Secondary Metabolites Profile Diversity of Lobostemon fruticosus Leaves Across Geographical Locations in the Western Cape

Lobostemon fruticosus (L.) H. Buek is an indigenous South African medicinal plant valued for its traditional therapeutic uses; however, information on its phytochemical variation and pyrrolizidine alkaloid (PA) content across geographical populations remains limited. This study investigated the secondary metabolite composition and PA accumulation in nine biological samples (three geographical locations × three biological replicates) of L. fruticosus collected from Rhodes Memorial, Doringrivier, and Grootnek Fontein in the Western Cape Province between January and March 2025 using untargeted UPLC-QTOF-MS and targeted LC-MS/MS, with values presented as mean ± standard deviation (SD). A total of 15 secondary metabolites of different classes were putatively annotated. Seven compounds, including kaempferol, jaceidin 7-rhamnoside, schizotenuin F, senburiside III, cosmosporaside B, lirioresinol A, and (−)-steganacin, are reported for the first time in L. fruticosus. Significant geographical variation (p < 0.05) was observed, with Doringrivier containing the highest relative abundances of rutin (4815.60 ± 18.96 mg CE g−1 DW), rosmarinic acid (3846.89 ± 285.78 mg CE g−1 DW), and rabdosiin (5142.10 ± 651.00 mg CE g−1 DW). Six of the ten targeted PAs were detected, with lycopsamine N-oxide being the predominant alkaloid (3.89 mg kg−1 in Grootnek Fontein). Principal component analysis explained 97.2% of the total metabolomic variation (PC1 = 72.6%; PC2 = 24.6%) and clearly separated the three geographical populations. The OPLS-DA model showed strong discrimination among populations (R2X = 0.725, R2Y = 0.998, and Q2 = 0.994), supporting the presence of location-specific chemotypic differences. The observed chemotypic differences may be associated with variation in soil properties, climatic conditions, water availability, altitude, and nutrient status among the study sites. Collectively, the results provide a foundation for chemotype selection, quality control, conservation, and the safe medicinal utilization of this species.