Genome-Wide Identification and Expression Profiling of the RNA-Directed DNA Methylation Pathway Genes in Cucumis sativus L.

The RNA-directed DNA methylation (RdDM) pathway is a crucial epigenetic mechanism governing plant responses to environmental stress. While the RdDM pathway has been extensively studied in <i>Arabidopsis thaliana</i>, the comprehensive understanding of its components in cucumber (<i>Cucumis sativus</i> L.) remains lacking. In this study, we performed a genome-wide identification and characterization of RdDM pathway genes in cucumber, followed by an analysis of their expression patterns across various tissues and under multiple abiotic stress conditions. A total of 67 putative <i>CsRdDM</i> genes were identified, which are unevenly distributed across the cucumber's chromosomes. Phylogenetic and gene structure analyses revealed considerable evolutionary divergence, particularly within the key Argonaute gene family (<i>CsAGO</i>). Crucially, the promoter regions of <i>CsRdDM</i> genes were found to contain cis-regulatory elements associated with abiotic stress, light signaling, and development, suggesting their potential involvement in complex regulatory networks. RT-qPCR assays confirmed that <i>CsRdDM</i> genes exhibit distinct and stress-specific transcriptional patterns. Notably, several genes such as <i>CsAGO4</i> and <i>CsIDN2</i> showed antagonistic expression between roots and leaves under drought (PEG-6000) stress, implying a sophisticated, tissue-specific defense mechanism. Among them, <i>CsAGO4</i> emerged as a candidate gene responsive to abiotic stress. Those findings provide new insights into the regulatory roles of <i>CsRdDM</i> genes under abiotic stress and highlight candidate genes for the genetic improvement of stress tolerance in cucumber.