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 highly associated with 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. Even though efforts have deciphered part of PDIs mode of action, more information is needed to understand the underlying pathways of their effectiveness. Here, salicylic acid (SA) loaded in chitosan nanoparticles, increased hypomethylation more than 25% on 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, 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 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 Overall design: All sequencing experiments were performed at Biomedical Research Foundation Academy of Athens on an Illumina NovaSeq 6000 sequencing system. Libraries were sequenced with 2 × 150 bp paired end reads at 30× coverage. According to NIH Roadmap Epigenomics Project the use of two biological replicates with a combined total coverage of 30× in sufficient for unbiased genome-wide DNA methylation profiling.