Metabolomic fingerprinting of Indonesian beetroot across Java agroecological zones: A tool for geographical authentication and quality assessment.

The metabolomic composition of beetroot (Beta vulgaris L.) is strongly shaped by environment, supporting geographical origin authentication. This study reports the first untargeted metabolomic profiling of Indonesian beetroot from Bandung (BDG), Semarang (SMG), and Malang (MLG) using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q/TOF-MS). A total of 92 metabolites were identified, including flavonoids, stilbenoids, alkaloids, glycosides, and phenolic derivatives. Multivariate analyses-principal component analysis (PCA), analysis of variance (ANOVA), and sparse partial least squares discriminant analysis (sPLS-DA)-achieved clear regional separation. Biomarkers were region-specific: BDG enriched in 2-hydroxy-3,4-dimethoxy-isoflavam-7-O-β-glucoside (loading weight > 0.8), MLG in 6-hydroxy-2-[2-(4'-methoxyphenyl)ethyl]chromone and decuroside VI (loading weight > 0.5), and SMG in licochalcone A and thalictricoside (loading weight > 0.5). Network analysis highlighted biosynthetic clustering (phenylpropanoid-stilbenoid in BDG, chromone-glycoside in MLG, chalcone-flavonoid in SMG), reflecting adaptation to altitude, humidity, and UV exposure. Findings provide metabolite markers for authentication, quality control, and region-specific cultivation strategies.