Single-cell transcriptomic atlas reveals that vascular tissues orchestrate cell fate transitions to initiate adventitious root formation in tomato

Abstract Adventitious root (AR) formation enables vegetative propagation critical for agriculture, conservation, and breeding, yet the cellular basis of AR competence in crop species remains poorly characterized. Most mechanistic studies rely on Arabidopsis, which exhibits constrained AR capacity compared to species dependent on clonal propagation. We constructed a single-cell transcriptomic atlas of tomato (Solanum lycopersicum) AR development comprising 7,920 cells across 12 cell types. Regulatory networks were inferred using hdWGCNA and MINI-EX, validated by RNA in situ hybridization and qPCR. Cross-dataset integration with shoot-borne root initiation data enabled developmental staging, while SATURN-based integration of 118,730 vascular cells from eight species permitted evolutionary comparison. CytoTRACE analysis revealed that vascular tissues—root stele and phloem—possess the highest developmental potential, supporting a model of latent stem cell-like identity rather than dedifferentiation-based reprogramming. Network analysis identified LEA3 as a central hub gene constitutively expressed throughout AR development, regulated by the DOF transcription factor DOF11. Cross-species integration demonstrated that tomato AR-initiating cells share transcriptomic similarity with woody dicots (Liriodendron, r = 0.46; Eucalyptus, r = 0.42) but not Arabidopsis (r = −0.02), with LEA3-containing macrogene weights highest in basal angiosperms and woody species. Our findings establish the DOF11-LEA3 axis as a conserved vascular identity module and suggest that AR competence represents an ancestral program retained in species with active cambial dynamics. These results reframe Arabidopsis as a derived rather than representative model for AR biology and identify molecular targets for enhancing vegetative propagation. Competing Interest Statement The authors have declared no competing interest.