Grafting and biodynamic nanosilica-induced physiological and transcriptomic modulation of chilli (Capsicum annuum L.) under drought stress.

Chilli (Capsicum annuum L.) is an economically important vegetable crop cultivated worldwide. Increasing drought stress associated with climate change has severely reduced chilli productivity. Although grafting and silicon-based nanomaterials have each been investigated independently as drought mitigation strategies in Solanaceae crops, this study represents, to our knowledge, the first investigation of their combined physiological, yield, and genome-wide transcriptomic effects in chilli under experimentally validated drought stress. Biodynamic nanosilica (BNS) is an α-quartz nanoparticle preparation (20-200 nm) derived from the biodynamic agricultural preparation BD501 through a vortex-triturating process, and distinct from chemically synthesised nanosilica in preparation method and surface bioavailability, applied as a foliar spray at 50 mg L-1. Five treatments were established: well-watered (WW), drought (D), grafting + BNS + drought (G+B+D), grafting + drought (G+D), and BNS + drought (B+D), each with three independent biological replicates. Under moderate-to-severe drought conditions (DSI 62-64%; VWC ~12% v/v at 14 days), the combined G+B+D treatment significantly improved plant height (3.05-fold over D), leaf relative water content (83% vs 49% in D), net photosynthetic rate (2.0-fold over D), water-use efficiency (+40%), and antioxidant enzyme activities (SOD: 3.1-fold; CAT: 2.8-fold over D), while reducing lipid peroxidation by 76%. Root architecture was also substantially enhanced, with a 4.1-fold increase in root length and a 3.1-fold increase in root surface area relative to D. Fruit yield increased by 79% relative to drought-stressed non-grafted plants. Transcriptomic analysis using Illumina NovaSeq 6000 identified 1,051 DEGs (431 upregulated, 620 downregulated; FDR < 0.05, |log2FC| > 1). Integrated transcriptomic-phenotypic concordance analysis revealed enrichment of MAPK signalling, ABA-mediated regulation (including ABA binding and (+)-ABA 8'-hydroxylase activity), and phenylpropanoid biosynthesis as the enriched pathways. Protein-protein interaction network analysis further revealed coordinated regulation of redox homeostasis, drought-responsive hormone signalling, and water transport gene modules in the combined treatment. These findings demonstrate that integrating grafting with biodynamic nanosilica is a promising strategy to enhance drought resilience and productivity in chilli, offering a sustainable approach for vegetable production under drought.