Comparative metabolomic profiling and biomarker identification reveal nutritional and antioxidant differences between Prunus tomentosa and Prunus avium

This study compares the nutritional and antioxidant attributes of <i>Prunus avium</i> and <i>Prunus tomentosa</i> while investigating their metabolite relationships. The results indicate that <i>P. tomentosa</i> has higher levels of vitamin C, total anthocyanins, soluble protein, Ca, K, Zn, and antioxidant capacity. Additionally, its pits demonstrate superior antioxidant and antimicrobial activities compared to those of <i>P. avium</i>. Metabolomic profiling using UPLC-QTOF-MS/MS identified 1019 metabolites, predominantly within flavonoids, organic acids, phenolic acids, and saccharides. Weighted gene co-expression network analysis linked these metabolites to nutritional and antioxidant traits, emphasizing key pathways such as phenylpropanoid and flavonoid biosynthesis. Multiple factor analysis affirmed the robustness of these findings, and random forest analysis pinpointed kaempferol 3-O-beta-D-galactopyranosyl-7-O-alpha-L-rhamnopyranoside, leucodelphidin, and quercetagetin as key contributors to nutritional and antioxidant attributes. In conclusion, this study identifies key biomarkers associated with nutritional and antioxidant properties, providing a scientific foundation for enhancing <i>P. tomentosa</i> cultivation and fruit quality improvement.