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

In agriculture, mineral nutrient uptake and deposition profoundly influences plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) uptake and deposition alters plant physiology and particularly improves defense response and stress mitigation. While genetic and molecular mechanisms of Si uptake and transport are well-studied in monocots, particularly rice, its role in dicot species, such as soybean, remains unclear at the cellular and molecular levels. Traditional bulk transcriptomics methods lack the resolution to uncover cellular heterogeneity. Here, we present a study utilizing single-nucleus RNA sequencing (snRNA-seq) to dissect cellular responses to Si accumulation in soybean leaves. Our analysis revealed distinct cellular populations, including a novel Si-induced cell cluster within vascular cells, suggesting a specific mechanism of Si distribution. Si treatment induced the expression of defense-related genes, particularly enriched in vascular cells, highlighting their specialized role in activating plant defense mechanisms. Moreover, Si modulated the expression of genes involved in RNA silencing, phytoalexin biosynthesis, and immune receptor signaling, suggesting transcriptional priming of genes involved in defense responses. We also investigated putative Si transporters, revealing differential expression patterns in response to Si treatment, suggesting presence of active and gradient-based transport mechanisms. Furthermore, by employing CRISPR/Cas9 genome editing we functionally validated the role of efflux Si transporters in composite soybean plants. Our findings shed light on the vital biotic stress regulatory networks governed by Si treatment in soybean leaves, paving potential strategies for enhancing stress tolerance and agronomic performance in crops.