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

Abstract DNA methylation at cytosine residues governs the regulation of stress responsive genes in plants to generate response against various environmental abiotic stress conditions. Here, we analyzed the epigenetic consequences of drought and salinity on cytosine methylation dynamics of promoter regions of stress responsive Germin-like protein (GLP) genes in rice (Oryza sativa). The bisulfite sequencing technique was employed to identify differential methylation status at cytosine residues in selected promoter region of three OsGLP genes (OsGLP4-1, OsGLP8-10 and OsGLP8-12) in leaves and roots of two elite Indica rice cultivars (tolerant KS282 and sensitive Super Basmati) under drought and salt stress. Our results identified cultivar, tissue and stress-dependent differentially methylated cytosine residues, however, the extent of methylation was found to be different depending upon CGN, CHG and CHH sequence contexts. Among all three OsGLP genes, promoter region of OsGLP8-12 was observed with most methylated and differentially methylated sites depending upon a particular variety, tissue or stress condition whereas no methylated sites were observed in promoter region of OsGLP4-1 in all samples. Moreover, in promoter regions of OsGLP8-10 and OsGLP8-12, several differentially methylated sites in response to stress treatments were identified either near or within cis-regulatory elements (CREs) involved in gene regulation or abiotic stress response indicating the association between promoter methylation and regulation of OsGLP genes under drought and salinity. This study provides insights to argue that altered methylation status of specific cytosine residues in the promoter regions of OsGLP genes can be a key regulatory mechanism associated with their regulation under abiotic stresses in contrasting rice cultivars.