**Background:** Waterlogging is a major abiotic stress that severely limits crop productivity worldwide, with over 17 million km² of agricultural land affected annually and losses exceeding $74 billion USD. Flooding events are increasing due to climate change, impacting 23% of the global population. Waterlogging causes oxygen depletion (hypoxia), leading to energy crises, accumulation of toxic metabolites (ethanol, lactic acid, ROS), stomatal closure, reduced photosynthesis, and increased susceptibility to diseases. Despite advances in understanding plant responses to other stresses, the molecular mechanisms of waterlogging signaling remain poorly understood. This review aims to provide a comprehensive overview of current knowledge on waterlogging stress effects, adaptive responses, signaling mechanisms, and the potential of multiomics and integrative approaches for developing tolerant cultivars.
**Methods:** The authors conducted a narrative review of the literature, synthesizing findings from studies on waterlogging stress in various crops including wheat, maize, rice, barley, soybean, and others. They examined classical breeding approaches (QTL mapping, marker-assisted selection), genetic engineering (overexpression/mutation of genes like *Sub1A*, *VHb*, *ERF* family members), and omics technologies (transcriptomics, proteomics, metabolomics) applied to waterlogging research. The review also discusses emerging tools such as panomics, high-throughput phenotyping, and genome editing (CRISPR/Cas9).
**Key Results:** The review identifies several key adaptive responses to waterlogging: formation of adventitious roots (ARs) and aerenchyma, radial oxygen loss (ROL) barriers, rapid stem elongation (low oxygen escape syndrome), and metabolic reprogramming (activation of glycolysis and fermentation). Hormonal regulation is critical, with ethylene (ET) and auxin promoting AR formation, while abscisic acid (ABA) negatively regulates ARs but promotes stomatal closure. Transcriptomic studies have identified numerous differentially expressed genes (DEGs) under waterlogging, including transcription factors from *ERF*, *NAC*, *MYB*, and *WRKY* families. For example, in maize, *ZmEREB180* (ERF-VII) positively controls AR development and ROS levels. In rice, the *Sub1A* gene confers submergence tolerance. Proteomic analyses in *Brassica napus* revealed proteins related to oxidation-reduction (BnaA09g29780D), ethylene response (BnaA09g07120D), and stress response (BnaC08g02330D). Metabolomic studies in *Medicago truncatula* showed accumulation of sugars, organic acids, alanine, and GABA under waterlogging. QTL mapping has identified loci for traits like leaf chlorosis, adventitious root formation, and survival in multiple crops, but comparison across species is hindered by lack of shared markers. Genetic engineering successes include overexpression of *Vitreoscilla* hemoglobin (*VHb*) in Arabidopsis improving root length and shoot dry weight, and *TaERFVII.1* in wheat enhancing chlorophyll content and grain weight.
**Clinical Implications:** The review emphasizes that while significant progress has been made in understanding waterlogging tolerance, major knowledge gaps remain, particularly in early signal perception (cell wall sensors, ion channels) and the role of the plant microbiome. The authors advocate for integrative multiomics (panomics) combined with high-throughput phenotyping and genome editing to decode the complexity of waterlogging signaling. Such approaches could identify key gene networks and biomarkers for breeding waterlogging-tolerant cultivars, ultimately reducing crop losses and enhancing food security in flood-prone regions. The development of standardized phenotyping protocols and the application of artificial intelligence are highlighted as future directions to accelerate progress.