Drought induces DNA methylation balance‐related genes in a stage-dependent manner during tomato fruit ripening

DNA methylation balance plays an important regulatory role in drought response and tolerance and also in the control of tomato fruit ripening, and its study may help to understand how fleshy fruits respond to drought. This work aimed to investigate how drought affects the expression profile of genes related to DNA methylation balance during tomato fruit ripening. Micro-Tom tomato plants were subjected to irrigated control (C) and two water deficit intensities (T1 and T2) treatments and analyzed for leaf gas exchange rates, leaf water potential (Ψ_w) and expression of genes encoding DNA methylases/demethylases during the mature green (MG), breaker (BR) and red ripe (RR) stages of fruit ripening. Water deficit promoted a significant reduction in the values of Ψ_w, photosynthetic rate (A), transpiration (E), stomatal conductance (gs), regardless of its applied intensity. In silico analysis of RNA-Seq data showed that CHROMOMETHYLASE 2 (SlCMT2) and DEMETER-LIKE 2 (SlDML2) were those, among all tomato DNA methylases/demethylases genes, that showed dramatic and opposite changes in expression during fruit ripening. Water deficit positively regulated the expression of SlCMT2 in the MG stage and SlDML2 in BR, with no significant variations in expression for these genes in the other stages of fruit ripening. These results show that genes related to DNA methylation balance have their expression further increased by water deficit in the fruit ripening stages in which they act, suggesting that drought enhances, but does not disrupt, the intrinsically programmed DNA methylation dynamics necessary for ripening progression.