Meta-analysis of drought and iron excess stress-responsive gene expression profiles in rice

• Integrated transcriptomic analysis reveals shared drought and iron stress responses in rice. • Identified ROS-related genes, transcription factors ( DREB2A, ERF95, ERF102 ), and phytohormone signaling pathways involved in both stresses. • Proposes a multilayered regulatory model involving Target–TF–miRNA interactions. • Findings provide candidate regulatory hubs for molecular breeding of stress-resilient rice varieties. Drought and iron (Fe) toxicity are major abiotic stresses that significantly limit rice productivity. While drought reduces water availability and thereby restricts Fe uptake, waterlogged or rainfed conditions increase soluble Fe levels. Despite these contrasting environments, both stresses trigger oxidative damage caused by reactive oxygen species (ROS). This raises key questions on how plants adjust to such distinct conditions, what responses are shared, and which are stress-specific. To address this, we performed a meta-analysis of transcriptome datasets for drought and Fe excess in the lowland aromatic rice variety Keteki Joha at two developmental stages. Common responses included upregulation of ROS scavenging systems, transcriptional regulation, and hormonal signaling pathways. In contrast, stress-specific responses showed distinct patterns. Under Fe toxicity, unique DEGs were enriched in antioxidant activity, peroxidase function, and ROS metabolism, highlighting the importance of redox defense. In parallel, several genes regulating Fe acquisition and homeostasis, including OsNAS1/2, OsHRZ2 , and IMA1 , were consistently downregulated, indicating a transcriptional shift to suppress further Fe uptake while enhancing compartmentalization and detoxification to maintain internal balance. Under drought, DEGs were mainly involved in RNA metabolism, protein folding, and vesicle-mediated transport, pointing to post-transcriptional and post-translational regulation as adaptive mechanisms. Additionally, 26 microRNAs (miRNAs) were identified as regulators of transcription factors under both stresses, suggesting an integrated miRNA–TF–target gene regulatory network. Together, these findings provide insights into the molecular basis of stress resilience and identify potential gene targets for crop improvement.