Harvest timing defines the metabolic signature of waxy yam: Environment and cultivation then fine-tune bioactive compounds

Harvest time, growth environment, and cultivation practices influence metabolic variations in waxy yam ( Dioscorea alata L.), yet their interactions are not well understood. Here, a metabolomics analysis was performed on waxy yam samples harvested at five time points under greenhouse and field conditions, with or without sleeve cultivation. Multivariate analysis revealed that harvest time was the primary factor driving 42.4% of metabolic variation, shifting from growth- and defense-related metabolites early stages to medicinally relevant bioactive compounds later. Moreover, 123 metabolites responded to interactions among all three factors, forming five harvest time-dependent clusters. Notably, field sleeve cultivation at later stages promoted the accumulation of flavonoids. These results indicate that harvest time establishes the core bioactive profile of waxy yam, whereas growth environment and cultivation practice act as modulators that can precisely enhance specific industrially relevant compounds. This study provides new insights into the interactive regulation of crop metabolism by agronomic factors and offers a metabolic basis for optimizing harvest timing and cultivation strategies to improve the quality consistency of waxy yam as an industrial crop with both nutritional and potential health-promoting value.