Silicon dioxide nanoparticles application triggers holistic multi-level reprogramming in Citrus sinensis trees

Silicon dioxide nanoparticles (SiO₂-NPs) have shown promise as plant biostimulants; however, their physiological, metabolic, and transcriptional effects in perennial fruit crops remain poorly understood. In this study, we evaluated the physiological, metabolic, and transcriptomic responses of Citrus sinensis leaves to repeated foliar spray applications of SiO₂-NPs under greenhouse conditions. Plants were foliar-sprayed every 15 days with SiO₂-NPs at 0, 200, 400, and 600 mg L⁻¹. SiO₂-NPs treatment significantly enhanced chlorophyll and phenolics accumulation, recording total chlorophyll of 10.08 mgL -1 and increased total phenolics to 171.0 mg g⁻¹ FW. Volatile organic compound profiling revealed concentration-dependent modulation of terpene emissions, including significant induction of sesquiterpenes. Transcriptome analysis identified 2,236 differentially expressed genes (1,619 upregulated and 617 downregulated), with significant enrichment in pathways associated with cell wall biosynthesis, cytoskeleton organization, hormone signaling, and photosynthetic function. SiO₂-NPs treatment significantly induces cell wall genes, including pectin methylesterases, expansins, arabinogalactan proteins, and kinesin motor proteins. Additionally, we recorded upregulation of cell cycle regulators, microtubule-associated proteins, and auxin-responsive transcription factors. SiO₂-NPs significantly enhanced primary metabolism, including a nearly ten-fold increase in glucose and accumulation of polyols and inositols. SiO₂‑NPs induced significant shifts in phytohormone profiles, elevating IAA from 19.8 to 56.4 µg/g FW, IBA from 255.3 to 664.7 µg/g FW, IPA from 176.4 to 292.4 µg/g FW, t JA from 35.0 to 62.8 µg/g FW, and ABA from 102.7 to 159.8 µg/g FW, while cinnamic and salicylic acid levels remained unchanged. Our results suggest that the application of SiO₂-NPs maintains plant integrity by coordinating cell wall remodeling, cytoskeletal organization, and hormone-mediated regulatory networks. • SiO₂-NPs enhanced Citrus primary and secondary metabolism in a dose-dependent manner. • Terpenoid VOC biosynthesis was strongly reprogrammed, with Geranial increasing 27.6-fold. • SiO₂-NPs triggered 2,236 DEGs enriched in cell cycle, cytoskeleton, and chromatin pathways. • Cell wall remodeling networks (PMEs, XOTs, AGPs, LTPs) were activated, • SiO₂-NPs upregulated auxin-, brassinosteroid-, and stress-responsive genes and increased levels of IAA, IBA, JA, and ABA.