About

Professor Siobhan Brady maps the gene networks that regulate the development of plant roots. Comparing these networks in different cell types across different species, including important crops such as tomato and sorghum, reveals how some plants adapt to frequent droughts and other harsh environmental conditions.

Research topics

• Biology
• Ecology
• Cell biology
• Political Science
• Computer Science
• Botany
• Genetics
• Sociology
• Biochemistry
• Engineering ethics
• Public relations
• Engineering

Selected publications

• Cell-specific Na ⁺ accumulation is linked to symplastic transport in tomato leaves

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-29

  articleOpen accessSenior authorCorresponding

  Abstract Soil salinization is a growing global threat that limits crop productivity. To cope with sodium (Na⁺) stress, plants have evolved tolerance mechanisms, including excluding Na⁺ from shoot tissues and tolerating elevated Na⁺ within shoots through tissue- and cellular-level mechanisms. Most current knowledge of Na⁺ accumulation comes from organ- or whole-plant measurements that lack the spatial resolution needed to resolve cellular tolerance mechanisms. Here, we used histological approaches to map leaf Na⁺ distribution in tomato ( Solanum ) species with contrasting salt-tolerance strategies. In the Na⁺-excluding domesticated tomato (cv. M82), Na⁺ was largely confined to the bundle sheath, whereas Na⁺-including wild relatives accumulated Na⁺ throughout the blade mesophyll. Consistent with these cell population-specific Na⁺ patterns, M82, but not S. pennellii , exhibited reduced symplastic transport and plasmodesmal permeability under salt stress. A genetic screen combined with transcriptome profiling implicated Plasmodesmata-Located Protein 1 ( PDLP1 ), a regulator of callose-mediated plasmodesmal closure, in establishing symplastic domains in M82 that restrict Na⁺ movement into the mesophyll. Moreover, PDLP1 expression negatively correlated with mesophyll Na + levels across wild and domesticated tomatoes. Collectively, these results link cellular Na⁺ enrichment patterns to symplastic connectivity and suggest that PDLP1 -mediated regulation of plasmodesmata contributes to leaf-level salt-tolerance strategies. Highlights Cell type-specific Na⁺ accumulation differs between domesticated tomato ( Solanum lycopersicum cv. M82) and its wild relative S. pennellii . Additional salt-tolerant wild tomato relatives exhibit leaf Na⁺ enrichment patterns similar to S. pennellii . Salt stress reduces symplastic transport and plasmodesmal permeability in M82 leaves but not in S. pennellii . An introgression line (IL6-4) between the two tomato species, which carries S. pennellii Plasmodesmata-Located Protein 1 ( SpPDLP1 ), shows S. pennellii -like Na⁺ enrichment patterns. PDLP1 expression shows a negative correlation with mesophyll Na + levels across tomato species.

  PublisherOA PDFDOI

• A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis[OPEN]

  UNC Libraries · 2026-04-11

  articleOpen access

  The cambium and procambium generate the majority of biomass in vascular plants. These meristems constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organization. However, how these functions are specified and integrated is unknown. Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis (<em>Arabidopsis thaliana</em>). Among these interactions was a feedforward loop containing transcription factors WUSCHEL HOMEOBOX RELATED14 (WOX14) and TARGET OF MONOPTEROS6 (TMO6), each of which regulates the expression of the gene encoding a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN4 (LBD4). PXY signaling in turn regulates the WOX14, TMO6, and LBD4 feedforward loop to control vascular proliferation. Genetic interaction between <em>LBD4</em> and <em>PXY</em> suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a mechanism that influences the recruitment of cells into the phloem lineage, and they define the role of PXY signaling in this context in determining the arrangement of vascular tissue.

  PublisherDOI

• Novel repressors of cambium activity in <i>Arabidopsis</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-31

  articleOpen access

  Abstract Wood is the greatest reservoir of terrestrial biomass and an essential carbon sink. Formed of xylem, it is derived from the cambium, a meristematic zone within plant stems from which phloem also forms. In Arabidopsis, cell division within the cambium is promoted by three major factors: auxin, cytokinin, and the TDIF-PXY ligand-receptor pair. Meristems and other stem cell populations are typically regulated by a balance between cell division-promoting factors and those that repress cell division to control meristem size, however few factors with cambium-repressing activity are known. Here we combined transcriptomics and transcriptional network analysis, which led to identification of related homeodomain zinc-finger transcription factors, ATHB23, ATHB30, and ATHB34, that repress cambium activity. These factors inhibit cambium activity by directly binding of promoters from a subset of auxin, cytokinin and TDIF-PXY transcriptional target genes, resulting in attenuation of their transcription. Our findings thus reveal a new mechanism underpinning balanced cambium activity.

  PublisherOA PDFDOI

• Drought drives reversible disengagement of root-mycorrhizal symbiosis

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-27

  preprintOpen access

  Abstract The increasing frequency and severity of droughts pose a major threat to agriculture, food security and ecosystems. Plants respond to water deficit by adjusting growth and metabolism to enhance survival; these adjustments impact the soil microorganisms interacting with plant roots. Plants establish symbiotic relationships with arbuscular mycorrhizal fungi which supply soil nutrients in exchange for carbon metabolites via an intricate dual-species interface within roots. These fungi are dependent upon host-derived photosynthates and are thus potentially vulnerable to plant perturbations during drought. Here, we demonstrate that the plant-mycorrhizal relationship is dynamic when water becomes limiting. During water deficit, rice de-prioritizes nutrient acquisition gene regulatory networks, including its AM symbiotic program, in a strategy conserved with tomato. The fungal symbiont correspondingly represses its growth, undergoing metabolic quiescence, coupled with decommissioning of hyphae within the host’s root. Following re-watering, the host re-engages with its partner fungus, re-invigorating fungal growth and arbuscule establishment. This coordinate, reversible and enduring inter-organismal association may aid host survival under transient stress, but suggests that mutualisms in native and crop plants are potentially fragile in increasingly erratic climates.

  PublisherOA PDFDOI

• Decoding nitrogen uptake efficiency in maize and sorghum: insights from comparative gene regulatory networks

  The Plant Journal · 2025-12-01

  articleOpen access

  Nitrogen (N) is an essential macronutrient for plant growth and yield, yet optimizing nitrogen use efficiency remains a challenge in agriculture. To better understand the regulatory basis of plant responses to N availability, we constructed a maize-specific nitrogen uptake efficiency gene regulatory network (mNUEGRN) comprising 1625 protein-DNA interactions (PDI) between 70 promoters and 301 transcription factors using enhanced yeast one-hybrid assays. We also projected a sorghum NUE GRN (spNUEGRN) based on maize orthologs and analyzed N-responsive subnetworks in both species using transcriptome profiling under N stress of early deprivation and recovery. Cross-species comparison with an existing Arabidopsis GRN revealed about 18% conserved interaction, corresponding to 11% of the mNUEGRN, particularly within the nitrate assimilation pathways. Notably, bZIP18 and bZIP30 emerged as central regulators in mNUEGRN, forming highly connected feed-forward loops (FFLs). From our time series data, we identified 19 236 and 23 864 differentially expressed genes in maize and sorghum, respectively. Gini correlation analysis uncovered 764 and 638 FFLs in mNUEGRN and spNUEGRN, respectively, of which 22 FFLs in maize and 35 in sorghum were identified in both leaf and root for each species. These FFLs may represent candidate regulatory motifs that contribute to modulating transcriptional responses under fluctuating N conditions, but their potential roles require further investigation. Together, our findings reveal evolutionarily conserved and species-specific regulatory strategies that mediate early N responsiveness, offering a foundation for engineering crops with improved NUE.

  PublisherOA PDFDOI

• Disentangling the importance of microbiological and physico-chemical properties of Ethiopian field soils for the Striga seed bank and sorghum infestations

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-04

  preprintOpen accessSenior authorCorresponding

  Abstract Striga hermonthica (Striga) is a parasitic weed that severely affects sorghum yields in sub-Saharan Africa. Recent studies highlighted the soil microbiome’s potential to suppress Striga through interference with specific stages in its life cycle. In this study, meta-analysis of 48 Ethiopian field soils revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga field occurrence. Striga infestation of sorghum and soil seedbank levels were negatively correlated with clay content and the nutrients potassium, sulfur, calcium, and carbon. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial compositions even in soils where Striga was not detected. Specific fungal and bacterial genera showed both positive and negative correlations with Striga measures, but patterns rarely held across taxonomic levels, highlighting the complexity of microbiome–Striga interactions. To begin to validate these correlations, we tested an isolate from the fungal genus Neocosmospora , which negatively correlated with the Striga seedbank, and showed that this isolate promotes Striga seed germination in vitro , suggesting potential for biological control of Striga. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil-Striga interactions.

  PublisherOA PDFDOI

• Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants

  The Plant Cell · 2025-05-01 · 26 citations

  reviewOpen access

  Research in Arabidopsis thaliana has a powerful influence on our understanding of gene functions and pathways. However, not everything translates from Arabidopsis to crops and other plants. Here, a group of experts consider instances where translation has been lost and why such translation is not possible or is challenging. First, despite great efforts, floral dip transformation has not succeeded in other species outside Brassicaceae. Second, due to gene duplications and losses throughout evolution, it can be complex to establish which genes are orthologs of Arabidopsis genes. Third, during evolution Arabidopsis has lost arbuscular mycorrhizal symbiosis. Fourth, other plants have evolved specialized cell types that are not present in Arabidopsis. Fifth, similarly, C4 photosynthesis cannot be studied in Arabidopsis, which is a C3 plant. Sixth, many other plant species have larger genomes, which has given rise to innovations in transcriptional regulation that are not present in Arabidopsis. Seventh, phenotypes such as acclimation to water stress can be challenging to translate due to different measurement strategies. And eighth, while the circadian oscillator is conserved, there are important nuances in the roles of circadian regulators in crop plants. A key theme emerging across these vignettes is that even when translation is lost, insights can still be gained through comparison with Arabidopsis.

  PublisherDOI

• A Way to Interact with the World: Complex and Diverse Spatiotemporal Cell Wall Thickenings in Plant Roots

  Annual Review of Plant Biology · 2025-01-02 · 12 citations

  reviewOpen accessSenior author

  Plant cells are defined by their walls, which, in addition to providing structural support and shape, are an integral component of the nonliving extracellular space called the apoplast. Cell wall thickenings are present in many different root cell types. They come in a variety of simple and more complex structures with varying composition of lignin and suberin and can change in response to environmental stressors. The majority of these root cell wall thickenings and cell types that contain them are absent in the model plant Arabidopsis thaliana despite being present in most plant species. As a result, we know very little regarding their developmental control and function. Increasing evidence suggests that these structures are critical for responding to and facilitating adaptation to a wide array of stresses that a plant root experiences. These structures function in blocking apoplastic transport, oxygen, and water loss and enhancing root penetrative strength. In this review, we describe the most common types of cell wall thickenings in the outer cell types of plant roots—the velamen, exodermal thickenings, the sclerenchyma, and phi thickenings. Their cell type dependency, morphology, composition, environmental responsiveness, and genetic control in vascular plants are discussed, as well as their potential to generate more stress-resilient roots in the face of a changing climate.

  PublisherDOI

• Transcription factors SlMYB41, SlMYB92, and SlWRKY71 regulate gene expression in the tomato exodermis

  Journal of Experimental Botany · 2025-04-08 · 9 citations

  articleOpen access

  Root barrier cell types, such as the endodermis and exodermis, are crucial for plant acclimation to environmental stresses. Deposition of suberin, a hydrophobic polymer, in these cell layers restricts the movement of molecules and plays a vital role in stress responses. This study investigates the role of SlMYB41, SlMYB92, and SlWRKY71 transcription factors (TFs) in regulating suberin biosynthesis in the tomato (Solanum lycopersicum) root exodermis by genetic perturbation. Genetic perturbation of these TFs altered exodermal suberin deposition patterns, indicating the SlMYBs as positive regulators and SlWRKY71 as a negative regulator of suberization. RNA sequencing revealed a significant overlap between differentially expressed genes regulated by these TFs, suggesting a shared regulatory network. Gene set enrichment analyses highlighted their role in lipid and suberin biosynthesis as well as over-representation of exodermis-enriched transcripts. Furthermore, transactivation assays demonstrated that these two MYBs promote the expression of suberin-related genes, while SlWRKY71 represses them. These results indicate a complex antagonistic relationship, advancing our understanding of the regulatory mechanisms controlling exodermis suberization in tomato roots.

  PublisherOA PDFDOI

• Developing future resilience from signatures of adaptation across the sorghum pangenome

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-06 · 1 citations

  preprintOpen access

  While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum, and many other crops that were not homogenized during the green revolution, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.

  PublisherOA PDFDOI

Recent grants

• RCN: Arabidopsis Research and Training for the 21st century (ART-21)

  NSF · $615k · 2015–2025

• Identification of Loci Regulating Root Architecture in Tomato

  NSF · $602k · 2011–2015

Frequent coauthors

• Philip N. Benfey

  Duke University

  85 shared

• Kaisa Kajala

  University of California, Davis

  36 shared

• David A. Orlando

  30 shared

• Julia Bailey‐Serres

  Utrecht University

  29 shared

• Shuang Song

  Syngenta (United States)

  25 shared

• Kanwarpal S. Dhugga

  Centro Internacional de Mejoramiento de Maíz Y Trigo

  25 shared

• J. Antoni Rafalski

  25 shared

• Allison Gaudinier

  University of California, Berkeley

  24 shared

Labs

• Brady LabPI