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Strawberry cultivation is associated with high mineral fertilizer doses and extensive use of chemical plant protection products. Based on previous research, we expected that chitin application to peat substrate would increase the nutrient availability and activate the plant systemic defense response, resulting in higher strawberry yields and fewer disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin treatment resulted in the attraction of plant growth–promoting fungi toward the plant root, such as species from genera Mortierella and Umbelopsis. In addition, by the end of the experiments 87 mg of mineral nitrogen (N) per liter of substrate was mineralized, which can be related to the observed increase in plant shoot biomass. This, however, led to nutrient imbalances in plant shoots and fruit; N concentration in the leaves increased over 30%, exceeding the optimal range, while phosphorous (P) and potassium (K) deficiencies occurred, with concentrations lower than 50% of the optimal range. This may explain the decreased fruit yield and disease resistance of the fruit toward Botrytis cinerea. In contrast, chitin caused a clear defense priming effect in the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in fewer foliar disease symptoms. Chitin causes positive effects on shoot growth and foliar disease resistance, but caution needs to be taken for nutrient imbalances leading to negative influences on root growth, fruit production, and disease susceptibility toward B. cinerea. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

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

Summary 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.

MicroRNAs miR390-5p, miR7694-3p miR1868 and miR1849 were found to be suitable miRNA reference genes for rice, under either infection with the root-knot nematode Meloidogyne graminicola or treatment with BABA. RT-qPCR is a widely used method to investigate the expression levels of genes under certain conditions. A key step, however, to have reliable results is the normalization of expression. For every experimental condition, suitable reference genes must be chosen. These reference genes must not be affected by differences in experimental conditions. MicroRNAs are regulatory RNA molecules, able to direct the expression levels of protein coding genes. In plants, their attributed functions range from roles in development to immunity. In this work, microRNAs (miRNAs) are evaluated for their suitability as reference genes in rice after infection with root-knot nematode Meloidogyne graminicola or after priming with beta-amino butyric acid. The evaluation was based on their amplification efficiency and their stability estimates according to geNorm, NormFinder and BestKeeper. All tested miRNAs, excluding one, were considered acceptable for normalization. Furthermore, miRNAs were validated using miRNA sequencing data. The set of microRNAs miR390-5p and miR7694-3p was found to be the most stable combination under the tested conditions. Another miRNA set consisting of miR7694-3p, miR1868 and miR1849 also shows potential to be used for miRNA expression normalization under experimental conditions beyond the scope of this study. This work is the first report on reference miRNAs in rice for the purpose of plant defence studies.

Background Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues. Results We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data. Conclusions To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies.

Background Sugar beet (Beta vulgaris subsp. vulgaris) is an economically important crop that provides nearly one third of the global sugar production. The beet cyst nematode (BCN), Heterodera schachtii, causes major yield losses in sugar beet and other crops worldwide. The most effective and economic approach to control this nematode is growing tolerant or resistant cultivars. To identify candidate genes involved in susceptibility and resistance, the transcriptome of sugar beet and BCN in compatible and incompatible interactions at two time points was studied using mRNA-seq. Results In the susceptible cultivar, most defense-related genes were induced at 4 dai while suppressed at 10 dai but in the resistant cultivar Nemakill, induction of genes involved in the plant defense response was observed at both time points. In the compatible interaction, alterations in phytohormone-related genes were detected. The effect of exogenous application of Methyl Jasmonate and ET-generator ethephon on susceptible plants was therefore investigated and the results revealed significant reduction in plant susceptibility. Genes putatively involved in the resistance of Nemakill were identified, such as genes involved in phenylpropanoid pathway and genes encoding CYSTM domain-containing proteins, F-box proteins, chitinase, galactono-1,4-lactone dehydrogenase and CASP-like protein. Also, the transcriptome of the BCN was analyzed in infected root samples and several novel potential nematode effector genes were found. Conclusions Our data provides detailed insights into the plant and nematode transcriptional changes occurring during compatible and incompatible interactions between sugar beet and BCN. Many important genes playing potential roles in susceptibility or resistance of sugar beet against BCN, as well as some BCN effectors with a potential role as avr proteins were identified. In addition, our findings indicate the effective role of jasmonate and ethylene in enhancing sugar beet defense response against BCN. This research provides new molecular insights into the plant-nematode interactions that can be used to design novel management strategies against BCN.

Rice (Oryza sativa) is one of the main staple crops worldwide but suffers from important yield losses due to different abiotic and biotic stresses. Analysis of quantitative trait loci (QTL) is a classical genetic method which enables the creation of more resistant cultivars but does not yield information on the genes directly involved or responsible for the desired traits. Lectins are known as proteins with diverse functions in plants. Some of them are abundant proteins in seeds and are considered as storage/defense proteins while other lectins are known as stress-inducible proteins, implicated in stress perception and signal transduction as part of plant innate immunity. We investigated the distribution of lectin sequences in different QTL related to stress tolerance/resistance, morphology, and physiology through mapping of the lectin sequences and QTL regions on the chromosomes and subsequent statistical analysis. Furthermore, the domain structure and evolutionary relationships of the lectins in O. sativa spp. indica and japonica were investigated. Our results revealed that lectin sequences are statistically overrepresented in QTLs for (a)biotic resistance/tolerance as well as in QTLs related to economically important traits such as eating quality and sterility. These findings contribute to the characterization of the QTL sequences and can provide valuable information to the breeders.

For more than three decades, Arabidopsis thaliana served as a model for plant biology research. At present only a few protein families have been studied in detail in Arabidopsis. This study focused on all sequences with lectin motifs in the genome of Arabidopsis. Based on amino acid sequence similarity (BLASTp searches), 217 putative lectin genes were retrieved belonging to 9 out of 12 different lectin families. The domain organization and genomic distribution for each lectin family were analyzed. Domain architecture analysis revealed that most of these lectin gene sequences are linked to other domains, often belonging to protein families with catalytic activity. Many protein domains identified are known to play a role in stress signaling and defense, suggesting a major contribution of the putative lectins in development and plant defense. This genome-wide screen for different lectin motifs will help to unravel the functional characteristics of lectins. In addition, phylogenetic trees and WebLogos were created and showed that most lectin sequences that share the same domain architecture evolved together. Furthermore, the amino acids responsible for carbohydrate binding are largely conserved. Our results provide information about the evolutionary relationships and functional divergence of the lectin motifs in A. thaliana.