About

Bastiaan Bargmann is an Assistant Professor at the School of Plant and Environmental Sciences at Virginia Tech. His research focuses on fundamental and translational studies aimed at crop improvement through genome editing and tissue culture techniques. His expertise includes crop improvement and domestication, molecular regulatory mechanisms, and applied genomic and data analysis. Bargmann's work aims to meet the increasing demands for food quantity and quality in a rapidly changing environment by developing new breeding techniques that enhance the development and refinement of novel traits in crops. His research involves understanding and improving the processes involved in the embryogenic and organogenic recovery of fertile plants from protoplast culture, with a focus on cell-identity establishment and growth-regulator signaling, in both model systems like Arabidopsis thaliana and relevant crop species. He is also dedicated to establishing next-generation breeding technologies, particularly gene-editing through CRISPR-Cas9, to increase precision and efficacy in plant breeding programs, ultimately aiming to develop crop varieties better suited for growers, processors, and consumers.

Research topics

• Biology
• Botany
• Biochemistry
• Molecular biology
• Biotechnology
• Cell biology
• Genetics

Selected publications

• From binding to networks: methods for identifying transcription factor targets in plant systems

  Frontiers in Plant Science · 2026-04-13

  articleOpen access

  Transcription factors (TFs) orchestrate gene expression programs by binding regulatory DNA sequences and modulating transcription of target genes. Identifying TF-target gene relationships is fundamental to understanding plant development, stress responses, and metabolic regulation. However, determining which genes a TF regulates remains technically challenging. This review provides a decision-oriented framework, that integrates experimental and computational plant TF-target identification. Placing emphasis on plant-specific constraints and practical method selection to guide researchers from initial TF discovery through comprehensive network characterization. We compare biochemical approaches (EMSA, Y1H), genome-wide mapping methods (ChIP-seq, DAP-seq, CUT&Tag), expression profiling techniques (RNA-seq on mutants and overexpression lines), and computational prediction tools (GENIE3, PTFSpot, ConnecTF). Critical trade-offs are discussed, between binding potential and functional regulation, throughput and resolution, and between different model and non-model plant systems. Finally, we highlight emerging technologies including high-throughput enhancer screening, single-cell approaches, and machine learning-based prediction platforms that promise to accelerate functional characterization of plant TFs and their regulatory networks.

  PublisherOA PDFDOI

• Automated Flow-Cytometric Readout of Reporter-Gene Activation in Transiently Transformed Protoplasts

  Methods in molecular biology · 2026-01-01

  book-chapterSenior author
  PublisherDOI

• Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

  Nature Communications · 2025-01-02 · 21 citations

  articleOpen access

  Single-cell RNA sequencing (scRNA-seq) is widely used in plant biology and is a powerful tool for studying cell identity and differentiation. However, the scarcity of known cell-type marker genes and the divergence of marker expression patterns limit the accuracy of cell-type identification and our capacity to investigate cell-type conservation in many species. To tackle this challenge, we devise a novel computational strategy called Orthologous Marker Gene Groups (OMGs), which can identify cell types in both model and non-model plant species and allows for rapid comparison of cell types across many published single-cell maps. Our method does not require cross-species data integration, while still accurately determining inter-species cellular similarities. We validate the method by analyzing published single-cell data from species with well-annotated single-cell maps, and we show our methods can capture majority of manually annotated cell types. The robustness of our method is further demonstrated by its ability to pertinently map cell clusters from 1 million cells, 268 cell clusters across 15 diverse plant species. We reveal 14 dominant groups with substantial conservation in shared cell-type markers across monocots and dicots. To facilitate the use of this method by the broad research community, we launch a user-friendly web-based tool called the OMG browser, which simplifies the process of cell-type identification in plant datasets for biologists.

  PublisherOA PDFDOI

• Disease signatures in whole plants and callus culture of Arabidopsis thaliana infected with the fungal plant pathogen Fusarium graminearum

  Plant Cell Tissue and Organ Culture (PCTOC) · 2025-09-01

  articleOpen access

  Abstract There is a growing need for scalable and high-throughput model systems to study plant-pathogen interactions and fungal secondary metabolite production. This research addresses that need by exploring the use of callus culture as a proxy for whole-plant infection dynamics and mycotoxin biosynthesis. Both callus and intact Arabidopsis thaliana plants were inoculated with the fungal pathogen, Fusarium graminearum. Disease progression in plants was evaluated using a visual Fusarium-Arabidopsis Disease (FAD) rating system, while ergosterol, a marker of fungal biomass, was quantified in callus. The mycotoxin, deoxynivalenol, (DON) was measured in both plants and callus. Three A. thaliana accessions with known differences in susceptibility were assessed at 7, 14, and 21 days post-inoculation (DPI). In all greenhouse experiments, inoculated plants exhibited symptoms and signs of infection including mycelial growth, drying, and constriction. The three A. thaliana accessions varied significantly in mean FAD ratings ( P = 0.03), when controlling for timepoint and experiment. DON was detected in flower and seed samples from infected A. thaliana plants. Inoculated calli exhibited symptoms of infection, and DON was measured in some but not all samples. Inconsistent DON detection may reflect detoxification by other fungi or the plants themselves. Mean ergosterol concentrations varied significantly across callus of different accessions ( P = 0.02), when controlling for timepoint and experiment. These findings highlight distinctions in disease markers based on accession-specific susceptibility and time post-inoculation. Collectively, the results support the potential of callus culture as a simplified yet informative system for studying plant-pathogen interactions and developing phytosensors for fungal pathogen detection in the future.

  PublisherOA PDFDOI

• Identifying direct TARGETs of transcription factors in wheat v1

  2025-04-02 · 2 citations

  preprintOpen access

  Transcription factors (TFs) are key regulators of expression of numerous genes. In wheat, many gene networks remain unresolved with the identification of TF target genes being particularly problematic. Methods developed for this purpose are not yet adequate. For example, ChIP-seq requires the use of transgenic plants which is still a lengthy process in wheat, while in vitro techniques such as DAP-seq are not effective on all families of TFs. To overcome these limitations, we have adapted the Arabidopsis thaliana TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) developed by Bargmann et al., 20131, to wheat. This in vivo system uses transformed protoplasts for the rapid, genome-wide identification of the direct targets of TFs.

  PublisherOA PDFDOI

• scCoBench: Benchmarking single cell RNA-seq co-expression using promoter-reporter lines

  Research Square · 2025-08-29

  preprintOpen access
  PublisherOA PDFDOI

• Glow with the Flow: Reproducible Analysis of Transiently Transformed Protoplasts Using Dual Fluorescent Reporters in R

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-29 · 1 citations

  preprintOpen accessCorresponding

  Transient transformation assays using protoplasts have become a widely employed technique in plant research. Positive fluorescent selection was subsequently developed to assess the effect of transient effector gene expression in only successfully transfected cells using flow cytometry. This process, though effective, often requires considerable manual effort and subjective judgment to quantify reporter gene expression in the intended cell populations. To address this, we introduce a new, open-source workflow based on the R programming language. This method enhances the reproducibility and scalability of such experiments, which enable rapid study of gene regulation and signal transduction in plants. This workflow is available at https://github.com/PlantSynBioLab/positive-fluorescence-selection.

  PublisherOA PDFDOI

• Identifying direct TARGETs of transcription factors in wheat v2

  2025-04-02

  preprintOpen access

  Transcription factors (TFs) are key regulators of expression of numerous genes. In wheat, many gene networks remain unresolved with the identification of TF target genes being particularly problematic. Methods developed for this purpose are not yet adequate. For example, ChIP-seq requires the use of transgenic plants which is still a lengthy process in wheat, while in vitro techniques such as DAP-seq are not effective on all families of TFs. To overcome these limitations, we have adapted the Arabidopsis thaliana TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) developed by Bargmann et al., 20131, to wheat. This in vivo system uses transformed protoplasts for the rapid, genome-wide identification of the direct targets of TFs.

  PublisherOA PDFDOI

• Transcriptional Tuning: How Auxin Strikes Unique Chords in Gene Regulation

  Physiologia Plantarum · 2025-04-29 · 2 citations

  reviewOpen accessSenior authorCorresponding

  Auxin is a central regulator of plant growth, development, and responses to environmental cues. How a single phytohormone mediates such a diverse array of developmental responses has remained a longstanding question in plant biology. Somehow, perception of the same auxin signal can lead to divergent responses in different organs, tissues, and cell types. These responses are primarily mediated by the nuclear auxin signaling pathway, composed of ARF transcription factors, Aux/IAA repressors, and TIR1/AFB auxin receptors, which act together to regulate auxin-dependent transcriptional changes. Transcriptional specificity likely arises through the functional diversity within these signaling components, forming many coordinated regulatory layers to generate unique transcriptional outputs. These layers include differential binding affinities for cis-regulatory elements, protein-protein interaction-specificity, subcellular localization, co-expression patterns, and protein turnover. In this review, we explore the experimental evidence of functional diversity within auxin signaling machinery and discuss how these differences could contribute to transcriptional output specificity.

  PublisherOA PDFDOI

• SAMPLS: A Prompt Engineering Approach Using Segment-Anything-Model for PLant Science Research

  Lecture notes in computer science · 2025-01-01

  book-chapter
  PublisherDOI

Recent grants

• Collaborative Research: Hormonal control of stamen filament growth

  NSF · $290k · 2024–2027

Frequent coauthors

• Gabriel Krouk

  Institut des Sciences des Plantes de Montpellier

  49 shared

• Gloria M. Coruzzi

  New York University

  45 shared

• Matthew D. Brooks

  Urbana University

  43 shared

• Kelsey M. Reed

  43 shared

• Ana M. Laxalt

  National University of Mar del Plata

  29 shared

• Bas ter Riet

  The Netherlands Cancer Institute

  28 shared

• Mark Estelle

  University of California, San Diego

  12 shared

• Kenneth D. Birnbaum

  New York University

  11 shared

Labs

• School of Plant and Environmental SciencesPI