Biology subjects

Herrera Estrella, L.

Publications and source records attributed to Herrera Estrella, L..

5 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

A spatiotemporal single-cell atlas reveals coordinated immune, metabolic, and nutrient exchange programs and a coumarin-centered metabolic switch during soybean arbusular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) establish intimate symbiosis with plant roots, yet the cell-type-specific regulatory and metabolic programs governing this interaction remain poorly resolved. Here, we integrate single-nucleus RNA sequencing (snRNA-seq) with spatial metabolomics across a temporal gradient of soybean root colonization (2-8 weeks post inoculation) to construct a high-resolution, multi-omic atlas of AMF symbiosis. Profiling 33,410 nuclei spanning all major root cell types, we uncover dynamic, cell-type-resolved transcriptional reprogramming coupled to spatially localized metabolite accumulation. Early colonization triggers a robust, epidermis-localized immune response alongside cortex-specific epigenetic reprogramming, mediated by RNA-directed DNA methylation machinery, suggesting active suppression of defense in fungal accommodation zones. Spatial metabolomics reveals a biphasic metabolic transition from flavonoid- and terpenoid-rich signaling states to lipid-dominated nutrient exchange, aligned with colonization progression. In parallel, coordinated carbon allocation and lipid biosynthesis pathways were activated in cortex and vascular tissues, supporting fungal dependence on host-derived fatty acids and sugars. Nutrient exchange programs, particularly nitrogen and phosphorus transport, exhibit strong pericycle and phloem specificity, highlighting systemic integration of symbiotic benefits. Through co-expression network analysis, we identify a previously uncharacterized coumarin-centered metabolic switch, governed by GmF6H1-2, that is essential for efficient colonization, as validated by natural loss-of-function variants. Collectively, this study provides a comprehensive, spatially resolved framework linking gene regulation, metabolism, and cell identity, revealing that AMF symbiosis is orchestrated through coordinated immune modulation, metabolic rewiring, and nutrient flux partitioning at single-cell resolution. Key pointsO_LIMulti-omic integration reveals cell-type-resolved symbiotic programs C_LIO_LISymbiosis requires spatially coordinated immune reprogramming C_LIO_LIA biphasic metabolic shift underpins colonization dynamics C_LIO_LICarbon and nutrient flux are partitioned across specialized cell types C_LIO_LIDiscovery of a coumarin-driven "metabolic GO-switch" controlling symbiosis C_LI

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↗

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↗