Stress-responsive transcription factor families are key components of the core abiotic stress response in maize

Abstract Abiotic stresses, including drought, salt, heat, cold, flooding, and low nitrogen, are harmful to agriculture and increasing in frequency due to climate change. Plants can experience multiple stresses within a single season, which elicit shared or overlapping responses. We searched for core stress-responsive genes in maize across stressors through meta-analysis of public RNA-seq data. Using nearly 1,900 RNA-seq samples with both set operations and random forest classification, we identified a core set of 744 stress-responsive genes across the six stressors. These are enriched in transcription factors, including the stress-responsive families AP2/ERF-ERF, NAC, bZIP, HSF, and C2C2-CO-like. Co-expression network analysis demonstrated that core transcription factors are co-expressed with stress-specific genes, supporting their role in regulating both generalized and stress-specific responses. This provides a valuable resource for understanding stress tolerance mechanisms and guiding future efforts to enhance maize resilience under climate change.