Molecular and hormonal regulation of plant responses to waterlogging stress: From fundamental mechanisms to potential strategies of crop tolerance engineering

Waterlogging is a major environmental constraint that severely restricts plant growth by causing oxygen deprivation and metabolic disruption in root zones. In response, plants activate sophisticated physiological and molecular mechanisms mediated by phytohormones under hypoxia. Although key hormones, including ethylene (ET), auxin (IAA), gibberellin (GA), abscisic acid (ABA), cytokinin (CK), jasmonic acid (JA), salicylic acid (SA), and brassinosteroid (BR), are known to play central roles in regulating waterlogging adaptation, a holistic understanding of how their intricate crosstalk orchestrates adaptive decisions remains fragmented. In this review, we synthesize recent advances to construct an integrated framework that spans initial oxygen sensing and hormone-driven morphological adaptations to critical metabolic and physiological adjustments under waterlogging. Particularly, we introduce the novel concept 'stress-metabolic integration and hormonal allocation' under waterlogging/hypoxia, which explains how redox, carbon, and hormones are quantitatively integrated to determine cell fate. We also highlight how synergistic and antagonistic interactions among major hormones fine-tune the balance between survival strategies and growth repression. Furthermore, we integrate hormonal treatments with practical and effective agronomic strategies to enhance crop waterlogging tolerance under field conditions. Beyond synthesis, we identify critical knowledge gaps and propose transformative research directions, offering a blueprint for the rational design of 'climate-resilient crops' through targeted manipulation of molecular and hormonal networks in practical agriculture.