Cell-type-specific response to silicon treatment in soybean leaves revealed by single-nucleus RNA sequencing and targeted gene editing

Mineral nutrient uptake and deposition profoundly influence plant development, stress resilience, and productivity.Silicon (Si), though classified as a non-essential element, significantly influences a plants physiology,particularly in fortifying defense responses and mitigating stress. While the genetic and molecularmechanisms of Si uptake and transport are well studied in monocots, particularly rice, their role in dicotspecies, such as soybean, remains unclear at the cellular and molecular levels. In this study, we utilizedsingle-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybeanleaves. We identified distinct cellular populations, including a unique Si-induced or Si-associated cell clusterwithin vascular cells, suggesting a specialized mechanism of Si distribution. Si treatment notably inducedthe expression of defense-related genes, with a pronounced enrichment in vascular cells, underscoring theirpivotal role in activating plant defense mechanisms. Moreover, Si modulated the expression of genesinvolved in phytoalexin biosynthesis, salicylic acid, and immune receptor signaling, suggesting transcriptionalpriming of genes involved in defense responses. Further investigation of Si transporters revealed preciseexpression of an Si efflux gene in epidermal cells in response to Si treatment. We also validated therole of efflux Si transporters using a Xenopus oocyte assay and CRISPR/Cas9 genome editing of compositesoybean plant roots. This study provides critical insights into the biotic stress regulatory networks influencedby Si treatment in soybean leaves at the single-cell level, thus laying the foundation for enhancingstress tolerance through optimized mineral nutrient uptake.