A single-cell and spatial transcriptomic atlas provides insights into the genetic regulation of secondary growth and specialized metabolism in the carrot taproot [Spatial Transcriptomics]

However, the regulatory mechanisms governing root thickening and cell-type-specific SM biosynthesis remain largely elusive. Here, we combined single-cell RNA sequencing and Stereo-seq spatial transcriptomics to construct a high-resolution spatiotemporal transcriptomic atlas of carrot taproots during secondary growth.

We resolved the cell fate trajectory of major vascular tissues and revealed that sequential expression of NAC transcription factors (TFs) drove xylem differentiation prior to phloem development. Spatiotemporal screening further identified DcERF1 as a critical positive regulator of the biosynthesis of falcarindiol, a vital anti-cancer SM. This study elucidates the regulatory mechanisms underlying carrot taproot secondary development and specialized metabolism, providing a valuable resource for improving the yield and nutritional quality of storage root crops.