Kshetry, A. O. | bioRxiv Science

bioRxiv2025

Developmental regulators enable rapid and efficient soybean transformation and CRISPR-mediated genome editing

Soybean transformation remains challenging and has not kept pace with the rapid advancement of genetic engineering technologies due to low efficiency, lengthy timelines, and genotype dependency. Here, we developed a streamlined transformation method by leveraging developmental regulators (DRs) to promote de novo shoot regeneration directly from growing soybean plants. By evaluating multiple DR combinations, our results showed that co-expression of WUSCHEL2 (WUS2) and isopentenyltransferase (IPT) achieved higher transformation efficiencies (15.2% to 22.3%) in Williams 82 and Bert varieties than individual DRs without requiring exogenous hormones or selection agents. Moreover, this method produces heritable transgenic events within 9-11 weeks and successfully delivers CRISPR-Cas9 components, generating heritable mutations with 20% efficiency. The temporal transcriptomic and gene regulatory network analyses revealed that WUS2/IPT synergistically modulates stress responses and activates developmental pathways, orchestrating a transition from initial stress adaptation to regenerative programming. Together, our findings demonstrate that this DR-enabled approach significantly enhances soybean transformation efficiency, reduces tissue culture requirements, and offers a promising genome editing platform for soybean improvement.

plant biology↗

bioRxiv2024

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

In agriculture, mineral nutrients uptake and deposition profoundly influence plant development, stress resilience, and productivity. Despite its classification as a non-essential element, silicon (Si) is crucial in plant physiology, particularly in 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 by 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 a mechanism of transcriptional priming of genes involved in defense responses. We further investigated putative Si transporters, revealing differential expression patterns in response to Si treatment, suggesting presence of active and gradient-based transport mechanisms. 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.

plant biology↗