Ancient Herb, Modern Metabolomics: Primary and Secondary Metabolite Profiling of Wild Fennel (Foeniculum vulgare Mill.) Accessions Under Drought

Fennel (Foeniculum vulgare Mill.) is an aromatic species of culinary and medicinal value, but the metabolic basis of its drought response and the extent of variation among wild populations remain poorly characterized. We investigated eleven wild fennel accessions from the Mediterranean region of Croatia under control and drought conditions, combining morphological measurements with targeted profiling of 78 primary and 55 secondary metabolites. Drought significantly reduced biomass, leaf area, length, and width, while leaf dry matter content increased. Primary metabolism shifted markedly: amino acids accumulated, with asparagine and arginine increasing by over 20-fold, whereas TCA-cycle (tricarboxylic acid cycle) organic acids declined. Pathway analysis identified Alanine, aspartate, and glutamate metabolism as most strongly affected by drought treatment. A decline in the GSH/GSSG ratio indicated oxidative stress under water shortage. Among secondary metabolites, free hydroxycinnamic acids and flavonoid aglycones accumulated while most glycosylated flavonoids declined, and eight compounds showed genotype-dependent responses in drought conditions. These results reveal accession-specific metabolic adjustments to drought and characterize Croatian wild fennel as a genetic resource with distinct phytochemical profiles relevant to future conservation and breeding.