Long-lasting defence priming by β-aminobutyric acid in tomato is marked by genome-wide changes in DNA methylation

Marco Catoni, Raul Alvarez-Venegas, Dawn Worrall, Geoff Holroyd, Aarón Barraza, Estrella Luna, Jurriaan Ton, Michael R Roberts

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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. Genes overlapping CHH DMRs were enriched for a small number of stress response-related gene ontology terms. In addition, there was significant enrichment of DMRs in the promoters of genes that are differentially expressed in response to infection with B. cinerea. However, the majority of genes that demonstrated priming did not contain DMRs, and nor was the overall distribution of methylated cytosines in primed 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 appears only to target a minority of 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.

Original languageEnglish
Article number836326
Number of pages13
JournalFrontiers in Plant Science
Publication statusPublished - 15 Apr 2022

Bibliographical note

Funding Information:
This work was funded by grants BB/G021791/1 and BB/L008939/1 from the United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) to MR and JT. RA-V acknowledges support from Conacyt CdF-2019/6360. EL was supported by a BBSRC Future Leader Fellowship (BB/P00556X/2). Part of the computational analysis described in this manuscript was performed using the University of Birmingham’s Compute and Storage for Life Sciences (CaStLeS) Service.

Publisher Copyright:
Copyright © 2022 Catoni, Alvarez-Venegas, Worrall, Holroyd, Barraza, Luna, Ton and Roberts.


  • DNA methylation
  • beta-aminobutyric acid
  • biotic stress
  • hypomethylation
  • induced resistance (IR)
  • priming
  • tomato

ASJC Scopus subject areas

  • Plant Science


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