Integrated Transcriptomic and Metabolomic Provide Insights into Strawberry Bioactive Compounds and Antioxidant Activities Under Varying Ecological Conditions

Strawberries are nutrient-rich fruits containing beneficial phytochemicals and bioactive compounds with significant health benefits. Among secondary metabolites, the polyphenolic compounds have been extensively studied. However, limited research exists on bioactive alkaloids in strawberry fruits. Additionally, the local “Akihime” strawberry variety cultivated in the high altitude of Zhaotong city is of inferior quality; in contrast, the “Red Face” variety cultivated in the lower altitude of Dandong city demonstrates superior quality attributes. This study aimed to introduce the “Red Face” strawberry variety from the lower altitude region of Dandong to the high altitudes of Zhaotong. The primary objectives were to enhance local strawberry quality and investigate the diversity of alkaloids and their biosynthesis genes in response to varying ecological conditions. In this study, a transcriptomic and LC–MS/MS approach identified several biosynthesis genes, 33 alkaloids, and 38 other bioactive compounds, reported for the first time in the strawberry fruits. Five alkaloids ergotamine, 3-indoleacrylic acid, L-pipecolic acid, 8-hydroxyquinoline, and indole, were abundantly found in both strawberry varieties. Principal component analysis and hierarchical cluster analysis revealed significant variation in the individual alkaloid compounds among the different strawberry varieties and ecological conditions. Cultivation of the “Red Face” variety at high-altitude environments modified the gene expressions and enhanced the total alkaloid contents and the antioxidant activity and capacity of strawberry fruits. Our study concluded that strawberries possess a diversity of bioactive alkaloid compounds, and introducing the “Red Face” variety at high-altitude environments produces superior quality of strawberry fruits with improved total alkaloid contents and antioxidant activities.