A central question in plant biology is whether natural transcriptome variation primarily reflects environmental adaptation or intrinsic genetic programs. Using transcriptomes from 665 natural Arabidopsis thaliana accessions, we show that inherited population structure, not environmental gradients, is the primary organizer of global transcriptome architecture. Genomic population structure uniquely explains 30.0% of transcriptome wide variation, while environmental variables account for only 2.5%. This architecture is dominated by a single co-expression program (proliferation Module Eigengene: prolifME), enriched for cell cycle regulation and ribosome biogenesis, regulated by a bipartite transcription factor architecture, and genetically encoded at discrete loci with broad trans regulatory effects. This proliferation program is associated with reduced plant size, biomass, growth rate and water use efficiency, and these relationships persist under common garden conditions. Gene contributions to this proliferation program are non randomly conserved in rice and maize across 150~200 million years of divergence. These findings identify an intrinsic transcriptional proliferation program as a primary state of plant population transcriptomes, conserved across plant species.

Understanding root system architecture is critical for improving crop productivity and resilience, yet phenotyping root traits such as root growth angle and rooting depth remains technically challenging, especially at high throughput. Here, we present ClearDepthIAS, a high-throughput imaging and analysis platform that enables nondestructive, automated quantification of root architecture traits in taproot system crops. By capturing and stitching 360° images of roots growing along the transparent walls of pots and applying deep learning-based segmentation (ClearDepth-WRT), we measured wall root shallowness (WRS)-a proxy for root growth angle-with high precision. We demonstrated for the tap root systems of soybean and canola that the system accurately detects root tips, quantifies their vertical distribution, and extracts biologically meaningful traits such as root area, distribution indices, and growth angles. Validation experiments in canola and soybean demonstrated that WRS can correlate with root crown architecture in mature plants, both in greenhouse and field settings. Furthermore, WRS and root distribution indices derived from ClearDepthIAS are predictors of early root architecture and can be correlated with root biomass distribution across soil depths under field conditions; however, environmental interactions may influence these relationships and weaken or even negate such correlations, as observed when comparing field to field variation in root system architecture. Our system enables efficient phenotyping of genetically diverse populations, with medium to high trait heritability, supporting its utility for genome-wide association studies and breeding. ClearDepthIAS accelerates the development of root ideotypes for improved resource acquisition and carbon sequestration, offering a scalable tool for supporting climate-resilient agriculture.

Calcium (Ca) availability is vital for optimal plant growth and immune signaling, yet the underlying mechanisms remain elusive. Here, we reveal that Arabidopsis vacuolar H⁺-pyrophosphatase (AVP1)-regulated cytosolic inorganic pyrophosphate (PPi) homeostasis governs leaf growth by maintaining cellulose synthesis to suppress autoimmune activation upon Ca deficiency. Ca deficiency reduces the AVP1 abundance, while AVP1 eliminates excess cytosolic PPi, which impairs guanosine triphosphate-dependent microtubule assembly and reduces cellulose synthase 3-mediated cellulose synthesis. This cell-wall disruption activates isochorismate synthase 1-mediated salicylic acid production, triggering autoimmune responses and inhibiting new leaf growth. Enhancing PPi hydrolysis genetically improves plant growth tolerance to low Ca availability (low-Ca). The link between Ca-dependent PPi metabolic regulation, autoimmunity, and leaf growth is conserved in tomato, highlighting the broad relevance of AVP1 and PPi homeostasis in plant resilience. Our findings offer potential strategies for improving crop tolerance to nutrient-limited environments.

Roots play a central role in plant growth, survival, and fitness and are increasingly recognized as key determinants of crop yield and sustainability traits, including soil carbon sequestration. While extensive research has focused on the regulatory mechanisms of root growth and development, the process of root aging and its impact on root growth has received considerably less attention. This is in part due to the technical challenges of sampling and analyzing older roots. However, growing evidence indicates that root growth often declines with age. In this review, we synthesize current knowledge on the molecular and physiological mechanisms regulating root growth and the mechanisms and effects of root aging, providing a conceptual bridge between 2 processes. Moreover, we discuss potential genetic and synthetic biology approaches and strategies to delay root aging or reactivate growth in old roots and how such interventions could ultimately enhance crop productivity and support plant-based strategies for climate change mitigation.

ABSTRACT Nitrogen is a critical nutrient necessary for plant growth and survival. Plasticity in root architecture helps adapt to soil nitrogen levels for optimal nitrogen uptake; the nitrate form of soil nitrogen is a major modulator of root architecture. Although details of nitrate-regulated primary and lateral root growth are known, nitrate-regulated formation of anchor roots, which arise from the collet, is not understood. In this work, we uncover a role for nitrate in the regulation of anchor root formation. We find that cytokinin inhibits anchor root formation with rising nitrate. These cytokinin effects on anchor root formation rely on regulated indole-3-butyric acid (IBA) to indole-3-acetic acid (IAA) conversion. These data point toward a mechanism by which nitrate controls a previously underappreciated aspect of nitrate-dependent root architecture driven by anchor roots. Summary Statement Elevated nitrate levels promote anchor root formation to alter root growth. In Arabidopsis, cytokinin restricts anchor root formation at elevated nitrate levels through indole-3-butyric acid (IBA) derived auxin.

The symbiotic interaction between soybean (Glycine max) and Bradyrhizobium japonicum results in the formation of root nodules, specialized organs that house nitrogen-fixing bacteria converting atmospheric N2 into plant-accessible ammonia (NH3). Accurate quantification of nodule traits is essential for understanding host–microbe interactions and genetic determinants of nodulation. However, traditional manual or semi-quantitative approaches are labor-intensive, subjective, and unsuitable for large-scale studies. Here, we present a high-throughput phenotyping pipeline based on the YOLO deep learning architecture for the automated detection and extraction of soybean root traits. The pipeline quantifies nodule count, dimensions, and spatial distribution, enabling measurement of 24 distinct nodulation-related traits. Using root images from 21-day-old hydroponically grown soybean plants, the model achieved a precision of 0.94, a recall of 0.95, and an F1 score of 0.94 for nodule detection, maintaining accuracy across count ranges. It processes 50 root images in 37 seconds on a single GPU (45 GB memory), representing a ~227-fold improvement in efficiency compared to manual scoring (~2 h 20 min). As proof of concept, we applied this pipeline in a genome-wide association study (GWAS) using the FarmCPU approach and identified 50 significant SNPs associated with multiple nodulation traits, including novel ones. Several candidate genes linked to these loci suggest potential new regulators of nodulation. This YOLO-based phenotyping framework provides a robust, scalable, and reproducible tool for trait discovery and genetic analysis, advancing research in legume genomics and crop improvement. To promote the adoption of this user-friendly nodulation phenotyping pipeline and to support its further development, we have made all essential resources publicly available at: https://github.com/Salk-Harnessing-Plants-Initiative/soybean-nodule-detection.

Membrane contact sites (MCSs) are fundamental for intracellular communication, but their role in intercellular communication remains unexplored. We show that in plants, plasmodesmata communication bridges function as atypical endoplasmic reticulum (ER)-plasma membrane (PM) tubular MCSs, operating at cell-cell interfaces. Similar to other MCSs, ER-PM apposition is controlled by a protein-lipid tethering complex, but uniquely, this serves intercellular communication. Combining high-resolution microscopy, molecular dynamics, and pharmacological and genetic approaches, we show that cell-cell trafficking is modulated through the combined action of multiple C2 domains transmembrane domain proteins (MCTPs) 3, 4, and 6 ER-PM tethers and phosphatidylinositol-4-phosphate (PI4P) lipid. Graded PI4P amounts regulate MCTP docking to the PM, their plasmodesmata localization, and cell-cell permeability. SAC7, an ER-localized PI4P-phosphatase, regulates MCTP4 accumulation at plasmodesmata and modulates cell-cell trafficking capacity in a cell-type-specific manner. Our findings expand MCS functions in information transmission from intracellular to intercellular cellular activities.

To identify novel genes engaged in plant epidermal development, we characterized the phenotypic variability of rosette leaf epidermis of 310 sequenced Arabidopsis thaliana accessions, focusing on trichome shape and distribution, compositional characteristics of the trichome cell wall, and histologically detectable metal ion distribution. Some of these traits correlated with cLimate parameters of our accession's locations of origin, suggesting environmental selection. A novel metal deposition pattern in stomatal guard cells was observed in some accessions. Subsequent GWAS analysis identified 1546 loci with protein sequence-altering SNPs associated with one or more traits, including 5 genes with previously reported relevant mutant phenotypes and 80 additional genes with known or predicted roles in relevant developmental and cellular processes. Some candidates, including GFS9/TT9, exhibited environmentally correlated allele distribution. Several large gene famiLies, namely DUF674, DUF784, DUF1262, DUF1985, DUF3741, cytochrome P450, receptor-Like kinases, Cys/His-rich C1 domain proteins and formins were overrepresented among the candidates for various traits, suggesting epidermal development-related functions. A possible participation of formins in guard cell metal deposition was supported by observations in available loss of function mutants. Screening of candidate gene lists against the STRING interactome database uncovered several predominantly nuclear protein interaction networks with possible novel roles in epidermal development.

The periderm provides a protective barrier in many seed plant species. The development of the suberized phellem, which forms the outermost layer of this important tissue, has become a trait of interest for enhancing both plant resilience to stresses and plant-mediated CO2 sequestration in soils. Despite its importance, very few genes driving phellem development are known. Employing single-nuclei sequencing, we have generated an expression census capturing the complete developmental progression of Arabidopsis root phellem cells, from their progenitor cell type, the pericycle, through to their maturation. With this, we identify a whole suite of genes underlying this process, including MYB67, which we show has a role in phellem cell maturation. Our expression census and functional discoveries represent a resource, expanding our comprehension of secondary growth in plants. These data can be used to fuel discoveries and engineering efforts relevant to plant resilience and climate change.

Maize (Zea mays L.) is the world's most productive grain crop and a cornerstone of global food supply. However, in temperate agricultural systems, maize exhibits 2 key anomalies. First, as a tropical species, maize cannot be planted in the cold conditions of early spring when light and natural soil nitrogen are available, resulting in a shorter growing season and creating a seasonal mismatch between nitrogen accessibility and demand. Second, maize kernel protein is a major nitrogen sink, driving fertilizer demand because of the scale of cultivation. This inefficient mismatch stems from modern maize's uses and the modest nutritional value of storage proteins. To address these anomalies, we established the Circular Economy that Reimagines Corn Agriculture initiative. Our vision requires advances in 3 research areas: (ⅰ) developing cold and frost tolerance during germination and early growth to enable the use of spring nitrogen and light resources; (ⅱ) reducing nitrogen allocation to grain by reducing low-quality storage proteins and developing alternative nitrogen sinks; and (ⅲ) stabilizing soil nitrogen by enhancing biological nitrification inhibition. We present blueprints for a nitrogen-efficient, cold-tolerant maize designed to utilize the full growing season, enabling farmers in temperate regions to fully leverage maize's C4 photosynthesis, reduce fertilizer inputs, increase yields, and minimize environmental impact.

Endomembrane trafficking (ET) plays a crucial role in plant adaptation to environmental stresses, yet its involvement in endodermal root suberization remains poorly understood. Here, we show that disruption of clathrin-mediated endocytosis (CME) or canonical exocytosis led to an ectopic suberin deposition in the Arabidopsis root endodermis toward the root tip. Genetic disruption of endocytosis phenocopied the effects of the CME inhibitor ES9-17, while genetic disruption of clathrin-independent endocytosis led to reduced suberization, suggesting distinct, pathway-specific roles in regulating suberin deposition. Ectopic suberization upon CME inhibition required the CIFs-SGN3-SGN1-RBOHF/D signaling axis, independent of abscisic acid. Notably, CME disruption led to the accumulation of RBOHF in the plasma membrane, driving NADPH oxidase-dependent H2O2 accumulation in the endodermis. Scavenging H2O2 or inhibiting NADPH oxidases abolished ET disruption-induced suberization, while exogenous H2O2 promoted it. Conversely, peroxidase activity inhibition reduced basal suberization but failed to suppress ET disruption-induced enhanced suberization, implicating reactive oxygen species (ROS) as a dominant driver. Our findings reveal a dual ET regulatory mechanism: exocytosis inhibition leads to suberization independently of known pathways, while CME impairment acts via RBOHF-mediated ROS to increase suberization on the endodermis. This study reveals that ET can control endodermal root suberization in Arabidopsis, linking membrane trafficking to apoplastic barrier formation through reactive oxygen species.

Plants are essential for life as we know it on Earth. They oxygenate the atmosphere, regulate the climate, and comprise much of the primary producers underpinning complex food systems. In the 1980s, a multinational group of plant scientists chose the small angiosperm-Arabidopsis thaliana-to serve as the model flowering plant for genetic and molecular studies that would be leveraged to produce vast new datasets, resources, and tools. The rationale they used to persuade funding agencies to make significant investments and focus intense effort on this single plant species was to produce a deep fundamental knowledge of the biology of plants and to apply this knowledge to valuable, but typically less tractable, plant species. Over the past 40 yr, Arabidopsis has emerged as the most powerful and versatile plant model to uncover core biological principles and served as a prototyping system to test advanced molecular and genetic concepts. We argue that the emerging challenges of accelerating climate instability and a rapidly growing global population call for renewed and robust investments in fundamental plant biology research. Leveraging the power of Arabidopsis research, resources, datasets, and global collaborative community is more important than ever. This commentary lays out a vigorous defense of foundational, i.e. "basic," plant science research; describes that often, Arabidopsis is preferable to working directly in crops; highlights several transformative applications generated from basic plant research; and makes the argument that plant science is vital to the survival of humanity.

While iron (Fe) is essential for life and plays important roles for almost all growth related processes, it can trigger cell death in both animals and plants. However, the underlying mechanisms for Fe-induced cell death in plants remain largely unknown. S-nitrosoglutathione reductase (GSNOR) has previously been reported to regulate nitric oxide homeostasis to prevent Fe-induced cell death within root meristems. Here, we found that in the absence of GSNOR, exposure to high Fe treatment results in DNA damage-dependent cell death specifically in vascular stem cells in root meristems within 48 h. Through a series of time-course transcriptomic analyses, we unveil that in the absence of GSNOR, mitochondrial dysfunction emerges as the most prominent response to high Fe treatment. Consistently, the application of mitochondrial respiratory inhibitors leads to stem cell death in root meristems, and pharmacological blockage of the voltage-dependent anion channel that is responsible for the release of mitochondrial-derived molecules into the cytosol or genetic changes that abolish the ANAC017- and ANAC013-mediated mitochondrial retrograde signaling effectively eliminate Fe-induced stem cell death in gsnor root meristems. We further identify the nuclear transcription factor ANAC044 as a mediator of this mitochondrial retrograde signaling. Disruption of ANAC044 completely abolishes the GSNOR-dependent, Fe-induced stem cell death in root meristems, while ectopic expression of ANAC044 causes severe root stem cell death. Collectively, our findings reveal a mechanism responsible for initiating Fe-induced stem cell death in the root meristem, which is the ANAC044-mediated GSNOR-regulated mitochondrial stress signaling pathway.

Studying the mechanisms that promote deep rooting in crops is crucial for engineering plant varieties with enhanced drought resilience and increased carbon sequestration capacity. Soil compaction is a major constraint on rooting depth, and to overcome this, root system penetrability needs to be enhanced. However, because of the limitations of current methods, phenotyping root penetrability remains a bottleneck. Here, we developed RootXplorer, a computer vision-based 3D phenotyping platform for high-throughput quantification of root penetration-related traits/phenotypes across dicot and monocot species. RootXplorer integrates a novel Phytagel-based cylinder system, a 3D imaging unit, and an automated software pipeline to extract root penetration-related traits with high precision and at a large scale. We demonstrate that RootXplorer enables large-scale diversity screenings in conditions replicating soil compaction effects in multiple species, revealing species-specific strategies for overcoming mechanical impedance. These findings highlight the utility and promise of RootXplorer for accelerating research on root architectural plasticity under controlled compaction conditions, identifying genotypes with varying tolerance to mechanical impedance, and supporting data-driven breeding decisions for developing soil compaction-resilient crop varieties. This technology has important implications for future plant breeding strategies and supports ongoing climate change mitigation efforts.

The Intergovernmental Panel on Climate Change estimates that societies may need to remove 5–16 GtCO _2 from the atmosphere annually to reach global net-zero CO _2 emissions within this century. Yet there has been little analysis of how quickly carbon dioxide removal (CDR) strategies could scale to meet this expected need. We develop a new integrated modeling approach for assessing scalability that combines insights from the history of analogous technological revolutions with information about the efficacy and specific constraints of CDR strategies. We illustrate our approach with genetically enhanced crops that grow larger roots and, in turn, increase soil carbon. Unlike many CDR technologies whose deployment will be slowed by the need for novel and costly infrastructures, history suggests that crop innovations can scale rapidly in countries that admit them. Within 13 years of first deployment, diffusion of enhanced crops could peak and remove 0.9–1.2 GtCO _2 yr ^–1 —about 7 times larger than all CO _2 offsets supplied today to the global voluntary offsets market. Upscaling depends on policy and politics, as they affect the total land area on which carbon-absorbing crops are allowed. Early scaling could allow crop engineering to play an outsized role in a portfolio of CDR strategies that, overall, scales to IPCC-like levels of carbon removal, even though carbon storage in soils is less permanent than geological storage.

Despite its significant relevance to drought adaptation, optimization of nutrient acquisition, and carbon sequestration in soil, genetic factors determining root depth remain poorly explored, mostly due to the limitations of the methods currently available to estimate it. Although several such methods have been developed for crops, their applicability to large-scale studies and those involving smaller, more fragile root systems is severely limited. To address this, we have developed ClearDepth, a simple, non-destructive, low-cost method. In ClearDepth, the root system develops naturally inside the soil in clear pots. As it expands, secondary roots reach the transparent walls of the pot ("wall roots"), becoming visible. The shallowness of each wall root is then measured (wall root shallowness, WRS), and the depth of the root system is expressed as the average of all single WRS measurements. We demonstrated the suitability of ClearDepth for root depth studies using Arabidopsis thaliana and Oryza sativa (rice), two species with contrasting root system architecture (RSA) and root size. The robustness and sensitivity of the WRS trait allow us not only to reproducibly discriminate between shallow and deep root systems but also to detect smaller yet significant differences in depth determined by the influence of environmental factors, such as light. Here, we present a comprehensive protocol for utilizing this method.

The pioneering plant scientist engineered roots for carbon sequestration and passionately advocated on behalf of women. The pioneering plant scientist engineered roots for carbon sequestration and passionately advocated on behalf of women.

Root system architecture (RSA) is central to plant adaptation and fitness, yet the design principles and regulatory mechanisms connecting RSA to environmental adaptation are not well understood. We developed Ariadne, a semi-automated software for quantifying cost-efficiency tradeoffs of RSA by mapping root networks onto a Pareto-optimality framework, which describes the balance between resource transport efficiency and construction cost. Applying Ariadne to Arabidopsis thaliana, we found that root architectures consistently assume Pareto-optimal forms across developmental stages, genotypes, and environmental conditions. Using the Discovery Engine, an engine that combines machine learning together with interpretability techniques, we found developmental stage, the hy5/chl1-5 genotype, and manganese availability as important determinants of the cost-efficiency tradeoff, with manganese exerting a unique influence not observed for other nutrients. These results reveal that RSA plasticity is genetically constrained to cost-efficiency optimal configurations and that developmental and environmental factors shift RSA on the pareto front, with manganese acting as a strong modulator of the transport efficiency and construction cost balance.

Calcium (Ca), an essential macronutrient, is crucial for the growth of young plant tissues, including the formation of lateral roots (LRs) that originate from pericycle cells in the inner root. The Casparian strip (CS) serves as an apoplastic barrier in the root endodermis, optimizing nutrient transport and facilitating plant adaptation to various environments. This study demonstrates that the integrity of the CS regulates local Ca-dependent LR emergence by controlling the lignification of the overlying endodermal cells in Arabidopsis. In mutants with disrupted CS integrity and compensatory lignin deposition, plants require sufficient Ca to maintain auxin gradients and the morphology of LR primordia, thereby promoting LR primordia through the endodermis. Both piperonylic acid treatment and genetic evidence indicate that excessive lignification of the overlying endodermal cells significantly delays LR emergence under low-Ca conditions compared with sufficient Ca. The receptor-like kinase SGN3/GSO1 mediates this excessive lignification. Importantly, the function of the CS in LR emergence is independent of Ca translocation from roots to shoots and, consequently, shoot growth dynamics. Overall, our study highlights the direct involvement of CS integrity in modulating Ca-dependent LR emergence by controlling cell wall stiffness through the lignification of overlying endodermal cells.

Due to global warming, it is important to understand how plants respond to high ambient temperature. Plant growth responses to high ambient temperature are termed thermomophogenesis and have been explored for more than a decade. However, this was mostly focused on the above-ground part of plants, the shoot. In this chapter, we describe a simple method to assess root growth phenotype to high ambient temperatures. In principle, this protocol can be applied for any other treatments to test overall seedling growth.