Transcriptomic Response of Tomato Leaves to Root-Applied Phyto-Courier

The application of nanotechnology in plant science is opening new opportunities to improve the delivery, stability and efficacy of bioactive compounds in agricultural systems. In particular, the use of nanocarriers to enhance the bioavailability of plant secondary metabolites, such as flavonoids, is gaining increasing attention due to their well-known roles in plant physiology and stress responses. Building upon previous developments of silicon-based nanoparticle delivery platforms (referred to as phyto-couriers), this study provides a comprehensive transcriptomic analysis to investigate the molecular responses induced in tomato leaves following root amendment of a rutin-loaded phyto-courier system (GS3-R; comprising silicon nanoparticles, lipids, amino acids and trehalose). Initial targeted qPCR analysis of nineteen genes comparing GS3-R with free rutin, the unloaded carrier and an empty hydrolysable polyvinyl alcohol (PVA) bag (B) used as the application control, under both non-stress and NaCl conditions, revealed treatment-dependent differences in gene expression and additional responses to salinity. To investigate the broader transcriptional response to GS3-R, RNA-Seq analysis was performed on leaves from GS3-R- and B-treated plants under non-stress conditions. Differentially expressed genes (DEGs) were identified using two analytical approaches to assess the robustness of the findings. The first analysis, based on Reads Per Kilobase Million—RPKM, identified 862 DEGs, while a count-based reanalysis using DESeq2 identified 1644 DEGs, of which 670 were shared and displayed concordant directions of differential expression. Functional enrichment analysis highlighted broadly consistent patterns across both analyses, involving phenylpropanoid and flavonoid biosynthesis, redox homeostasis, membrane transport, photosynthesis, phytohormone-associated pathways and cell wall organisation. These findings show that root application of the GS3-R phyto-courier is associated with molecular responses in aerial tissues and offer a transcriptome-wide overview of the biological processes responsive to the complete formulation. The study identifies candidate molecular pathways associated with the plant response to this formulation and establishes a robust molecular foundation for future investigations aimed at elucidating the physiological significance of these pathways under stress conditions.