Assessment of DNA methylation pattern under drought stress using methylation-sensitive randomly amplified polymorphism analysis in rice

Abstract

DNA methylation is known to regulate gene expression when plants are exposed to abiotic stress such as drought. Therefore, insight into DNA methylation pattern would be useful for a better understanding of the expression profile of genes associated with drought adaptation. In the present study, we attempted to analyse the DNA methylation pattern at the whole-genome level and the expression of a few drought-responsive genes in rice under different regimes of soil water status, i.e. puddled, 100 and 60% field capacities (FC). The methylation-sensitive randomly amplified polymorphic DNA analysis was employed to identify DNA methylation pattern. We observed an increase in DNA methylation at 60% FC, and reduced methylation under 100% FC compared to puddled condition. The genes such as protein phosphatases (PP2C) and phenylalanine ammonia-lyase (PAL) having CpG islands in their promoter region had lower expression level under 100 and 60% FC compared to puddled conditions. Heat shock protein 70 (HSP70) and RNA helicase 25 (RH25), with no CpG islands in their promoter region, exhibited enhanced expression compared to puddled plants. In rice, increased DNA methylation seems to be an important mechanism associated with drought responses, which probably regulates the methylation-sensitive gene expression. The drought-induced changes in DNA methylation would contribute for epigenetic mechanism. The study provided evidence to argue that drought-induced increased methylation might be one of the major mechanisms associated with acclimation responses in field crops like rice.

The promoters of OsGLP genes exhibited differentially methylated sites under drought and salt stress in rice cultivars

“…A study on whole genome methylome showed that promoter methylation seemed to be associated with tissue speci c gene expression in plants (Surdonja et al 2017). Moreover, in accordance with our study, drought stress has been documented to induce cultivar and site speci c alteration in methylation status of DNA in two contrasting rice varieties with an increased differential methylation in promoters of abiotic stress responsive genes including drought stress (Sapna et al 2020; W. S. Wang et al 2011;Zheng et al 2013). In view of previous reports as well as current study it can be suggested that differentially methylated sites in the promoter regions of OsGLP genes may play a role in modulating their cultivar and tissue speci c expression in response to drought stress.…”

“…DNA methylation, methylation of cytosine nucleotides to 5-methylcytosine, is one of the most important epigenetic marks in genomes of eukaryotes that plays signi cant role in governing chromatin structure, replication and gene regulation (Sapna et al 2020). In plants, cytosine methylation occurs at three different types of sequence contexts: CGN, CHG and CHH (where N = A, C, T or G and H = A, C, T).…”

Genome-wide identification of MBD gene family members in Eleutherococcus senticosus with their expression motifs under drought stress and DNA demethylation

“…Plants also respond to drought stress by reducing water loss and enhancing water absorption capacity [ 36 ]. It has been suggested that drought induced increases in DNA methylation may be one of the main mechanisms by which plants respond to drought stress [ 37 ]. In maize, the MBD genes of Zea mays L. showed a similar expression motif under drought stress [ 38 ].…”

Stress memory responses and seed priming correlate with drought tolerance in plants: an overview

“…When on the other hand differential DNA methylation patterns were analyzed in rice plants using drought susceptible lines, drought tolerant lines, and their F1 hybrids DNA methylation was correlated with drought tolerance, and hypo-methylation of DNA was an indicator of drought tolerance (Joel 2013 ). DNA methylation patterns identified by DNA analysis provide evidence for drought-induced DNA methylation associated with acclimation responses in rice (Sapna et al 2020 ). Genome-wide bisulphite sequencing of rice plants uncovered that dynamic and distinct patterns of differentially methylated DNA regions are related to drought stress memory.…”