Decoding plant responses to waterlogging: from stress signals to molecular mechanisms and their future implications

Climate change and global warming drastically alter ecosystems, intensifying extreme weather events such as heavy rainfall and glacier melting, leading to increased soil flooding and threatening agriculture. Waterlogging, a direct consequence of prolonged soil saturation, severely affects plant growth by causing hypoxia, impaired nutrient uptake, photosynthesis inhibition, energy depletion, and microbiome disturbances, ultimately leading to plant mortality. Despite research progress in mitigating waterlogging stress, the molecular mechanisms underlying plant perception and their subsequent adaptive responses remain largely unclear. Recent advancements in molecular, biochemical, and multi-omics technologies have enabled significant progress in understanding the molecular mechanisms of plant responses to stress conditions. In this review, we highlight the metabolic pathways and key genes that could be targeted to enhance waterlogging tolerance and discuss how advanced techniques can be implemented to understand waterlogging responses and develop resistant cultivars. We review molecular insights into how ethylene and hypoxia signaling pathways trigger waterlogging responses and highlight key factors involved in energy metabolism and phytohormone signaling pathways, along with possible directions for further study.