The CLE41 peptide, like all other TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) family CLE peptides, promotes cell division in (pro-)cambium vascular meristem and prevents xylem differentiation. In this work, we analyzed the differential gene expression in the radish primary-growing P35S:RsCLE41-1 roots using the RNA-seq. Our analysis of transcriptomic data revealed a total of 62 differentially expressed genes between transgenic radish roots overexpressing the RsCLE41-1 gene and the glucuronidase ( GUS) gene. For genes associated with late embryogenesis, response to abscisic acid and auxin-dependent xylem cell fate determination, an increase in the expression in P35S:RsCLE41-1 roots was found. Among those downregulated, stress-associated genes prevailed. Moreover, several genes involved in xylem specification were also downregulated in the roots with RsCLE41-1 overexpression. Unexpectedly, none of the well-known targets of TDIFs, such as WOX4 and WOX14, were identified as DEGs in our experiment. Herein, we discuss a suggestion that the activation of pathways associated with desiccation resistance, which are more characteristic of late embryogenesis, in roots with RsCLE41-overexpression may be a consequence of water deficiency onset due to impaired vascular specification.