Four onion (Allium cepa L.) cultivars with different bulb colors (yellow Y14, red R12, red R10 and white W3) were characterized for phenotypic, metabolic, volatile, antioxidant, flavor and transcriptomic variations, to unravel key metabolites and molecular mechanisms responsible for quality differentiation. Y14 possessed the maximum bulb weight (535.34 g) and diameter (13.10 cm), along with the highest total phenolic content (3.10 mg·g⁻¹), showing superior yield and antioxidant properties. In R12, upregulated expression of carotenoid biosynthetic genes enhanced carotenoid accumulation, resulting in vivid bulb color. R10 had high total phenols (3.89 mg·g⁻¹) and the richest sweet-associated volatiles, featuring strong antioxidant activity and distinct sweetness. By contrast, W3 exhibited moderate flavor but inferior performance in yield, antioxidant capacity, pigment and volatile levels relative to the other three cultivars. Comprehensive assessment indicated that Y14 serves as an excellent processing material, R12 and R10 are ideal for fresh consumption and functional food development, and W3 is well-suited for raw salads. This study lays a theoretical foundation for onion quality improvement, targeted breeding and efficient utilization.

The effects of ambient storage (A), cold storage (C), and frozen storage (F) on the quality, metabolomic characteristics, and sulfur-related aroma of red onion ‘Kewei Red 10’ (R10) and yellow onion ‘Kewei Yellow 14’ (Y14) were investigated using integrated non-targeted and volatile metabolomics. Ambient storage accelerated shrinkage, firmness loss, and sensory deterioration in both cultivars, whereas low-temperature storage effectively delayed quality decline. R10 exhibited better tolerance to frozen storage, while Y14 performed better under cold storage. Metabolomic analysis revealed that amino acids and lipid-related metabolites were closely associated with onion senescence in both cultivars. In contrast, flavonoids were enriched in preservation-associated subclasses in R10, whereas organic acids and their derivatives were more strongly associated with delayed senescence in Y14. Volatile metabolomic analysis identified sulfur compounds and heterocyclic sulfur compounds as the major contributors to onion aroma. Sulfur-related volatiles showed distinct cultivar-dependent accumulation patterns, with many sulfur compounds accumulating prominently in ambient-stored R10-A, whereas cold-stored Y14-C maintained relatively higher levels of characteristic onion-like aroma compounds. These findings demonstrate distinct metabolic adaptation strategies between red and yellow onions during storage and suggest that cultivar-specific storage conditions are required to optimize both shelf life and flavor quality.