Integrated genomic and transcriptomic profiling provide insights into silicon-mediated resistance to the fall armyworm

Silicon (Si) is known to be involved in enhancing plant defense against insect pests. However, the underlying mechanisms by which Si accumulation in rice (Oryza sativa L.) confer resistance to insects remain poorly understood. This study explored the impact of Si accumulation on plant-insect interactions and defense mechanisms in rice when infested by the fall armyworm (Spodoptera frugiperda Smith). We utilized three OsLsi1 silicon transporter mutants of the wild-type Nipponbare with varying levels of Si uptake: (i) >95% deficient (Lsi1-L), (ii) ~55% deficient (Lsi1-M), and (iii) similar to wild type (Lsi1-WT) and wild type cultivar Nipponbare (WT). Further, these mutants' gene expression and phytohormone levels in these mutants were compared were compared to WT using whole-genome re-sequencing (WGRS) and RNA sequencing (RNA-seq), and candidate genes associated with Si-mediated resistance were identified. RNA-seq analysis revealed 2644 differentially expressed genes (DEGs) in the WT and 2204 in the mut95 under herbivory compared to control plants. Under herbivory, DEGs related to phytohormone metabolism and stress responses were significantly enriched. We will identify candidate genes by integrating WGRS and RNA-seq profiles with functional annotation. This study provides crucial insights into the genes and mechanisms underlying Si-mediated resistance in rice.