Salicylic Acid Reprograms Multi‐Omics Regulatory Networks to Enhance Waterlogging Tolerance in Waxy Maize ( Zea mays L. var. Ceratina ) Seedlings

Waxy maize ( Zea mays L. var. ceratina ) is a high‐amylopectin crop particularly vulnerable to waterlogging stress during early development, resulting in severe yield losses. Salicylic acid (SA) is a crucial signalling molecule that modulates plant stress responses, yet its role in waterlogging tolerance remains poorly understood. Here, we integrated physiological, transcriptomic, and metabolomic analyses to elucidate how exogenous SA enhances waterlogging tolerance in waxy maize seedlings. Waterlogging markedly suppressed pigment biosynthesis, PSII photochemical efficiency, and carbon fixation, accompanied by excessive accumulation of reactive oxygen species (ROS) and lipid peroxidation. Exogenous SA significantly alleviated these effects by stabilizing chlorophyll pigments, restoring ΦPSII and qP, and reducing ROS and malondialdehyde levels, thereby sustaining photosynthetic activity and redox homeostasis. Multi‐omics integration revealed 5281 differentially expressed genes (DEGs) and 223 differentially accumulated metabolites (DAMs) responsive to waterlogging and exogenous SA. Correlation network analysis further revealed 22 key DEGs and 20 key DAMs strongly associated with endogenous SA, photosynthetic, redox, and growth‐related traits. Notably, transcription factors from the TCP, MYB‐related, G2‐like, and NAC families were identified as potential key regulators linking SA signalling to adaptive physiological responses. Under normal conditions, SA up‐regulated Psb28 and ATPγ , enhancing PSII assembly and ATP synthesis. Under waterlogging, SA redirected carbon flux through ME , AlaAT , and the pentose phosphate pathway, sustaining NADPH regeneration, energy homeostasis, and stress adaptation. Collectively, our findings demonstrate that exogenous SA enhances waterlogging tolerance in waxy maize by reprogramming transcriptional and metabolic networks to maintain photosynthetic function, carbon flux, and energy–redox balance. This study provides mechanistic insights and reveals potential avenues for improving maize resilience through molecular breeding and agronomic management.