Stress-specific metabolic and physiological responses to drought and waterlogging in Allium cepa L. and Allium × cornutum Clementi ex Vis.

Increasing variability in water availability, caused by changing climatic conditions, is a major constraint for onion production. The present study investigated the physiological, metabolic and molecular responses of the diploid onion Allium cepa L. and the triploid hybrid Allium × cornutum Clementi ex Visiani under drought and waterlogging. Plants were exposed to controlled stress conditions, and responses were evaluated through relative water content (RWC), electrolyte leakage (EL), photosynthetic pigments, amino acid composition, total phenolic content (TPC), individual phenolic compounds and expression of antioxidant genes (CAT, SOD, AOX). Allium × cornutum showed a more pronounced response to drought, characterized by higher RWC, stable chlorophyll and carotenoid levels, increased accumulation of free amino acids and phenolic compounds, especially chlorogenic acid and quercetin glycosides, with significant upregulation of the antioxidant genes SOD and CAT. Allium cepa responded more strongly to waterlogging, showing increased amino acid levels, accumulation of quercetin and its glycosides, a marked increase in α-aminobutyric acid (AABA) concentration and higher expression of CAT and SOD. These results show distinct metabolic responses and physiological changes to drought and waterlogging, reflecting stress-specific adjustments under extreme water conditions and contributing to a better understanding of water stress adaptation in Allium species.