MALDI-MSI-based spatial metabolite mapping of Rheum tanguticum roots across growth years reveals functional food potential

The extraordinary chemodiversity of secondary metabolites in Rheum tanguticum Maxim. ex Balf. underpins its promise as a great Food-Medicine Homology crop. Elucidating how these metabolites accumulate and are spatially organized during root maturation is therefore an essential prerequisite for quality-oriented cultivation and processing. Here, we harvested roots at three developmental stages and integrated MALDI-MSI, UPLC-ESI-MS/MS and RNA-seq to dissect the morphological, metabolic and transcriptional dynamics governing quality formation. Quantitative and imaging results indicate that AQs and flavonoids account for a significant proportion of the bioactive constituents in rhubarb roots and exhibit complementary spatial gradients that expand centripetally with root age. Transcriptome co-mapping identified stage-specific PKSIII and MYBs expression hotspots that precisely colocalize with these metabolite maxima, providing the first genetic evidence for their coordinated biosynthesis in R. tanguticum . These findings not only redefine the spatiotemporal blueprint of metabolite accumulation in rhubarb roots, but also offer high-resolution targets for marker-assisted breeding and targeted processing strategies to maximize both medicinal efficacy and functional-food value. • The comprehensive spatial map of root metabolites in R. tanguticum now exists. • Differential spatiotemporal patterns of AQs/flavonoids enable food use of roots. • New finding: Diphyllin. • Stage-specific MALDI-MSI traces every step of AQ and flavonoid biosynthesis. • Key gene for food-target metabolite mined