Unraveling the genetic mechanisms of waterlogging stress through the leaf metabolome of a sweet corn panel

BACKGROUND: Sweet corn is a crop with global economic importance, yet it is highly susceptible to waterlogging stress. The molecular and metabolic mechanisms underlying its waterlogging response remain poorly understood. RESULTS: We used an integrated multi-omics approach to investigate the genetic and biochemical basis of waterlogging tolerance in a diverse panel of 185 super sweet corn inbred lines. Waterlogging reduced seedling growth by 21-35%, and transcriptomic analysis identified 295 DEGs, including downregulated nitrogen assimilation genes (e.g., Zmgln2) and upregulated stress-responsive transcription factors involved in calcium ion transport pathways. Metabolomic analysis identified 75 DAMs, particularly amino acids and other organic acids that are associated with anaerobic metabolism. GWAS pinpointed a pleiotropic locus, Zmhpc1, that regulates glycerol-related metabolism and associated agronomic traits. CONCLUSIONS: Our findings provide novel insights into the adaptive responses to waterlogging stress and identify promising candidate genes for developing climate-resilient sweet corn varieties, offering practical applications for breeding waterlogging-tolerant sweet corn.