Siobhan Mary Brady

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 moderately salt-tolerant, Na+-excluding domesticated tomato (cv. M82), Na+ was largely confined to the bundle sheath, whereas in salt-tolerant, Na+-including wild relatives, Na+ accumulated throughout the blade mesophyll. Consistent with these cell population-specific Na+ patterns, M82, but not Solanum pennellii, exhibited reduced symplastic transport and plasmodesma permeability under salt stress. A genetic screen combined with transcriptome profiling implicated Plasmodesmata-Located Protein 1 (PDLP1), a regulator of callose-mediated plasmodesma closure, in establishing symplastic domains in M82 that restrict Na+ movement into the mesophyll. Moreover, PDLP1 expression was 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.

Root anatomical barriers, including the suberized and lignified walls of the endodermis and exodermis, and cortical aerenchyma, regulate water and nutrient transport, gas exchange, and rhizosphere interaction. Their adaptive function places them as an important target for breeding environmentally resilient plant species. Quantifying these structures at high resolution is a manual bottleneck that limits experimental scale. We present RADIX (Root Anatomy Deep- learning Image segmentation across species and platforms), a framework that adapts a large self-supervised vision-transformer foundation encoder (DINOv3), pre-trained on billions of natural images, to root anatomy by fine-tuning its encoder with a dense-prediction-transformer decoder. Transferring these general-purpose vision encoders to a specialized biological domain with a high-quality annotated dataset is what allows RADIX to generalize across species and imaging platforms. We train and evaluate it on the first expert-annotated benchmark of root anatomical structures at scale, comprising 1,695 high-quality fluorescence images spanning 17 monocot and dicot species, six anatomical structures, and three imaging platforms. RADIX segments all six structures at inter-annotator-level accuracy and generalizes to unseen species, genotypes, growth conditions, and an imaging platform from an independent laboratory. A single unified model surpasses monocot- and dicot-specialist models without sacrificing in-group accuracy. Predicted masks yield aerenchyma and suberin/lignin measurements matching expert annotation at ∼1.2 s per image with a single GPU, reducing weeks of manual analysis to minutes. Applying RADIX across genotypes, microbial treatments, and growth systems, we show that these cell type features form a coordinated, multidimensional, and context-dependent system shaped by genetic and environmental factors.

Background: Striga hermonthica ( Striga ) is a parasitic weed that severely affects sorghum yield in sub-Saharan Africa. Recent studies highlighted the soil microbiome’s potential to suppress Striga through interference with specific stages in its life cycle. Results: Statistical analyses of data collected from 48 Ethiopian sorghum field soils sampled across a > 1000-km-transect revealed that microbial communities and their interactions with soil physico-chemical properties correlated with Striga occurrence in the field. Striga infestation of sorghum and seedbank levels were negatively correlated with potassium and sulfur soil content and positively correlated with calcium and magnesium nutrient profile proportions. Microbiome analyses indicated that fungal communities were more responsive than bacteria to changes in Striga infestation and seedbank levels, with distinct microbial composition 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. 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. The data and analysis methods are integrated and shared in a public Shiny App for broader analysis and continued research on soil- Striga interactions. Conclusions: This study highlights the complexity of soil-microbiome- Striga interactions and the potential for observational studies to reveal candidates for biological control of Striga .

Nitrate induces widespread transcriptional reprogramming in plants, but how transcription factors coordinate these responses across cell types and evolve across species with divergent root patterning remains unclear. Using single-cell transcriptomics in Arabidopsis thaliana and Solanum lycopersicum (tomato) under varying nitrate conditions, we demonstrate that many transcriptional responses are cell type and developmental stage-specific. Arabidopsis NIN-LIKE PROTEIN 7 (NLP7) directly modulates both broadly expressed and cell-type-specific targets, but is not required to establish the cell type specific nature of these patterns. Comparative analysis reveals evolutionary shifts; key nitrogen programs are localized to different cell types in tomato, with the exodermis as a major regulatory hub. Identification of tomato NLP7a and NLP7b direct targets at cellular resolution supports their role in direct modulation of cell type N-transcriptional programs. This is evidenced by NLP7-controlled exodermal cell wall remodeling in low nitrate, highlighting functional conservation despite divergent cellular topographies.

Nitrogen (N) is an essential macronutrient and its bioavailability plays a major role in tuning plant development to the environmental nutrient status. To find novel factors in early root system architecture responses to N conditions, we performed Arabidopsis thaliana root transcriptome profiling of a short-term time course in limiting and sufficient N conditions. Using this data, we inferred transcriptional regulatory networks in each condition, which revealed the N-condition specific jasmonate responses. We found that the transcription factor (TF) ERF107 plays a generalized role in lateral root development while LBD13 is specific to N-limiting conditions. Further, we used a lateral root single-cell-identity specific transcriptome dataset to model the roles of TFs in early stages of lateral root development. We linked the N time course transcriptomics, lateral root mutant phenotypes and cell type-specific profiling approaches to find and test the roles of TFs that are involved in early root patterning responses to N conditions.

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.

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops¹, like that of the grain and bioenergy crop sorghum^2,3,4,5, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets⁶. Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

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.

SUMMARY: 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.