Cultivar-Dependent Variation in Silicon Accumulation and Phytolith Formation Revealed by Comparative Proteomic Analysis in Rice

Silicon is a key determinant of growth, productivity, and stress adaptation in rice (Oryza sativa L.). Silicon accumulation and its deposition as phytoliths contribute to plant performance and environmental resilience. However, although the physiological functions of silicon and the mechanisms governing its uptake and transport have been extensively studied, the proteomic basis underlying cultivar-dependent variation in silicon accumulation and phytolith formation remains poorly understood. In this study, silicon concentration, phytolith content, and proteomic profiles were compared in roots and shoots of three rice cultivars, Chai Nat 1 (CNT), Khao Dawk Mali 105 (KDML105), and RD51, at the flowering stage. RD51 exhibited the highest silicon concentration and phytolith accumulation in shoots, whereas CNT accumulated the highest silicon concentration in roots. Proteomic analysis identified 4086 and 4115 protein groups in roots and shoots, respectively, revealing cultivar-specific differences in protein abundance. Principal component analysis and differential abundance analysis demonstrated the greatest proteomic divergence between CNT and RD51, particularly in shoots. Functional enrichment analysis indicated that KDML105 was enriched in transport- and sulfur metabolism-related processes, whereas RD51 showed enrichment of mitochondrial respiration, energy production, and associated metabolic pathways. Protein–protein interaction (PPI) network analysis further revealed functional associations between silicon transporter proteins and proteins involved in transport, signaling, and respiratory metabolism. Collectively, these findings provide novel insights into the proteomic mechanisms underlying silicon accumulation and phytolith formation in rice. The superior silicon accumulation and phytolith production observed in RD51 highlight its potential as a valuable genetic resource for enhancing phytolith production, improving silicon-use efficiency, and strengthening climate resilience in rice.