A Genome-Wide DNA Methylation Survey Reveals Salicylic Acid-Induced Distinct Hypomethylation Linked to Defense Responses Against Biotrophic Pathogens

DNA methylation is a conserved regulatory mechanism of gene expression, genome stability, and development, and is highly associated with the effective induction of defense responses for plant priming. In the Green Deal era, the use of plant defense inducers (PDIs), compounds that activate defense and prime plants against imminent pathogen attacks, is a safe and environmentally sustainable approach to support plants against pathogens. Though efforts have succeeded at deciphering part of the mode of action of PDIs, more information is needed to understand the underlying pathways of their effectiveness. Here, salicylic acid (SA), loaded in chitosan nanoparticles, increased hypomethylation by more than 25% for 56 genomic regions that corresponded to defense-related genes, such as pectin lyases, defensins and leucine-rich repeat transmembrane protein kinases against the biotrophic fungal pathogen Podosphaera xanthii. A genomic region of the promoter of SKP1A, which is a core member of the SCF E3 ubiquitin ligase complex, was found to be a differentially methylated region (DMR), with 60% hypomethylation, both after PDI application and pathogen inoculation, possibly indicating a similar activation mechanism. Examination of this DMR revealed the presence of SA-, auxin-, and defense-related cis-elements. Investigation of the proteins associated with the above cis-elements showed significant upregulation in expression after PDI. Moreover, association of the identified DMR with transcriptomics showed enrichment of the SA pathway. Overall, these findings shed light on the epigenetic mechanisms that underlie SA-related defense priming in plants.