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Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [small RNA-seq]

ABSTRACT: Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. Grafting experiments were done to assess the systemic nature of this signal, which was further characterised by small RNA (sRNA) sequencing of scions. Only BABA-treated seedlings displayed induced resistance (IR). DNA methylation analysis revealed seedling-specific changes, which occurred in the context of lower basal methylation. BABA-IR was found to be transmissible from primed rootstock to grafted unprimed scions. In these scions, we identified a subset of mobile 24 nt sRNAs associated with primed genes to infection in fruit. Our results demonstrate the functional association of a systemic signal with long lasting IR and priming. Through integrated omics approaches we have identified markers of long-lasting priming in tomato fruit which could also serve as targets for durable resistance in other crops.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE273943 | GEO | 2024/11/17

REPOSITORIES: GEO

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Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [RNA-seq]

Project description:Tomato is a major global crop however its production is limited by Botrytis cinerea. Due to the toxicity of post-harvest pesticide application, alternative control methods such as priming are being investigated. Plants were treated with β-aminobutyric (BABA) at two developmental stages and resistance against B. cinerea was tested in fruit tissue and in progenies. DNA methylation and RNA sequencing were conducted to characterise the (epi)genetic changes associated with long-lasting resistance. Grafting experiments were done to assess the systemic nature of this signal, which was further characterised by small RNA (sRNA) sequencing of scions. Only BABA-treated seedlings displayed induced resistance (IR). DNA methylation analysis revealed seedling-specific changes, which occurred in the context of lower basal methylation. BABA-IR was found to be transmissible from primed rootstock to grafted unprimed scions. In these scions, we identified a subset of mobile 24 nt sRNAs associated with primed genes to infection in fruit. Our results demonstrate the functional association of a systemic signal with long lasting IR and priming. Through integrated omics approaches we have identified markers of long-lasting priming in tomato fruit which could also serve as targets for durable resistance in other crops.

2024-11-17 | GSE273944 | GEO

Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato [WGBS]

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BABA-induced pathogen resistance: a multi-omics analysis of the tomato response reveals a hyper-receptive status strongly involving ethylene

Project description:Prior exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with stronger defence responses. b-aminobutyric acid (BABA) is an endogenous stress metabolite that induces resistance protecting various plants towards diverse stresses. In this study, by integrating BABA-induced changes in selected metabolites with transcriptome and proteome data, we generated a global map of the molecular processes operating in BABA-induced resistance (BABA-IR) in tomato. BABA significantly restricts the growth of the pathogens Oidium neolycopersici and Phytophthora parasitica but not Botrytis cinerea. A cluster analysis of the upregulated processes showed that BABA acts mainly as a stress factor in tomato. The main factor distinguishing BABA-IR from other stress conditions was the extensive induction of signalling and perception machinery playing a key role in defence priming. Interestingly, the signalling processes and immune response activated during BABA-IR in tomato differed from those in Arabidopsis with substantial enrichment of genes associated with jasmonic acid and ethylene signalling and no change in Asp levels. Our results revealed key differences between the effect of BABA on tomato and other model plants studied until now. Surprisingly, salicylic acid is not involved in BABA downstream signalization whereas ethylene and jasmonic acid play a crucial role.

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Long-lasting priming by β-amino butyric acid is marked by DNA hypomethylation

Project description:Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed state, whereby responses to future stress encounters are enhanced. Stress priming can be long-lasting and likely involves epigenetic regulation of stress-responsive gene expression. However, the molecular events underlying priming are not well understood. Here, we characterise epigenetic changes in tomato plants primed for pathogen resistance by treatment with β-aminobutyric acid (BABA). We used whole genome bisulphite sequencing to construct tomato methylomes from control plants and plants treated with BABA at the seedling stage, and a parallel transcriptome analysis to identify genes primed for the response to inoculation by the fungal pathogen, Botrytis cinerea. Genomes of plants treated with BABA showed a significant reduction in global cytosine methylation, especially in CHH sequence contexts. Analysis of differentially methylated regions (DMRs) revealed that CHH DMRs were almost exclusively hypomethylated and were enriched in gene promoters and in DNA transposons located in the chromosome arms. Although there was some enrichment of stress response-related gene ontology terms in genes overlapping CHH DMRs, there was no significant enrichment of DMRs amongst a set of 747 primed defence genes, and nor was the pattern of methylation in these genes altered by BABA treatment. Hence, we conclude that whilst BABA treatment of tomato seedlings results in characteristic changes in genome-wide DNA methylation, CHH hypomethylation does not appear to directly target genes showing primed responses to pathogen infection. Instead, methylation may confer priming via in-trans regulation, acting at a distance from defence genes, and/or by targeting a smaller group of regulatory genes controlling stress responses.

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Priming resistance of tomato to Botrytis cinerea infection by root drench treatment with beta-aminobutyric acid.

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Project description:Inbred parental lines of two cultivars (cv Moneyberg and cv Bolstar Granda) of the model crop tomato were primed (induced for resistance) during four different moments in their development, i.e. once in the vegetative phase (time window 1), once in the generative phase at early flowering (time window 2), multiple times in the generative phase during flowering (time window 3), and once during ripening of the first fruit bunch (time window 4). The primers were ß-aminobutyric acid (BABA), 2,6-dichloroisonicotinic acid (INA), methyljasmonate (MeJA), and water as control; they were selected for their ability to induce different plant resistance pathways. After collecting seed batches from these plants we here look at the effect of priming the tomato plants with those different chemicals on the plant genome methylation level.

2023-12-31 | GSE229117 | GEO

ELICITOM

Project description:ELICITOM project aims to decipher the complex regulation of tomato induced resistance to pathogens. Here, we use a classical elicitor of tomato defenses, ie beta-aminobutyric acid (BABA). This unusual amino acid triggers a strong resistance to the oomycete pathogen Phytophthora parasitica as well as to Oidium neolycopersici (powdery mildew) to a lesser extent. No resistance could be observed towards the grey mold (Botrytis cinerea). Transcriptomic data were generated from RNA extracted from tomato leaves (Solanum lycopercum cv "Marmande") sprayed with 10 mM BABA compared to control organs treated with water, 24 h after treatment. Mapping was achieved on Solanum lycopersicum cv Heinz1706 genome (release ITAG2,3).

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Expression data of tomato fruit responses to Botrytis cinerea

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Project description:Tomato fruit ripening is associated with a dramatic increase in susceptibility to the fungal pathogen Botrytis cinerea, the causal agent of gray mold. Mature green fruit, prior to ripening, are largely resistant to B. cinerea, whereas red fruit, at the end of ripening, are susceptible to B. cinerea infection. We used microarrays to detail the gene expression changes that are induced by B. cinerea when tomato fruit at unripe and ripe stages are infected. Experiment Overall Design: Tomato fruit at mature green and red ripe stages were wound inoculated with a water suspension of B. cinerea conidia. Twenty four hours post inoculation fruit pericarp and epicarp tissue around and including the inoculation sites was collected and the total RNA extracted. Total RNA was also collected from healthy and mock inoculated fruit.

2009-06-01 | E-GEOD-14637 | biostudies-arrayexpress

Genome-wide high-throughput small RNA sequence analysis of B. cinerea-infected tomato leaf and fruit

Project description:We profiled small RNAs obtained from B. cinerea-infected tomato leaf and fruit during a time course. Examination of small RNAs from B. cinerea-treated tomato leaf and fruit tissue over a time course.

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