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Rice is the important crop for more than half of the world population. However, drought can have a devastating impact on rice growth and reduce yield drastically. Understanding the response of rice to drought stress is especially important for crop breeding. Previously we found that rice enhanced its tolerance to drought stresses via stress memory mechanisms. Numerous memory genes were identified to play important roles in the process. DNA methylation was reported to mediate tolerance via regulating gene expression and enhances the survival rate of rice encountering drought stress. However, how DNA methylation involved in stress memory is still not clear. In this study, genome-wide bisulphite sequencing at a single base resolution methylome profiling level was performed and analyzed in rice cultivar under recurrent drought stresses and recovery treatments. We found that rice drought stress memory-related differentially methylated regions (DMRs) showed dynamic and distinct patterns. The drought-memory DMRs may regulate Transposable elements and gene expression to cope with short-term repeated drought stresses. Our findings of drought-memory DMRs can explain mechanisms of rice drought stress memory in a new perspective on global methylome details. Using epigenetic markers to breed drought-resistant rice would become a feasible way in the future research.

Plants are sensitive to external environmental conditions and the mechanisms of stress tolerance in plants are complex. As one of the most significant epigenetic phenomena, DNA methylation plays a crucial role in plants’ adaptation to environmental changes. Recent research has improved our understanding of the relationship between DNA methylation and stress tolerance. Here, we review the mechanism of DNA methylation and discuss recent reports of the dynamics of DNA methylation in plants under abiotic stress conditions, including high salt concentration, drought, and extreme temperatures. The DNA methylation plays important functions during the response to stress in plants, but the differential variations of which were exhibiting in different species. The consistent or the specific mechanisms of DNA methylation need further exploration.