Integrated metabolomic and transcriptomic analysis unravels the biosynthetic mechanism of characteristic aroma compounds in red-fleshed 'Yexiang' mango pulp

Abstract

Mango pulp aroma comprises diverse volatile organic compounds that determine fruit flavor quality and commercial value. The ‘Yexiang’ mango is distinguished by its sweet flavor and delicate texture. In particular, the red-fleshed variant exhibits a distinctive aroma compared with the traditional yellow-fleshed variant. To elucidate the mechanism underlying this distinctive aroma, red- and yellow-fleshed ‘Yexiang’ mangoes from the same orchard were comparatively analyzed. The pulp of the red-fleshed fruit exhibited a deeper yellow color with a reddish hue, emitted a distinctive citrus-like aroma, and had a higher sugar-acid ratio. Volatile metabolomic analysis showed that terpenoids represented the largest class of differential metabolites, with limonene emerging as the monoterpene most closely associated with the distinctive aroma. Transcriptomic analysis showed that, from 90 days after flowering to postharvest ripening, most differentially expressed genes were enriched in metabolic and secondary metabolite biosynthesis pathways. Among them, genes encoding 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and DXS2 were identified as candidate regulators of limonene biosynthesis. Targeted GC–MS quantification confirmed that limonene content was significantly higher in red-fleshed fruit at 80, 90, and 97 DAF. ELISA assays demonstrated significantly elevated total DXS protein content in red-fleshed pulp, matching the trend of limonene accumulation. In addition, qRT-PCR verified the upregulation of DXS and DXS2 at specific stages, indicating that enhanced precursor supply through the MEP pathway drives limonene accumulation and characteristic aroma formation. These findings clarify the molecular basis of citrus-like aroma biosynthesis in red-fleshed 'Yexiang' mango, offering practical guidance for fruit quality breeding and cultivation management.