Integrated transcriptomic and physiological analyses elucidate the role of silicon nanoparticles in chromium detoxification in Brassica napus

• Si-NPs reduce chromium uptake and enhance photosynthesis in B. napus under stress. • RNA-seq reveals Si-NPs reprogram the transcriptome, boosting antioxidant and detoxification genes. • Nitrogen and amino acid metabolism are identified as central hubs for Si-NP-mediated Cr tolerance. • Si-NPs act as nano-elicitors, actively rewiring defense networks rather than just blocking metal uptake. Chromium (Cr), a pervasive and toxic heavy metal contaminant of agricultural soils, poses a significant threat to crop productivity and food safety. Silicon nanoparticles (Si-NPs) represent a promising nano-enabled strategy for mitigating heavy metal toxicity in plants. However, the molecular mechanisms by which Si-NPs confer Cr tolerance in major crops such as Brassica napus are not fully elucidated. This study investigated the physiological and transcriptomic responses of B. napus to Cr stress and the protective role of Si-NPs. We found that Si-NPs application significantly improved plant growth and biomass while reducing Cr translocation to shoots. Physiologically, Si-NPs alleviated Cr-induced oxidative stress by enhancing antioxidant defense and reducing reactive oxygen species and lipid peroxidation. RNA-seq analysis revealed that Cr stress profoundly dysregulated genes involved in metal transport, oxidative response, and phenylpropanoid biosynthesis. Crucially, Si-NPs induced a protective transcriptional reprogramming, upregulating genes associated with metal chelation and sequestration (e.g., metallothioneins, ABC transporters), antioxidant enzymes, and the biosynthesis of lignin and flavonoids. These changes are consistent with enhanced metal detoxification and reinforced cell walls, effectively reducing Cr mobility and toxicity. Our findings decipher the key molecular pathways through which Si-NPs enhance Cr tolerance in B. napus , providing crucial insights for developing Si-NP-based strategies to cultivate crops in Cr-contaminated environments.