Transcriptomic Analysis of Radish (Raphanus sativus L.) Roots with CLE41 Overexpression

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.