Spatial transcriptome analysis reveals de novo regeneration of poplar roots

Propagation through cuttings is a well-established and effective technique for plant multiplication. This study explores the regeneration of poplar roots using spatial transcriptomics to map a detailed developmental trajectory. Mapping of the time-series transcriptome data revealed notable alterations in gene expression during root development, particularly in the activation of cytokinin-responsive genes. Our analysis identified six distinct clusters during the second and third stages, each corresponding to specific anatomical regions with unique gene expression profiles. Auxin response <i>cis</i>-elements (AuxREs) were prevalent in the promoters of these cytokinin-responsive genes, indicating a regulatory interplay between auxin and cytokinin. Pseudo-temporal trajectory analysis mapped the differentiation from cambium cells to root primordium cells, revealing a complex pattern of cell differentiation. <i>SAC56</i> and <i>LOS1</i> emerged as potential novel biomarkers for enhancing root regeneration, with distinct spatial expression patterns confirmed by <i>in situ</i> hybridization. This comprehensive spatial analysis enhances our understanding of the molecular interactions driving root regeneration and provides insights for improving plant propagation techniques.