Integrative transcriptomic and epigenomic analyses reveal GhERF114 as a negative regulator of drought and salt stress tolerance in cotton

Abiotic stresses such as salt and drought severely impair cotton ( Gossypium hirsutum ) productivity by disrupting photosynthesis, growth, and fiber development. Although transcription factors (TFs) are key regulators in the process of abiotic stress adaptation, their specific roles in cotton remain not fully elucidated. Here, we integrated transcriptomic and CUT&Tag analyses to identify GhERF114 , an AP2/ERF family transcription factor, as a key negative regulator of drought and salt tolerance. GhERF114 is highly expressed in roots and rapidly induced by salt stress. The functional validation results in cotton using virus-induced gene silencing (VIGS) technology demonstrated that GhERF114 -silenced plants exhibited enhanced stress resistance, maintaining higher chlorophyll content, relative leaf water content (RLWC), and antioxidant enzyme activity, while accumulating less malondialdehyde and reactive oxygen species (ROS). In contrast, overexpressing GhERF114 in Arabidopsis leads to its hypersensitivity to salt and drought, accompanied by severe wilting, elevated ROS, and weakened antioxidant defenses. Comprehensive metabolomic profiling further revealed that GhERF114 overexpression disrupted lipid and carbohydrate metabolism under salt stress, reducing metabolites involved in galactose, fructose, and mannose pathways. This metabolic imbalance likely compromises osmotic adjustment and energy homeostasis, aligning with the reduced stress tolerance phenotype. Collectively, these findings demonstrate that GhERF114 impairs abiotic stress resilience by suppressing ROS scavenging capacity and perturbing key metabolic and hormonal signaling pathways. This study identifies GhERF114 as a negative regulator of tolerance to salt stress and drought stress, and provides a potential molecular target for enhancing cotton stress resilience through breeding. • An integrated multi-omics analysis revealed that salt stress induces genome-wide alterations. • Discovery of GhERF114 as a key gene involved in salt and drought tolerance. • Arabidopsis plants overexpressing GhERF114 provide robust genetic evidence for its negative regulatory role.