The Use of PTI-Marker Genes to Identify Novel Compounds that Establish Induced Resistance in Rice

Molecular analysis of broad-spectrum induced resistance in rice by the green leaf volatile Z-3-hexenyl acetate

Green leaf volatiles (GLVs), volatile organic compounds released by plants upon tissue damage, are key signaling molecules in plant immunity. The ability of exogenous GLV application to trigger an induced resistance (IR) phenotype against arthropod pests has been widely reported, but its effectiveness against plant pathogens is less well understood. In this study, we combined mRNA sequencing-based transcriptomics and phytohormone measurements with multispectral imaging-based precision phenotyping to gain insights into the molecular basis of Z-3-hexenyl acetate-induced resistance (Z-3-HAC-IR) in rice. Furthermore, we evaluated the efficacy of Z-3-HAC-IR against a panel of economically significant rice pathogens: Pyricularia oryzae, Rhizoctonia solani, Xanthomonas oryzae pv. oryzae, Cochliobolus miyabeanus, and Meloidogyne graminicola. Our data revealed rapid induction of jasmonate metabolism and systemic induction of plant immune responses upon Z-3-HAC exposure, as well as a transient allocation cost due to accelerated chlorophyll degradation and nutrient remobilization. Z-3-HAC-IR proved effective against all tested pathogens except for C. miyabeanus, including against the (hemi)biotrophs M. graminicola, X. oryzae pv. oryzae, and P. oryzae. The Z-3-HAC-IR phenotype was lost in the jasmonate (JA)-deficient hebiba mutant, which confirms the causal role of JA in Z-3-HAC-IR. Together, our results show that GLV exposure in rice induces broad-spectrum, JA-mediated disease resistance with limited allocation costs, and may thus be a promising alternative crop protection approach.

Acetyl-Proteomic Profiling of Sorghum bicolor Seedlings after Chitin Treatment Reveals the Involvement of Acetylated Chlorophyll a/b Binding Proteins in the Innate Immune Response

Plant pathogen-associated molecular pattern-triggered immunity (PTI) is affected by post-translational modifications, but the role of acetylation in the PTI responses of Sorghum bicolor remains unclear. In this study, a comprehensive acetyl-proteomic analysis was performed on sorghum seedlings treated with chitin based on label-free protein quantification. Chitin rapidly induced 15 PTI-related genes and 5 defense enzymes. Acetylation was upregulated in sorghum after the chitin treatment, and 579, 895, and 929 acetylated proteins, peptides, and sites, respectively, were identified using high-performance liquid chromatography-tandem mass spectrometry. Acetylation and expression of chlorophyll a/b binding proteins (Lhcs) were significantly upregulated, and they were localized in chloroplasts. Additionally, we found that the expression of Lhcs in vivo enhanced chitin-mediated acetylation. The findings of this study provide a comprehensive assessment of the lysine acetylome in sorghum and a foundation for future study into the regulatory mechanisms of acetylation during chlorophyll synthesis.

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.

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.

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.

Recognition and Response in Plant-Nematode Interactions

Plant-parasitic nematodes spend much of their lives inside or in contact with host tissue, and molecular interactions constantly occur and shape the outcome of parasitism. Eggs of these parasites generally hatch in the soil, and the juveniles must locate and infect an appropriate host before their stored energy is exhausted. Components of host exudate are evaluated by the nematode and direct its migration to its infection site. Host plants recognize approaching nematodes before physical contact through molecules released by the nematodes and launch a defense response. In turn, nematodes deploy numerous mechanisms to counteract plant defenses. This review focuses on these early stages of the interaction between plants and nematodes. We discuss how nematodes perceive and find suitable hosts, how plants perceive and mount a defense response against the approaching parasites, and how nematodes fight back against host defenses.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.

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.

MeWRKY IIas, Subfamily Genes of WRKY Transcription Factors From Cassava, Play an Important Role in Disease Resistance

Cassava (Manihot esculenta Crantz) is an important tropical crop for food, fodder, and energy. Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) occurs in all cassava growing regions and threatens global cassava production. WRKY transcription factor family plays the essential roles during plant growth, development, and abiotic or biotic stress. Particularly, previous studies have revealed the important role of the group IIa WRKY genes in plant disease resistance. However, a comprehensive analysis of group IIa subfamily in cassava is still missing. Here, we identified 102 WRKY members, which were classified into three groups, I, II, and III. Transient expression showed that six MeWRKY IIas were localized in the nucleus. MeWRKY IIas transcripts accumulated significantly in response to SA, JA, and Xam. Overexpression of MeWRKY27 and MeWRKY33 in Arabidopsis enhanced its resistance to Pst DC3000. In contrast, silencing of MeWRKY27 and MeWRKY33 in cassava enhanced its susceptibility to Xam. Co-expression network analysis showed that different downstream genes are regulated by different MeWRKY IIa members. The functional analysis of downstream genes will provide clues for clarifying molecular mechanism of cassava disease resistance. Collectively, our results suggest that MeWRKY IIas are regulated by SA, JA signaling, and coordinate response to Xam infection.

The Aquaporin TaPIP2;10 Confers Resistance to Two Fungal Diseases in Wheat

Plants employ aquaporins (AQPs) of the plasma membrane intrinsic protein (PIP) family to import environmental substrates, thereby affecting various processes, such as the cellular responses regulated by the signaling molecule hydrogen peroxide (H₂O₂). Common wheat (Triticum aestivum) contains 24 candidate members of the PIP family, designated as TaPIP1;1 to TaPIP1;12 and TaPIP2;1 to TaPIP2;12. None of these TaPIP candidates have been characterized for substrate selectivity or defense responses in their source plant. Here, we report that T. aestivum AQP TaPIP2;10 facilitates the cellular uptake of H₂O₂ to confer resistance against powdery mildew and Fusarium head blight, two devastating fungal diseases in wheat throughout the world. In wheat, the apoplastic H₂O₂ signal is induced by fungal attack, while TaPIP2;10 is stimulated to translocate this H₂O₂ into the cytoplasm, where it activates defense responses to restrict further attack. TaPIP2;10-mediated transport of H₂O₂ is essential for pathogen-associated molecular pattern-triggered plant immunity (PTI). Typical PTI responses are induced by the fungal infection and intensified by overexpression of the TaPIP2;10 gene. TaPIP2;10 overexpression causes a 70% enhancement in wheat resistance to powdery mildew and an 86% enhancement in resistance to Fusarium head blight. By reducing the disease severities, TaPIP2;10 overexpression brings about >37% increase in wheat grain yield. These results verify the feasibility of using an immunity-relevant AQP to concomitantly improve crop productivity and immunity.

The phenylpropanoid pathway inhibitor piperonylic acid induces broad-spectrum pest and disease resistance in plants

Although many phenylpropanoid pathway-derived molecules act as physical and chemical barriers to pests and pathogens, comparatively little is known about their role in regulating plant immunity. To explore this research field, we transiently perturbed the phenylpropanoid pathway through application of the CINNAMIC ACID-4-HYDROXYLASE (C4H) inhibitor piperonylic acid (PA). Using bioassays involving diverse pests and pathogens, we show that transient C4H inhibition triggers systemic, broad-spectrum resistance in higher plants without affecting growth. PA treatment enhances tomato (Solanum lycopersicum) resistance in field and laboratory conditions, thereby illustrating the potential of phenylpropanoid pathway perturbation in crop protection. At the molecular level, transcriptome and metabolome analyses reveal that transient C4H inhibition in tomato reprograms phenylpropanoid and flavonoid metabolism, systemically induces immune signalling and pathogenesis-related genes, and locally affects reactive oxygen species metabolism. Furthermore, C4H inhibition primes cell wall modification and phenolic compound accumulation in response to root-knot nematode infection. Although PA treatment induces local accumulation of the phytohormone salicylic acid, the PA resistance phenotype is preserved in tomato plants expressing the salicylic acid-degrading NahG construct. Together, our results demonstrate that transient phenylpropanoid pathway perturbation is a conserved inducer of plant resistance and thus highlight the crucial regulatory role of this pathway in plant immunity.

Biotechnological advances with applicability in potatoes for resistance against root-knot nematodes

Potato production is negatively affected by root-knot nematodes (Meloidogyne spp.). There are no commercially available potato cultivars that are resistant to root-knot nematodes. To reduce the reliance on chemical controls, genetic engineering for nematode resistance in potato shows promise. Genetically modified potatoes that silence a parasitism gene or that express toxic protease inhibitors display reduced nematode infections. Modifying potato immune responses may also offer new opportunities for nematode resistance in potato. Plant defense elicitors, including those secreted by modified bacteria, enhanced resistance against root-knot nematodes in potato. The use of transgenic bacteria as delivery vehicles of defense-related molecules presents several possibilities for sophisticated nematode management and because this does not involve transgenic plants, it may garner greater public acceptance.

The Induced Resistance Lexicon: Do's and Don'ts

To be protected from biological threats, plants have evolved an immune system comprising constitutive and inducible defenses. For example, upon perception of certain stimuli, plants can develop a conditioned state of enhanced defensive capacity against upcoming pathogens and pests, resulting in a phenotype called 'induced resistance' (IR). To tackle the confusing lexicon currently used in the IR field, we propose a widely applicable code of practice concerning the terminology and description of IR phenotypes using two main phenotypical aspects: local versus systemic resistance, and direct versus primed defense responses. Our general framework aims to improve uniformity and consistency in future scientific communication, which should help to avoid further misinterpretations and facilitate the accessibility and impact of this research field.

Altering the Sex Pheromone Cyclo(l-Pro-l-Pro) of the Diatom Seminavis robusta towards a Chemical Probe

As a major group of algae, diatoms are responsible for a substantial part of the primary production on the planet. Pennate diatoms have a predominantly benthic lifestyle and are the most species-rich diatom group, with members of the raphid clades being motile and generally having heterothallic sexual reproduction. It was recently shown that the model species Seminavis robusta uses multiple sexual cues during mating, including cyclo(l-Pro-l-Pro) as an attraction pheromone. Elaboration of the pheromone-detection system is a key aspect in elucidating pennate diatom life-cycle regulation that could yield novel fundamental insights into diatom speciation. This study reports the synthesis and bio-evaluation of seven novel pheromone analogs containing small structural alterations to the cyclo(l-Pro-l-Pro) pheromone. Toxicity, attraction, and interference assays were applied to assess their potential activity as a pheromone. Most of our analogs show a moderate-to-good bioactivity and low-to-no phytotoxicity. The pheromone activity of azide- and diazirine-containing analogs was unaffected and induced a similar mating behavior as the natural pheromone. These results demonstrate that the introduction of confined structural modifications can be used to develop a chemical probe based on the diazirine- and/or azide-containing analogs to study the pheromone-detection system of S. robusta.

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat

AIM

To establish a gene co-expression network for identifying principal modules and hub genes that are associated with drought resistance mechanisms, analyzing their mechanisms, and exploring candidate genes.

METHODS AND FINDINGS

42 data sets including PRJNA380841 and PRJNA369686 were used to construct the co-expression network through weighted gene co-expression network analysis (WGCNA). A total of 1,896,897,901 (284.30 Gb) clean reads and 35,021 differentially expressed genes (DEGs) were obtained from 42 samples. Functional enrichment analysis indicated that photosynthesis, DNA replication, glycolysis/gluconeogenesis, starch and sucrose metabolism, arginine and proline metabolism, and cell cycle were significantly influenced by drought stress. Furthermore, the DEGs with similar expression patterns, detected by K-means clustering, were grouped into 29 clusters. Genes involved in the modules, such as dark turquoise, yellow, and brown, were found to be appreciably linked with drought resistance. Twelve central, greatly correlated genes in stage-specific modules were subsequently confirmed and validated at the transcription levels, including TraesCS7D01G417600.1 (PP2C), TraesCS5B01G565300.1 (ERF), TraesCS4A01G068200.1 (HSP), TraesCS2D01G033200.1 (HSP90), TraesCS6B01G425300.1 (RBD), TraesCS7A01G499200.1 (P450), TraesCS4A01G118400.1 (MYB), TraesCS2B01G415500.1 (STK), TraesCS1A01G129300.1 (MYB), TraesCS2D01G326900.1 (ALDH), TraesCS3D01G227400.1 (WRKY), and TraesCS3B01G144800.1 (GT).

CONCLUSIONS

Analyzing the response of wheat to drought stress during different growth stages, we have detected three modules and 12 hub genes that are associated with drought resistance mechanisms, and five of those genes are newly identified for drought resistance. The references provided by these modules will promote the understanding of the drought-resistance mechanism. In addition, the candidate genes can be used as a basis of transgenic or molecular marker-assisted selection for improving the drought resistance and increasing the yields of wheat.

Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants

A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants.