Biology subjects

Patil, G. B.

Publications and source records attributed to Patil, G. B..

6 recordsLinked to original sources

bioRxiv2026

Developmental regulator-mediated transcriptional reprogramming reveals novel regulators of somatic embryogenesis in sorghum

Recalcitrance to genetic transformation remains a fundamental bottleneck in crop improvement, driven by genotype-specific barriers that include entrenched defense transcriptional states, limited embryogenic competence, and inadequate hormonal reprogramming potential. Here, we present a multi-layered transcriptomic analysis of somatic embryogenesis (SE) and regeneration in two sorghum genotypes (forage Tx2910 and grain Tx2783), two explant types (immature embryos and leaf bases), and three developmental regulator (DR) treatments (GRF-GIF, WUS, and BBM+WUS). This design lets us separate genotype, explant, and DR-specific regulatory programs. Using in-depth transcriptomics analysis (bulk RNAseq and single nucleus transcriptomics), we identified the molecular logic by which DRs override genotype-specific barriers and redirect somatic cells toward embryogenic and regeneration-competent states. Compared to Tx2910, the transformation-recalcitrant sorghum line Tx2783 shows a stronger defense response to both Agrobacterium infection plus culture stress and depends more heavily on DR-driven transcriptional reprogramming to exit this defense-locked state. WUS acts as an early, broad suppressor of defense and stress signaling while activating fate-specification programs, whereas GRF-GIF drives a delayed but pronounced transcriptional shift toward cell proliferation and morphogenesis. Integrative gene network analyses further identified a prioritized set of sorghum-specific transcription factors with potential to increase regeneration efficiency. Among the top candidates, we identified that SbEREB167 and SbEREB174 (AP2/EREBP family) efficiently induce SE and regeneration in sorghum. Collectively, this study establishes the transcriptional architecture underlying DR-mediated transformation across sorghum types and identifies novel regulators that hold potential to improve plant transformation across recalcitrant cereal species.

plant biology↗

bioRxiv2026

Cell-type-resolved transcriptional reprogramming in resistant soybean roots reveals cambial activation and early syncytium initiation upon nematode infection

Soybean cyst nematode (SCN) is the most destructive pathogen of soybean, yet the cellular basis of host resistance remains poorly understood. Here, we present a high-quality, cell-type-resolved atlas of root responses during early SCN infection in the highly resistant genotype PI437654, capturing transcriptional states across all major tissues, including rare syncytial cells. Our analyses reveal that resistance is mediated not by a localized defense but by coordinated, multicell reprogramming spanning invasion layers, vascular tissues, and feeding site-associated cells. We identify the vascular cambium as the primary cellular origin of SCN-induced syncytia, resolving a long-standing question in nematology. Mechanistically, resistance arises from disruption of key processes required for feeding site establishment, secretory stress via imbalanced vesicle trafficking, suppression of endoreduplication to prevent hypertrophic syncytial growth, and activation of autophagy to maintain cellular homeostasis. Spatially organized hormone signaling networks, including jasmonic acid, salicylic acid, and ethylene pathways, further reinforce defense, with GmJAZ1 functioning as a central regulator of JA-SA crosstalk. Collectively, PI437654 enforces resistance by targeting host cell identity, nutrient sink formation, and sustained parasitism, deploying a multilayered, tissue-specific defense strategy. This study provides a mechanistic, systems-level framework for SCN resistance and establishes a single-cell resource capturing rare root cell states, offering actionable targets for engineering durable nematode resistance. Key pointsO_LISoybean cyst nematode (SCN) is the most destructive pathogen of soybean worldwide, yet the cellular basis of early host responses and feeding site initiation remains poorly understood. C_LIO_LIUsing single-nucleus RNA sequencing (snRNA-seq), we generated a cell-type-resolved atlas of early SCN infection in roots of a unique and highly resistant soybean genotype PI437654. Trajectory analysis integrated with syncytium marker genes revealed that cambium cells are selectively targeted as the cellular origin of syncytium formation. C_LIO_LISCN infection triggers extensive cell-type-specific transcriptional reprogramming, particularly in vascular tissues (xylem, phloem, and cambium), involving pathways related to cell cycle and endoreduplication, vesicle trafficking, autophagy, and phytohormone signaling. C_LIO_LIFunctional validation demonstrated enhanced autophagy activation in infected roots via increased GFP-GmATG8a-labeled autophagic puncta, while overexpression of the jasmonic acid regulator GmJAZ1 significantly enhanced SCN resistance in susceptible soybean. C_LIO_LITogether, these findings define the cellular origin of SCN-induced syncytia and reveal coordinated cell-type-specific defense programs, providing a mechanistic framework for engineering durable resistance to SCN. C_LI

plant biology↗

bioRxiv2026

A Grass-Specific Structural Feature of Myosin VIII Regulates Protoxylem Development and Hydraulic Conductance in Sorghum

Sorghum (Sorghum bicolor), a C grass adapted to hot semi-arid environments, depends on reinforced xylem vessels to maintain hydraulic conductance under high evaporative demand. During protoxylem differentiation, coordinated microtubule and actin dynamics guide secondary cell wall (SCW) deposition; however, whether actin-based motors directly regulate vascular architecture and hydraulic performance has remained unknown. Here, we identify HEAT-SENSITIVE 1 (HS1), a previously uncharacterized myosin VIII, as a central regulator of protoxylem integrity and water transport in sorghum. The hs1 mutant exhibited severe leaf scorching under field conditions. The hs1 mutant displayed severe leaf scorching under field conditions, accompanied by pronounced protoxylem defects under controlled environments, including vessel collapse, reduced lumen area, and attenuated lignified SCWs. These structural abnormalities compromised longitudinal hydraulic conductance, diminished whole-plant water use, and rendered expanding leaves unable to meet transpirational demand, resulting in transient water deficit and thermal injury. HS1 encoded a grass-specific myosin VIII with a grass-specific N-terminal extension exhibiting high intrinsic disorder and lineage-specific substitutions in the motor domain. Molecular and single-cell transcriptome analyses positioned HS1 within differentiating protoxylem cells of developing leaves, revealing pronounced temporal and cell-type specificity. Furthermore bulk transcriptome profiling and quantitative lignin measurements indicated that HS1 promoted lignin-associated SCW biosynthesis during protoxylem differentiation, functionally linking actin-based motor activity to wall reinforcement. HS1 encodes a grass-specific myosin VIII distinguished by an extended intrinsically disordered N-terminal region and lineage-specific substitutions within the motor domain, suggesting evolutionary specialization. Consistant with core developmental role, reduced nucleotide diversity at the HS1 locus across diverse sorghum accessions further supported strong evolutionary constraint. Together, these findings established HS1 as the first actin-based motor protein shown to control xylem architecture and hydraulic function in plants.

plant biology↗

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↗

bioRxiv2025

Shoot at Site: Advancing in planta transformation, regeneration and gene-editing through a cascade of wounding-mediated developmental regulators

Developing transgenic and/or gene-edited plants largely depends on tedious, lengthy, and costly in vitro regeneration protocols. While plants have remarkable regeneration ability, not all species, genotypes or even explants exhibit the same transformation and regeneration potential under in vitro conditions. To tackle this bottleneck, we have developed a seamless and user-friendly system to induce transgenic and gene-edited de novo meristems via a synthetic cascade comprising a wound-induced regeneration pathway, plant developmental regulators (DRs) and gene-editing reagents. WOUND INDUCED DEDIFFERENTIATION 1 (WIND1) is used as a transcriptional regulator to control the expression of various DR genes through ENHANCER OF SHOOT REGENERATION 1 (ESR1) promoter. This cascade was strategically applied in planta to the non-meristematic internode of N. benthamiana to induce meristematic activity and regenerate de novo shoots with knock-out mutations of the phytoene desaturase (PDS) gene. This synthetic toolkit was further applied successfully to tomato and soybean. This methodology offers a transformative approach to overcome barriers in plant biotechnology, potentially accelerating the generation of transgenic and gene-edited plants without reliance on conventional tissue-culture intermediates.

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↗