of Meloidogyne incognita after exposure to sub-lethal concentrations (0.25, 1, 2, and 5 ppm) of ethoprophos, fenamiphos, and oxamyl were investigated. Although the tested concentrations did not show nematicidal properties in vitro, they reduced root galls by at least 30% at 0.25 ppm and up to 67% at 5 ppm in pots, besides disrupting nematode fertility. For all three nematicides at 2 ppm, a chemotaxis assay showed that ≤ 11% of the nematode population was successfully oriented to the host roots, compared to 44% in the control. Ethoprophos and fenamiphos at 5 ppm showed poor inhibitory effects on acetylcholinesterase (AChE) activity (5.6% and 12.5%, respectively). In contrast, the same nematicides were shown to be strong ATPase inhibitors, causing 82.4% and 82.8% inhibition, respectively. At the same concentration, oxamyl moderately inhibited AChE and ATPase-specific activities, the inhibition being 22.5% and 35.2%, respectively. This study suggests that the use of very low nematicide concentrations could be a promising strategy for nematode management. Furthermore, it has also highlighted the role of ATPases as a possible target site for suppressing nematode activity in the development of future nematicides.

Overexpression of the GmEXPA1 gene reduces plant susceptibility to Meloidogyne incognita

The overexpression of the soybean GmEXPA1 gene reduces plant susceptibility to M. incognita by the increase of root lignification. Plant expansins are enzymes that act in a pH-dependent manner in the plant cell wall loosening and are associated with improved tolerance or resistance to abiotic or biotic stresses. Plant-parasitic nematodes (PPN) can alter the expression profile of several expansin genes in infected root cells. Studies have shown that overexpression or downregulation of particular expansin genes can reduce plant susceptibility to PPNs. Root-knot nematodes (RKN) are obligate sedentary endoparasites of the genus Meloidogyne spp. of which M. incognita is one of the most reported species. Herein, using a transcriptome dataset and real-time PCR assays were identified an expansin A gene (GmEXPA1; Glyma.02G109100) that is upregulated in the soybean nematode-resistant genotype PI595099 compared to the susceptible cultivar BRS133 during plant parasitism by M. incognita. To understand the role of the GmEXPA1 gene during the interaction between soybean plant and M. incognita were generated stable A. thaliana and N. tabacum transgenic lines. Remarkably, both A. thaliana and N. tabacum transgenic lines overexpressing the GmEXPA1 gene showed reduced susceptibility to M. incognita. Furthermore, plant growth, biomass accumulation, and seed yield were not affected in these transgenic lines. Interestingly, significant upregulation of the NtACC oxidase and NtEFE26 genes, involved in ethylene biosynthesis, and NtCCR and Nt4CL genes, involved in lignin biosynthesis, was observed in roots of the N. tabacum transgenic lines, which also showed higher lignin content. These data suggested a possible link between GmEXPA1 gene expression and increased lignification of the root cell wall. Therefore, these data support that engineering of the GmEXPA1 gene in soybean offers a powerful biotechnology tool to assist in RKN management.

Phytochemical Analysis and Binding Interaction of Cotton Seed Cake Derived Compounds with Target Protein of Meloidogyne incognita for Nematicidal Evaluation

The root-knot nematode Meloidogyne incognita is one of the most damaging plant-parasitic nematodes and is responsible for significant crop losses worldwide. Rising human health and environmental concerns have led to the withdrawal of commonly used chemical nematicides. There has been a tremendous demand for eco-friendly bio-nematicides with beneficial properties to the nematode hosting plants, which encourages the need for alternative nematode management practices. The current study was undertaken to determine the nematicidal potential of cotton seed cake (CSC) against second-stage juvenile (J2) hatching, J2 mortality, and J2 penetration of M. incognita in tomato plants in vitro. J2s and egg masses of M. incognita were exposed to four concentrations (250, 500, 750, and 1000 mg/L) of CSC extracts. The higher J2 mortality and inhibition of J2 hatching were found at 1000 mg/L, while the least effective result was observed at 250 mg/L of the CSC extract. The CSC extract applied with the concentrations mentioned above also showed inhibition of J2 penetration in tomato roots; 1000 mg/L showed the highest inhibition of penetration, while 250 mg/L displayed the least inhibition. Using gas chromatography-mass spectroscopy, we identified 11 compounds, out of which 9,12-Octadecadienoic acid, Hexadecanoic acid, and Tetradecanoic acid were found as major compounds. Subsequently, in silico molecular docking was conducted to confirm the nematicidal behavior of CSC based on binding interactions of the above three major compounds with the targeted protein acetylcholine esterase (AChE) of M. incognita. The values of binding free energy are -5.3, -4.5, and -4.9 kcal/mol, observed for 9,12-Octadecadienoic acid, n-Hexadecanoic acid, and Tetradecanoic acid, respectively, suggesting that 9,12-Octadecadienoic acid binds with the receptor AChE more efficiently than the other two ligands. This study indicates that CSC has nematicidal potential that can be used to control M. incognita for sustainable agriculture.

Breeding for disease resistance in soybean: a global perspective

KEY MESSAGE

This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.

Is the Arbuscular Mycorrhizal Fungus Funneliformis mosseae a Suitable Agent to Control Criconematid Populations?

Several studies have shown the potential of using mycorrhizal fungi in increasing the plant yield by simultaneously reducing damages caused by pathogens. Plant parasitic nematodes (PPNs) are among the most feared pathogens for crops. This study aimed to evaluate the effects of Funneliformis mosseae as a mycorrhizal fungus on the population abundance of three world widespread species of nematodes from the family Criconematidae: Mesocriconema xenoplax, Mesocriconema antipolitanum, and Criconemides informis. Pure and highly abundant populations of each species were collected from Urmia city in Northwestern Iran, after the identification morphological and morphometric characteristics. The experiments were carried out in greenhouse conditions on three different rhizospheres of alfalfa, sugar beet, and wheat. After five months, the final population of nematodes and fungus, and the root surface on host plants inoculated and non-inoculated with the fungus F. mosseae, were evaluated. The results showed that the population of nematodes was increased in the presence of the fungus. It could be assumed that the extension of the host surface level of roots by the fungus resulted in more feeding sites for nematode activity and, consequently, higher population densities. In this study, the fungus did not seem to play a suitable role in controlling ectoparasitic nematode growth. However, since there are still many open questions about mycorrhizal fungi’s role in agriculture, more research should be conducted.

Pea Breeding for Resistance to Rhizospheric Pathogens

Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.

Virulence and Reproductive Fitness of Meloidogyne paranaensis Field Populations in Coffee Genotypes

The aim of this study was to characterize Meloidogyne paranaensis populations collected from infested coffee crops. Methodologies used to characterize the 11 studied populations from municipalities in Paraná and Minas Gerais States involved the morphological analysis of perineal patterns, biochemical analysis by isozyme electrophoresis, sequencing of internal transcribes spacer 1 (ITS-1) and D2/D3 ribosomal DNA (rDNA) regions, reproductive fitness, and virulence characterization in coffee genotypes. Morphological evaluations showed the existence of variation between populations, although the majority of them showed typical perineal patterns. The biochemical identification was based on α-esterase isozyme analyses and resulted in the appearance of three distinct profiles: P1 (typical), P2 (atypical), and a nondescribed profile, P2b. BLAST of the ITS-1 and D2/D3 rDNA regions indicated homology (>95%) with other sequences deposited in GenBank. For reproductive fitness and virulence characterization, 13 coffee genotypes (5 Coffea arabica and 8 C. canephora) were inoculated with 11 M. paranaensis populations. Variation in the reproductive fitness of populations was observed for cultivar Mundo Novo, a genotype without resistance genes, and variation in the virulence of populations was observed in genotypes carrying resistance genes. Three populations exhibited virulence combined with high reproductive fitness, while one showed virulence with low reproductive fitness. Some hosts were resistant to 11 populations, while one of the hosts was resistant to only one population, indicating the presence of different resistance genes. Nevertheless, no relationship was observed between the origin of population and their variations in perineal patterns, esterase profiles, phylogeny, or reproductive fitness in coffee genotypes, or between the different characterizations, although differences were observed within each characteristic.

Overexpression of a soybean Globin (GmGlb1-1) gene reduces plant susceptibility to Meloidogyne incognita

The overexpression of the GmGlb1-1 gene reduces plant susceptibility to Meloidogyne incognita. Non-symbiotic globin class #1 (Glb1) genes are expressed in different plant organs, have a high affinity for oxygen, and are related to nitric oxide (NO) turnover. Previous studies showed that soybean Glb1 genes are upregulated in soybean plants under flooding conditions. Herein, the GmGlb1-1 gene was identified in soybean as being upregulated in the nematode-resistant genotype PI595099 compared to the nematode-susceptible cultivar BRS133 during plant parasitism by Meloidogyne incognita. The Arabidopsis thaliana and Nicotiana tabacum transgenic lines overexpressing the GmGlb1-1 gene showed reduced susceptibility to M. incognita. Consistently, gall morphology data indicated that pJ2 nematodes that infected the transgenic lines showed developmental alterations and delayed parasitism progress. Although no significant changes in biomass and seed yield were detected, the transgenic lines showed an elongated, etiolation-like growth under well-irrigation, and also developed more axillary roots under flooding conditions. In addition, transgenic lines showed upregulation of some important genes involved in plant defense response to oxidative stress. In agreement, higher hydrogen peroxide accumulation and reduced activity of reactive oxygen species (ROS) detoxification enzymes were also observed in these transgenic lines. Thus, based on our data and previous studies, it was hypothesized that constitutive overexpression of the GmGlb1-1 gene can interfere in the dynamics of ROS production and NO scavenging, enhancing the acquired systemic acclimation to biotic and abiotic stresses, and improving the cellular homeostasis. Therefore, these collective data suggest that ectopic or nematode-induced overexpression, or enhanced expression of the GmGlb1-1 gene using CRISPR/dCas9 offers great potential for application in commercial soybean cultivars aiming to reduce plant susceptibility to M. incognita.

Root-Knot Nematode (Meloidogyne incognita) Control Using a Combination of Lactiplantibacillus plantarum WiKim0090 and Copper Sulfate

Lactic acid bacteria (LAB) exert antagonistic activity against root-knot nematodes, mainly by producing organic acids via carbohydrate fermentation. However, they have not yet been used for root-knot nematode (Meloidogyne incognita) control owing to a lack of economic feasibility and effectiveness. In this study, we aimed to isolate organic acid-producing LAB from kimchi (Korean traditional fermented cabbage) and evaluated their nematicidal activity. Among the 234 strains isolated, those showing the highest nematicidal activity were selected and identified as Lactiplantibacillus plantarum WiKim0090. Nematicidal activity and egg hatch inhibitory activity of WiKim0090 culture filtrate were dose dependent. Nematode mortality 3 days after treatment with 2.5% of the culture filtrate was 100%, with a 50% lethal concentration of 1.41%. In pot tests, the inhibitory activity of an L. plantarum WiKim0090-copper sulfate mixture on gall formation increased. Compared to abamectin application, which is a commercial nematicide, a higher control value was observed using the WiKim0090-copper sulfate mixture, indicating that this combination can be effective in controlling the root-knot nematode.

Rooting Out the Mechanisms of Root-Knot Nematode-Plant Interactions

Root-knot nematodes (RKNs; Meloidogyne spp.) engage in complex parasitic interactions with many different host plants around the world, initiating elaborate feeding sites and disrupting host root architecture. Although RKNs have been the focus of research for many decades, new molecular tools have provided useful insights into the biological mechanisms these pests use to infect and manipulate their hosts. From identifying host defense mechanisms underlying resistance to RKNs to characterizing nematode effectors that alter host cellular functions, the past decade of research has significantly expanded our understanding of RKN-plant interactions, and the increasing number of quality parasite and host genomes promises to enhance future research efforts into RKNs. In this review, we have highlighted recent discoveries, summarized the current understanding within the field, and provided links to new and useful resources for researchers. Our goal is to offer insights and tools to support the study of molecular RKN-plant interactions.

Fumigant Activity of Bacterial Volatile Organic Compounds against the Nematodes Caenorhabditis elegans and Meloidogyne incognita

Plant-parasitic nematodes infect a diversity of crops, resulting in severe economic losses in agriculture. Microbial volatile organic compounds (VOCs) are potential agents to control plant-parasitic nematodes and other pests. In this study, VOCs emitted by a dozen bacterial strains were analyzed using solid-phase microextraction followed by gas chromatography-mass spectrometry. Fumigant toxicity of selected VOCs, including dimethyl disulfide (DMDS), 2-butanone, 2-pentanone, 2-nonanone, 2-undecanone, anisole, 2,5-dimethylfuran, glyoxylic acid, and S-methyl thioacetate (MTA) was then tested against Caenorhabditis elegans. DMDS and MTA exhibited much stronger fumigant toxicity than the others. Probit analysis suggested that the values of LC₅₀ were 8.57 and 1.43 μg/cm³ air for DMDS and MTA, respectively. MTA also showed stronger fumigant toxicity than DMDS against the root-knot nematode Meloidogyne incognita, suggesting the application potential of MTA.

Combined effects of vermicompost and vermicompost leachate on the early growth of Meloidogyne incognita stressed Withania somnifera (L.) Dunal

Roots of Withania somnifera, an important medicinal herb, are prone to the infection of Meloidogyne incognita (a root parasitic nematode). The infection lowers the quality and quantity of plant material and poses a challenge in crop cultivation and obtaining desirable yield. In the present study, in vitro inhibitory activity of vermicompost leachate (Vcom-L) was assessed against % hatch and survival of M. incognita in a 96 h assay. Then, Vcom-L was used as soil supplement in combination with vermicompost (Vcom) to evaluate their nematode inhibitory and stress alleviating effect in W. somnifera, in a pot experiment. Root galling intensity and growth performance of nematode-stressed W. somnifera raised from seeds pre-soaked in distilled water (DW), Vcom-L, vermicompost tea (Vcom-T) and different dilutions of Vcom-L were assessed. We observed 79% suppression of egg hatching and 89% juvenile (J2) mortality after 96 h compared to control, at 100% concentration of Vcom-L. Significant reduction in gall formation with increase in growth parameters of seedlings was observed after combined application of Vcom (60% or 100%) + Vcom-L and was evident as enhancement in seedling biomass and contents of chlorophyll and protein. However, proline, total phenolics and malondialdehyde (MDA) content declined significantly in these combinations compared to the control (0% Vcom). Activity of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidise (APX), guaiacol peroxidise (GPX) and glutathione reductase (GR) declined with Vcom as well as Vcom + Vcom-L and corresponded with decline in the accumulation of reactive oxygen species in leaves. Further, 1:5 and 1:10 dilutions of Vcom-L in combination with Vcom (60%) proved beneficial in mitigating the nematode-induced stress in W. somnifera. Present results showed the potential of Vcom and Vcom-L in standardised combination as an effective strategy in controlling the pathogenicity of M. incognita in medicinal plants such as W. somnifera.

In planta RNAi approach targeting three M. incognita effector genes disturbed the process of infection and reduced plant susceptibility

Meloidogyne incognita is the most economically important species of the root-knot nematode complex causing damage to several crops worldwide. During parasitism in host plants, M. incognita secretes several effector proteins to suppress the plant immune system, manipulate the plant cell cycle, and promote parasitism. Several effector proteins have been identified, but their relationship with plant parasitism by M. incognita has not been fully confirmed. Herein, the Minc01696, Minc00344, and Minc00801 putative effector genes were evaluated to assess their importance during soybean and Nicotiana tabacum parasitism by M. incognita. For this study, we used in planta RNAi technology to overexpress dsRNA molecules capable of producing siRNAs that target and downregulate these nematode effector genes. Soybean composite roots and N. tabacum lines were successfully generated, and susceptibility level to M. incognita was evaluated. Consistently, both transgenic soybean roots and transgenic N. tabacum lines carrying the RNAi strategy showed reduced susceptibility to M. incognita. The number of galls per plant and the number of egg masses per plant were reduced by up to 85% in transgenic soybean roots, supported by the downregulation of effector genes in M. incognita during parasitism. Similarly, the number of galls per plant, the number of egg masses per plant, and the nematode reproduction factor were reduced by up to 83% in transgenic N. tabacum lines, which was also supported by the downregulation of the Minc00801 effector gene during parasitism. Therefore, our data indicate that all three effector genes can be a target in the development of new biotechnological tools based on the RNAi strategy in economically important crops for M. incognita control.

Transcriptional changes of biochemical pathways in Meloidogyne incognita in response to non-fumigant nematicides

Meloidogyne incognita is a destructive and economically important agricultural pest. Similar to other plant-parasitic nematodes, management of M. incognita relies heavily on chemical controls. As old, broad spectrum, and toxic nematicides leave the market, replacements have entered including fluensulfone, fluazaindolizine, and fluopyram that are plant-parasitic nematode specific in target and less toxic to applicators. However, there is limited research into their modes-of-action and other off-target cellular effects caused by these nematicides in plant-parasitic nematodes. This study aimed to broaden the knowledge about these new nematicides by examining the transcriptional changes in M. incognita second-stage juveniles (J2) after 24-h exposure to fluensulfone, fluazaindolizine, and fluopyram as well as oxamyl, an older non-fumigant nematicide. Total RNA was extracted and sequenced using Illumina HiSeq to investigate transcriptional changes in the citric acid cycle, the glyoxylate pathway, [Formula: see text]-fatty acid oxidation pathway, oxidative phosphorylation, and acetylcholine neuron components. Observed transcriptional changes in M. incognita exposed to fluopyram and oxamyl corresponded to their respective modes-of-action. Potential targets for fluensulfone and fluazaindolizine were identified in the [Formula: see text]-fatty acid oxidation pathway and 2-oxoglutarate dehydrogenase of the citric acid cycle, respectively. This study provides a foundation for understanding how potential nematicide resistance could develop, identifies cellular pathways as potential nematicide targets, and determines targets for confirming unknown modes-of-action.

Transcriptional response of Meloidogyne incognita to non-fumigant nematicides

There is limited research about the impacts of new nematicides, including fluazaindolizine, fluopyram, and fluensulfone, on the plant-parasitic nematode Meloidogyne incognita, despite it being a pervasive agricultural pest. In this study, M. incognita second-stage juveniles were exposed for 24-h to fluensulfone, fluazaindolizine, fluopyram, and oxamyl and total RNA was extracted and sequenced using next-generation sequencing to determine gene expression. The effects of nematicide exposure on cellular detoxification pathways, common differentially expressed (DE) genes, and fatty acid and retinol-binding genes were examined. Fluopyram and oxamyl had the smallest impacts on the M. incognita transcriptome with 48 and 151 genes that were DE, respectively. These compounds also elicited a weak response in the cellular detoxification pathway and fatty acid and retinol-binding (FAR) genes. Fluensulfone and fluazaindolizine produced robust transcriptional responses with 1208 and 2611 DE genes, respectively. These compounds had strong impacts on cellular detoxification, causing differential regulation of transcription factors and genes in the detox pathway. These compounds strongly down-regulated FAR genes between 52-85%. Having a greater understanding of how these compounds function at a molecular level will help to promote proper stewardship, aid with nematicide discovery, and help to stay a step ahead of nematicide resistance.

The differential impact of four tropical species of root-knot nematodes (Meloidogyne spp.) on biofortified cassava

Cassava plays an important food security role in Africa. Although a hardy crop in general, average yields are low, while traditional cultivars tend to be low in nutrients and vitamins. Substantial efforts have therefore been made to improve the nutritional quality of cassava through the development of biofortified cultivars. Although root-knot nematodes (RKN) are among the various important constraints affecting production, details on the impact of different species of RKN on cassava productivity are scarce. In this study, six popular cultivars of biofortified cassava were evaluated for their response to M. arenaria, M. enterolobii, M. incognita, M. javanica and a combination of all four species, in pots. All tested cultivars were susceptible to the four Meloidogyne species, but some cultivars showed a tolerance to M. arenaria infection. Galling damage was observed on feeder roots of inoculated plants, with nematode reproduction factors ranging between 2.3 and 9.5. Plant height, stem girth and fresh plant mass were significantly lower for most cultivars by as much as 70% following RKN infection. The highest root galling and damage were observed in plants following inoculation with a combination of the four species. As individual species inoculations, M. incognita and M. javanica were the most damaging, with the least damage observed in plants inoculated with M. arenaria only. These results confirm the pathogenicity of M. arenaria, M. incognita and M. javanica and further illustrate the potential of M. enterolobii to impact cassava production, while combined species infections demonstrate the greater levels of damage that these may cause.

Exploring Machine Learning Algorithms to Unveil Genomic Regions Associated With Resistance to Southern Root-Knot Nematode in Soybeans

Southern root-knot nematode [SRKN, Meloidogyne incognita (Kofold & White) Chitwood] is a plant-parasitic nematode challenging to control due to its short life cycle, a wide range of hosts, and limited management options, of which genetic resistance is the main option to efficiently control the damage caused by SRKN. To date, a major quantitative trait locus (QTL) mapped on chromosome (Chr.) 10 plays an essential role in resistance to SRKN in soybean varieties. The confidence of discovered trait-loci associations by traditional methods is often limited by the assumptions of individual single nucleotide polymorphisms (SNPs) always acting independently as well as the phenotype following a Gaussian distribution. Therefore, the objective of this study was to conduct machine learning (ML)-based genome-wide association studies (GWAS) utilizing Random Forest (RF) and Support Vector Machine (SVM) algorithms to unveil novel regions of the soybean genome associated with resistance to SRKN. A total of 717 breeding lines derived from 330 unique bi-parental populations were genotyped with the Illumina Infinium BARCSoySNP6K BeadChip and phenotyped for SRKN resistance in a greenhouse. A GWAS pipeline involving a supervised feature dimension reduction based on Variable Importance in Projection (VIP) and SNP detection based on classification accuracy was proposed. Minor effect SNPs were detected by the proposed ML-GWAS methodology but not identified using Bayesian-information and linkage-disequilibrium Iteratively Nested Keyway (BLINK), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Enriched Compressed Mixed Linear Model (ECMLM) models. Besides the genomic region on Chr. 10 that can explain most of SRKN resistance variance, additional minor effects SNPs were also identified on Chrs. 10 and 11. The findings in this study demonstrated that overfitting in GWAS may lead to lower prediction accuracy, and the detection of significant SNPs based on classification accuracy limited false-positive associations. The expansion of the basis of the genetic resistance to SRKN can potentially reduce the selection pressure over the major QTL on Chr. 10 and achieve higher levels of resistance.

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

Meloidogyne incognita (Root-knot nematode) and Alternaria alternata (fungus) were among the dominant parasites of the medicinal plant Withania somnifera. Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of W. somnifera (host plant), M. incognita (root-knot nematode) and A. alternata (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of W. somnifera and M. incognita was found to be A-T biased while A. alternata had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of W. somnifera and M. incognita while natural selection was the main force affecting CUB of A. alternata. Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship.

The Biocontrol Functions of Bacillus velezensis Strain Bv-25 Against Meloidogyne incognita

Meloidogyne incognita is obligate parasitic nematode with a wide variety of hosts that causes huge economic losses every year. In an effort to identify novel bacterial biocontrols against M. incognita, the nematicidal activity of Bacillus velezensis strain Bv-25 obtained from cucumber rhizosphere soil was measured. Strain Bv-25 could inhibit the egg hatching of M. incognita and had strong nematicidal activity, with the mortality rate of second-stage M. incognita juveniles (J2s) at 100% within 12 h of exposure to Bv-25 fermentation broth. The M. incognita genes ord-1, mpk-1, and flp-18 were suppressed by Bv-25 fumigation treatment after 48 h. Strain Bv-25 could colonize cucumber roots, with 5.94 × 107 colony-forming units/g attached within 24 h, effectively reducing the infection rate with J2s by 98.6%. The bacteria up-regulated the expression levels of cucumber defense response genes pr1, pr3, and lox1 and induced resistance to M. incognita in split-root trials. Potted trials showed that Bv-25 reduced cucumber root knots by 73.8%. The field experiment demonstrated that disease index was reduced by 61.6%, cucumber height increased by 14.4%, and yield increased by 36.5% in Bv-25-treated plants compared with control. To summarize, B. velezensis strain Bv-25 strain has good potential to control root-knot nematodes both when colonizing the plant roots and through its volatile compounds.

Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection

Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

Bioefficacy evaluation of ferrocenyl chalcones against Meloidogyne incognita and Sclerotium rolfsii infestation in tomato

The present study reports, bioefficacy evaluation of effective compounds against Meloidogyne incognita and Sclerotium rolfsii in pot cultured tomato. The identified five most effective compounds, i.e. (2E)-1-(4-Methylphenyl)-3-ferrocenyl-prop-2-en-1-one (6g), (2E)-1-(4-Methoxyphenyl)-3-ferrocenyl-prop-2-en-1-one (6h), (2E)-1-(3-Bromophenyl)-3-ferrocenyl-prop-2-en-1-one (6j), (2E)-1-(2,4-Dichlorophenyl)-3-ferrocenyl-prop-2-en-1-one (6k) and (2E)-1-(3,5-Dichloro-2-hydroxyphenyl)-3-ferrocenyl-prop-2-en-1-one (6p) along with Carbofuran 3G as positive control were tested at 20, 40 and 80 ppm by soil drenching and root dipping methods. The study revealed that all plant growth parameters were positively influenced by these compounds. The presence of an electron releasing group positively influenced the efficacy, and the activity was highest in compounds 6g and 6h at 80 ppm. Based on in vitro results against S. rolfsii, (2E)-1-Ferrocenyl-3-(4-bromophenyl)-prop-2-en-1-one (3b), (2E)-1-Ferrocenyl-3-(2,6-dichlorophenyl)-prop-2-en-1-one (3o) and (2E)-1-(5-Chloro-2-hydroxyphenyl)-3-ferrocenyl-prop-2-en-1-one (6o) along with Tebuconazole 25.9% EC and Hexaconazole 5% SC as positive control were evaluated. The shoot length was found to be highest (24.50 cm) in plants treated with 3b followed by 3o and 6o at 1000 ppm. The percent disease incidence was significantly decreased as compared to control. The percent disease incidence was found to be minimum in plants treated with 3b at 1000 ppm. However, root dipping was not as effective as soil drenching. Therefore, ferrocenyl chalcone derivatives proved to be of great fungicidal and nematicidal potential opening new opportunities for expanding their effectiveness as new pest control agents.

Classification Methods and Identification of Reniform Nematode Resistance in Known Soybean Cyst Nematode-Resistant Soybean Genotypes

Plant parasitic nematodes are a major yield-limiting factor of soybean in the United States and Canada. It has been indicated that soybean cyst nematode (SCN; Heterodera glycines Ichinohe) and reniform nematode (RN; Rotylenchulus reniformis Linford and Oliveira) resistance could be genetically related. For many years, fragmentary data have shown this relationship. This report evaluates RN reproduction on 418 plant introductions (PIs) selected from the U.S. Department of Agriculture Soybean Germplasm Collection with reported SCN resistance. The germplasm was divided into two tests of 214 PIs reported as resistant and 204 PIs reported as moderately resistant to SCN. The defining and reporting of RN resistance changed several times in the last 30 years, causing inconsistencies in RN resistance classification among multiple experiments. Comparison of four RN resistance classification methods was performed: (i) ≤10% as compared with the susceptible check, (ii) using normalized reproduction index (RI) values, and using (iii) transformed data log10(x), and (iv) transformed data log10(x + 1) in an optimal univariate k-means clustering analysis. The method of transformed data log10(x) was selected as the most accurate for classification of RN resistance. Among 418 PIs with reported SCN resistance, the log10(x) method grouped 59 PIs (15%) as resistant and 130 PIs (31%) as moderately resistant to RN. Genotyping of a subset of the most resistant PIs to both nematode species revealed their strong correlation with rhg1-a allele. This research identified genotypes with resistance to two nematode species and potential new sources of RN resistance that could be valuable to breeders in developing resistant cultivars.