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.

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.

Abstract 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.

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 sorghum2-5, 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.

Abstract 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.

Branched broomrape (Phelipanche ramosa) is an obligate root parasitic weed that threatens tomato production in many regions. Progress in understanding host resistance mechanisms has been hindered by the parasite's subterranean life cycle and the technical limitations of traditional soil-based assays. Here, we introduce an integrated experimental framework that enables molecular, genetic, and cellular analysis of broomrape parasitism in tomato under controlled conditions. We implemented a transparent, soil-less co-cultivation system for non-destructive, real-time monitoring of broomrape development on tomato roots, and a dual-compartment in vitro co-culture system supporting parasite infection of transgenic hairy roots. This methodology enabled rapid functional testing of candidate host resistance genes, exemplified by CRISPR-edited mutants of the tomato transcription factor SCHIZORIZA (SlSCZ), which displayed localized lignin accumulation at the parasite entry site in the root. The observed lignification suggests a role for this gene in regulating inducible cell wall lignification against broomrape. Together, these tomato-focused integrated methods enable reproducible imaging, genetic perturbation, and high-resolution analysis of host-parasite interfaces. These provide a scalable platform for dissecting broomrape resistance and accelerating resistance gene discovery in tomato and a critical tool for combating the devastating consequences of this parasite on agriculture.

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.

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. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, IOS-211980, DGE-1922642 National Institute of Food and Agriculture, 2019-67013-29313, 2022-67012-36716, 1026477

Plant roots dynamically respond to nitrogen availability by executing a signaling and transcriptional cascade resulting in altered plant growth that is optimized for nutrient uptake. The NIN-LIKE PROTEIN 7 (NLP7) transcription factor senses nitrogen and, along with its paralog NLP6, partially coordinates transcriptional responses. While the post-translational regulation of NLP6 and NLP7 is well established, their upstream transcriptional regulation remains understudied in Arabidopsis (Arabidopsis thaliana) and other plant species. Here, we dissected a known sub-circuit upstream of NLP6 and NLP7 in Arabidopsis, which was predicted to contain multiple multi-node feedforward loops suggestive of an optimized design principle of nitrogen transcriptional regulation. This sub-circuit comprises AUXIN RESPONSE FACTOR 18 (ARF18), ARF9, DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 26 (DREB26), Arabidopsis NAC-DOMAIN CONTAINING PROTEIN 32 (ANAC032), NLP6 and NLP7 and their regulation of NITRITE REDUCTASE 1 (NIR1). Conservation and divergence of this circuit and its influence on nitrogen-dependent root system architecture were similarly assessed in tomato (Solanum lycopersicum). The specific binding sites of these factors within their respective promoters and their putative cis-regulatory architectures were identified. The direct or indirect nature of these interactions was validated in planta. The resulting models were genetically validated in varying concentrations of available nitrate by measuring the transcriptional output of the network revealing rewiring of nitrogen regulation across distinct plant lineages.

Plants are essential for human survival. Over the past three decades, work with the reference plant Arabidopsis thaliana has significantly advanced plant biology research. One key event was the sequencing of its genome 25 years ago, which fostered many subsequent research technologies and datasets. Arabidopsis has been instrumental in elucidating plant-specific aspects of biology, developing research tools, and translating findings to crop improvement. It not only serves as a model for understanding plant biology and but also biology in other fields, with discoveries in Arabidopsis also having led to applications in human health, including insights into immunity, protein degradation, and circadian rhythms. Arabidopsis research has also fostered the development of tools useful for the wider biological research community, such as optogenetic systems and auxin-based degrons. This 4th Multinational Arabidopsis Steering Committee Roadmap outlines future directions, with emphasis on computational approaches, research support, translation to crops, conference accessibility, coordinated research efforts, climate change mitigation, sustainable production, and fundamental research. Arabidopsis will remain a nexus for discovery, innovation, and application, driving advances in both plant and human biology to the year 2030, and beyond.

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.

Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.

Plant roots integrate environmental signals with development using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates flow of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation but is absent in the tomato endodermis. Instead, suberin is present in the exodermis, a cell type that is absent in the model organism Arabidopsis thaliana . Here we demonstrate that the suberin regulatory network has the same parts driving suberin production in the tomato exodermis and the Arabidopsis endodermis. Despite this co-option of network components, the network has undergone rewiring to drive distinct spatial expression and with distinct contributions of specific genes. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response and that the exodermal barrier serves an equivalent function to that of the endodermis and can act in its place.

Wood constitutes the largest reservoir of terrestrial biomass. Composed of xylem, it arises from one side of the vascular cambium, a bifacial stem cell niche that also produces phloem on the opposing side. It is currently unknown which molecular factors endow cambium stem cell identity. Here we show that TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) ligand-activated PHLOEM INTERCALATED WITH XYLEM (PXY) receptors promote the expression of CAMBIUM-EXPRESSED AINTEGUMENTA-LIKE (CAIL) transcription factors to define cambium stem cell identity in the Arabidopsis root. By sequestrating the phloem-originated TDIF, xylem-expressed PXY confines the TDIF signaling front, resulting in the activation of CAIL expression and stem cell identity in only a narrow domain. Our findings show how signals emanating from cells on opposing sides ensure robust yet dynamically adjustable positioning of a bifacial stem cell layer.

Plants shed organs such as leaves, petals, or fruits through the process of abscission. Monitoring cues such as age, resource availability, and biotic and abiotic stresses allow plants to abscise organs in a timely manner. How these signals are integrated into the molecular pathways that drive abscission is largely unknown. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) gene is one of the main drivers of floral organ abscission in Arabidopsis and is known to transcriptionally respond to most abscission-regulating cues. By interrogating the IDA promoter in silico and in vitro, we identified transcription factors that could potentially modulate IDA expression. We probed the importance of ERF- and WRKY-binding sites for IDA expression during floral organ abscission, with WRKYs being of special relevance to mediate IDA up-regulation in response to biotic stress in tissues destined for separation. We further characterized WRKY57 as a positive regulator of IDA and IDA-like gene expression in abscission zones. Our findings highlight the promise of promoter element-targeted approaches to modulate the responsiveness of the IDA signaling pathway to harness controlled abscission timing for improved crop productivity.

Plant roots navigate the soil ecosystem with each cell type uniquely responding to environmental stimuli. Below ground, the plant's response to its surroundings is orchestrated at the cellular level, including morphological and molecular adaptations that shape root system architecture as well as tissue and organ functionality. Our understanding of the transcriptional responses at cell type resolution has been profoundly enhanced by studies of the model plant Arabidopsis thaliana. However, both a comprehensive view of the transcriptional basis of these cellular responses to single and combinatorial environmental cues in diverse plant species remains elusive. In this review, we highlight the ability of root cell types to undergo specific anatomical or morphological changes in response to abiotic and biotic stresses or cues and how they collectively contribute to the plant's overall physiology. We further explore interconnections between stress and the temporal nature of developmental pathways and discuss examples of how this transcriptional reprogramming influences cell type identity and function. Finally, we highlight the power of single-cell and spatial transcriptomic approaches to refine our understanding of how environmental factors fine tune root spatiotemporal development. These complex root system responses underscore the importance of spatiotemporal transcriptional mapping, with significant implications for enhanced agricultural resilience.

The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank'of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.

Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root’s response to abiotic and biotic stimuli. In tomato roots, the exodermis forms a genetically distinct polar lignin cap (PLC) barrier from the Casparian strip. SlSCZ and SlEXO1 repress PLC deposition in inner layers. The PLC cannot fully compensate for the CS as a mineral ion barrier.

An archetype of collaboration, community development and vision, who made fundamental contributions to biology through his studies on the often-unseen part of the plant, the root.

The root parasitic weed Striga hermonthica has a devastating effect on sorghum and other cereal crops in Sub-Saharan Africa. Available Striga management strategies are rarely sufficient or not widely accessible or affordable. Identification of soil- or plant-associated microorganisms that interfere in the Striga infection cycle holds potential for development of complementary biological control measures. Such inoculants should be preferably based on microbes native to the regions of their application. We developed a method to assess microbiome-based soil suppressiveness to Striga with a minimal amount of field-collected soil. We previously used this method to identify the mechanisms of microbe-mediated suppression of Striga infection and to test individual microbial strains. Here, we present protocols to assess the functional potential of the soil microbiome and individual bacterial taxa that adversely affect Striga parasitism in sorghum via three major known suppression mechanisms. These methods can be further extended to other Striga hosts and other root parasitic weeds.