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

The metabolomic composition of beetroot (<i>Beta vulgaris</i> 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.