An integrated analysis of transcriptome and metabolome reveals aerenchyma-mediated antioxidant defense and energy metabolism conferring high waterlogging tolerance in sea barley

• Waterlogging hinders the growth of barley, while sea barley was little influenced by such stress. • Constitutive aerenchyma was observed in roots of sea barley, and it could be significantly induced by waterlogging. • Transcriptome analysis revealed some stress-responsive factors involved in aerenchyma formation under waterlogging. • Multi-omics analysis uncovered high waterlogging tolerance associated with active TCA cycle and sugar reserve in sea barley. Waterlogging is a major abiotic stress restricting crop production, and its frequency is increasing due to global climate change. Although some genes related to respiration and carbohydrate metabolism under waterlogging have been identified, the key elements regulating waterlogging tolerance remain unclear. In this study, we found sea barley ( Hordeum marinum , accession H559), a wild relative of Triticeae species, exhibited much higher waterlogging tolerance than barley ( Hordeum vulgare , cultivar ZU9). This tolerance was directly associated with well-developed aerenchyma, under both normal and waterlogging conditions. After 20-day of waterlogging, 2,348 and 867 differentially expressed genes (DEGs) in roots were detected in sea barley and barley, respectively. Transcriptomic analysis revealed that the key stress-responsive transcription factors (such as bHLH121 and MYB2 ) involved in aerenchyma formation were significantly up-regulated in sea barley, while remained little change in barley. Metabolomic analysis further showed that superior waterlogging tolerance of sea barley was due to its ability to mitigate oxidative stress and energy deficit by maintaining higher sugar content and an active tricarboxylic acid (TCA) cycle, both of which depended on well-developed aerenchyma. This study enhances our understanding of waterlogging tolerance mechanisms at both transcriptomic and metabolic levels, providing valuable insights for genetic breeding for waterlogging-tolerant cultivars.