Silicon Modulates the Expression of Copper-Responsive Transporters and Non-Coding RNAs in Cucumber Subjected to Copper Stress

Excess copper (Cu) disrupts metal homeostasis and induces oxidative stress in plants. Silicon (Si) is known to mitigate heavy metal toxicity, yet the molecular basis of its protective role under Cu stress remains insufficiently understood. To address this, an exploratory transcriptome-wide screening was performed to identify candidate differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs), and microRNAs responsive to excess Cu and/or Si in cucumber (Cucumis sativus cv. Chinese Long). Genes encoding metal transporters and selected miRNA–target pairs were further analyzed by qRT-PCR. Silicon alone modulated the expression of numerous candidate DEGs, notably enhancing the expression of metal transporter genes. Exposure to excess Cu suppressed genes involved in metal uptake while upregulating those associated with efflux and metal redistribution. Application of Si under Cu stress mitigated these transcriptional alterations. Cu stress repressed miR398 and miR408, concomitantly increasing the expression of their targets: superoxide dismutase (SOD) and plantacyanin (PCY). Furthermore, excess Cu downregulated miR390, resulting in increased expression of its predicted lncRNA target. The addition of Si to Cu-stressed plants further enhanced SOD expression while attenuating the upregulation of PCY and the lncRNA. The results demonstrated that Si modulates both coding and non-coding RNA expression under optimal and Cu-stress conditions, revealing post-transcriptional gene expression regulation as an additional layer of Si’s effect on plants. When integrated with previously reported physiological and biochemical data, these findings advance our understanding of the molecular basis of Si-mediated heavy metal tolerance in plants.