Exogenous melatonin enhances flooding tolerance in maize and is associated with coordinated redox, metabolic, and chloroplast responses

Flooding stress (FS) at the maize seedling stage disrupts energy metabolism and redox homeostasis, impairing photosynthesis and causing cellular damage. This study evaluated whether exogenous melatonin (MT) alleviates FS injury in maize and characterized physiological and molecular responses associated with this protection. Maize seedlings were subjected to a 2 × 2 design (CK, CK-MT, FS, and FS-MT), while transcriptomic, metabolomic, and hormone profiling focused on CK, FS, and FS-MT. FS reduced net photosynthetic rate and stomatal conductance by 61.93% and 77.98%, respectively, increased H2O2 by 194.15%, and decreased leaf area. Relative to FS, MT increased leaf area by 25.46%, net photosynthetic rate by 79.98%, stomatal conductance by 155.58%, Fv/Fm by 3.35%, and relative water content by 10.22%, while decreasing H2O2, NO, and ethanol levels by 23.27%, 12.67%, and 13.86%, respectively. MT restored SOD and CAT activities toward CK levels and further enhanced POD and APX activities. Multi-omics analyses revealed treatment-associated changes in RBOH-associated ROS responses, NADPH-related metabolic pathways, antioxidant-related genes, ZmPIP expression, osmotic and fermentative metabolism, and hormone profiles. These responses were accompanied by improved chloroplast ultrastructure, reduced qualitative TUNEL-positive signals, and an 18.24% increase in projected grain yield relative to FS. Collectively, the key novel finding is that MT-associated improvement under flooding coincided with coordinated redox, osmotic, fermentative, and chloroplast responses across physiological and multi-omics layers. These treatment-associated patterns support an integrated stress-alleviation response but do not establish a causal role for NADPH regeneration or a flooding-specific MT molecular mechanism.