Integrative phenomics, metabolomics, and flavoromics reveal key quality indicators during the formation of flavor and bioactive compounds in Alpinia hainanensis (Zingiberaceae) fruit.

Abstract

Alpinia hainanensis seed (AHS) is a traditional spice and medicinal material with limited studies on its flavor and bioactive chemistry. This study integrated anatomical and microstructural analyses, flavor traits, and full-spectrum metabolome profiling using GC-MS and UPLC-MS/MS to characterize AHS quality. A total of 1543 metabolites were identified, with 41 key flavor compounds showing spatiotemporal specificity. Boiled and dried mature AHS exhibited optimal flavor with large dried fruit, dark and heavy seeds, and strong pungency. Different bioactive compounds peaked across 4-10 weeks post-anthesis, indicating stage-specific medicinal potential. Oil cell traits correlated with bioactive compounds of pinocembrin, cardamonin, and 3-carene accumulation, while bitterness correlated with pinocembrin. Postharvest processing enhanced seed pungency and increased peel terpenoids, supporting value-added utilization. Metabolite accumulation was associated with galactose, fatty acid, terpene, and phenylpropanoid pathways. These findings provide a foundation for refining A. hainanensis harvesting, processing, and utilization.