Word count: 5338 25 26Highlight: Bisulphite sequencing revealed single base resolution DNA methylation, and 27 cultivar-specific differential methylation patterns and correlation with gene expression that 28 control desiccation and salinity stress response in the rice cultivars. 29 30 2 Abstract 31 DNA methylation is an epigenetic mark that controls gene expression in response to internal and 32 environmental cues. In this study, we sought to understand the role of DNA methylation in 33 response to desiccation and salinity stresses in three rice cultivars (IR64, stress-sensitive; 34Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) via bisulphite sequencing. We 35 identified DNA methylation patterns in different genomic/genic regions and analysed their 36 correlation with gene expression. Methylation in CG context within gene body and methylation 37 in CHH context in distal promoter regions were positively correlated with gene expression. 38However, methylation in other sequence contexts and genic regions was negatively correlated 39 with gene expression. DNA methylation was found to be most dynamic in CHH context under 40 stress condition(s) in the rice cultivars. The expression profiles of genes involved in de-novo 41 methylation were correlated with methylation dynamics. Hypomethylation in Nagina 22 and 42 hypermethylation in Pokkali in response to desiccation and salinity stress, respectively, were 43 correlated with higher expression of abiotic stress response related genes. Our results suggest an 44 important role of DNA methylation in abiotic stress responses in rice in cultivar-specific 45 manner. This study provides useful resource of DNA methylomes that can be integrated with 46 other data to understand abiotic stress response in rice. 47 48 49