Drought stress induces variation in DNA methylation pattern in a genotype-dependent manner in chickpea

When plants are exposed to harsh environmental conditions, such as extreme temperatures or drought, certain genes are turned on or off. This process can be controlled by a chemical modification to their DNA called methylation. Here, we examined the impact of DNA methylation during drought stress on two chickpea genotypes, ICC 1882 (drought sensitive, DS) and ICC 4958 (drought tolerant, DT) chickpea genotypes via whole-genome bisulfite sequencing. A higher degree of hypomethylation in the DT genotype and more hypermethylation in the DS genotype were observed. A positive correlation was observed between CG methylation with genes and CHH methylation with TEs. Functional annotation of differentially methylated regions associated with differentially expressed genes revealed distinct pathways enriched in DS, such as enrichment of genes involved in root development, telomere maintenance, ion transport, and regulation of gene expression, while pathways like apoptosis, silencing by miRNAs, programmed cell death and carotenoid metabolic processes were enriched in DT genotype. Further, small RNA distribution and non-CWA context methylation density in TEs suggested the role of the RdDM pathway in mediating CHH hypermethylation in transposable elements. Overall, we observed distinct genes are differentially expressed and differentially methylated under drought stress in sensitive and tolerant genotypes.