Root gravitropism is regulated by an auxin gradient, causing the root to reorient downwards with gravity. Transcriptional activator auxin response factors (ARFs), such as ARF5, ARF6, ARF7, ARF8, and ARF19, play key roles in auxin signaling in seedling root tissues. ARF7 and ARF19 are both required for root gravitropism, but their regulatory relationship with each other and other activating ARFs remains unknown. Here, we identify that rapid and transient upregulation of ARF19 during gravitropic stimulus is functionally important. ARF7 and ARF8 are required to activate ARF19 upregulation via auxin response elements (AuxREs) in its promoter, while our data indicate that ARF19 does not self-activate. ARF7 can replace ARF19 but not vice versa. Although ARF7 shares overlapping targets with ARF19, they also have distinct functionally important targets, such as ARF19. Our results show that ARF7 and ARF19 have sub-functionalized, with ARF19 acting as an auxin response enhancer for a subset of ARF7 target genes.

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum , a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

Plant phenotyping increasingly relies on (semi-)automated image-based analysis workflows to improve its accuracy and scalability. However, many existing solutions remain overly complex, difficult to reimplement and maintain, and pose high barriers for users without substantial computational expertise. To address these challenges, we introduce PhenoAssistant: a pioneering AI-driven system that streamlines plant phenotyping via intuitive natural language interaction. PhenoAssistant leverages a large language model to orchestrate a curated toolkit supporting tasks including automated phenotype extraction, data visualisation and automated model training. We validate PhenoAssistant through several representative case studies and a set of evaluation tasks. By significantly lowering technical hurdles, PhenoAssistant underscores the promise of AI-driven methodologies to democratising AI adoption in plant biology.

Plant roots play myriad roles that include foraging for resources in complex soil environments. Within this highly dynamic soil environment roots must sense, interact with, and acclimate to factors such as water availability, microbiota, and heterogeneous distribution of nutrients. To aid their acclimation, roots alter their growth and development to optimize their architecture and actively regulate the physical, chemical, and biological properties of their rhizosphere. Understanding the complex interactions between roots and rhizosphere is critical for designing future crops with improved root traits better adapted to diverse and challenging soil conditions. However, studying roots and their interactions with soil under real-world conditions presents significant challenges. Addressing these challenges demands developing realistic laboratory-based model systems and innovative field-based root imaging techniques. Our review surveys the current knowledge and recent advances in understanding root-environment interactions while proposing future solutions to study roots under more "real-life" soil conditions.

Both chronic and acute drought alter the composition and physiology of soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Currently, little is known about how the resulting precipitation legacy effects manifest at the molecular and physiological levels and how they influence neighboring plants, especially in the context of subsequent drought. We characterized metagenomes of six prairie soils spanning a steep precipitation gradient in Kansas, USA. By statistically controlling for variation in soil porosity and elemental profiles, we identified bacterial taxa and functional gene categories associated with precipitation. This microbial precipitation legacy persisted through a 5-month-long experimental drought and mitigated the negative physiological effects of acute drought for a wild grass species that is native to the precipitation gradient, but not for the domesticated crop species maize. In particular, microbiota with a low-precipitation legacy altered transcription of a subset of host genes that mediate transpiration and intrinsic water use efficiency during drought. Our results show how long-term exposure to water stress alters soil microbial communities with consequences for the drought responses of neighboring plants.

BACKGROUND:The reconstruction of 3-dimensional (3D) plant models can offer advantages over traditional 2-dimensional approaches by more accurately capturing the complex structure and characteristics of different crops. Conventional 3D reconstruction techniques often produce sparse or noisy representations of plants using software or are expensive to capture in hardware. Recently, view synthesis models have been developed that can generate detailed 3D scenes, and even 3D models, from only RGB images and camera poses. These models offer unparalleled accuracy but are currently data hungry, requiring large numbers of views with very accurate camera calibration. RESULTS:In this study, we present a view synthesis dataset comprising 20 individual wheat plants captured across 6 different time frames over a 15-week growth period. We develop a camera capture system using 2 robotic arms combined with a turntable, controlled by a re-deployable and flexible image capture framework. We trained each plant instance using two recent view synthesis models: 3D Gaussian splatting (3DGS) and neural radiance fields (NeRF). Our results show that both 3DGS and NeRF produce high-fidelity reconstructed images of a plant subject from views not captured in the initial training sets. We also show that these approaches can be used to generate accurate 3D representations of these plants as point clouds, with 0.74-mm and 1.43-mm average accuracy compared with a handheld scanner for 3DGS and NeRF, respectively. CONCLUSION:We believe that these new methods will be transformative in the field of 3D plant phenotyping, plant reconstruction, and active vision. To further this cause, we release all robot configuration and control software, alongside our extensive multiview dataset. We also release all scripts necessary to train both 3DGS and NeRF, all trained models data, and final 3D point cloud representations. Our dataset can be accessed via https://plantimages.nottingham.ac.uk/ or https://https://doi.org/10.5524/102661. Our software can be accessed via https://github.com/Lewis-Stuart-11/3D-Plant-View-Synthesis.

Soils are highly heterogeneous and dynamic systems, experiencing a constant flow of plant root exudates and moisture fluctuations that affect nutrient distribution, soil physicochemical properties, and microbial metabolisms. Plant roots adjust their development within the soil matrix (growth, branching, root angle, and anatomical features) by integrating local environmental conditions with physiologically informed signals. These physiological responses and the adaptability of roots are commonly defined as plasticity. Although genetically determined, root plasticity is modulated by local fluctuations in water and nutrient availability, environmental changes, and soil properties as well as by the root-associated microbiota. Roots and their vicinity are colonized by taxonomically and functionally diverse microbial species. Specific members within these communities can establish chemical communication with plants via root-derived signals, thereby tapping into the plant's hormonal and developmental network, influencing root plasticity. Given that most root traits associated with plasticity have been discovered under axenic conditions, our knowledge of the multiple potential mechanisms by which members of the root-associated microbiota modulate root plastic responses is still limited. In this review, we explore the recent progress in this field and identify specific avenues for future research toward advancing molecular and ecological understanding of microbial-mediated root plasticity in terrestrial systems.

SUMOylation is essential in plant and animal cells, but it remains unknown how small ubiquitin-like modifier (SUMO) components act in concert to modify specific targets in response to environmental stresses. In this study, we characterize every SUMO component in the Arabidopsis root to create a complete SUMO Cell Atlas in eukaryotes. This unique resource reveals wide spatial variation, where SUMO proteins and proteases have subfunctionalized in both their expression and subcellular localization. During stress, SUMO conjugation is mainly driven by tissue-specific regulation of the SUMO E2-conjugating enzyme. Stress-specific modulation of the SUMO pathway reveals unique combinations of proteases being targeted for regulation in distinct root tissues by salt, osmotic, and biotic signals. Our SUMO Cell Atlas resources reveal how this posttranslational modification (PTM) influences cellular- and tissue-scale adaptations during root development and stress responses. To our knowledge, we provide the first comprehensive study elucidating how multiple stress inputs can regulate an entire PTM system.

Pearl millet (Pennisetum glaucum) thrives in arid and nutrient-poor environments, establishing its role as a crucial cereal crop for food security in sub-Saharan Africa. Despite its remarkable adaptability, its yields remain below genetic potential, primarily due to limited water and nutrient availability. In this study, we conducted ionomic profiling and genome-wide association studies (GWAS) in field conditions across two growing seasons to unravel the genetic basis of nutrient acquisition in pearl millet. Soil ion content analyses revealed significant differences in nutrient distribution between field sites, while certain ions, such as phosphorus (P) and zinc (Zn), consistently displayed stratified accumulation patterns across years, suggesting stable depth-dependent trends. Evaluation of a genetically diverse panel of inbred lines revealed substantial variation in leaf ion concentrations, with high heritability estimates. Correlations between leaf ion content and root anatomical or agromorphological traits highlighted the intricate interplay between genetic and environmental factors shaping leaf ion accumulation. These analyses also uncovered potential trade-offs in nutrient acquisition strategies. GWAS identified genomic regions associated with leaf ion concentrations, and the integration of genetic and gene expression data facilitated the identification of candidate genes implicated in ion transport and homeostasis. Our findings provide valuable insights into the genetic regulation of nutrient acquisition in pearl millet, offering potential targets for breeding nutrient-efficient and climate-resilient varieties. This study underscores the importance of integrating genetic, physiological, and root architectural traits to enhance agricultural productivity and sustainability in resource-constrained environments.

Pearl millet is a key food security grain crop in the world's drylands due to its tolerance to abiotic stresses. However, its yield remains low and is negatively impacted by climate change. Root phenes are potential targets to improve crop productivity and resilience to environmental stress. However, the sheer number of combinations resulting from interactions of multiple phenes is a challenge for empirical research. In silico approaches are a plausible alternative to assess the utility of different phene combinations in varying states over diverse environmental contexts. Here, we developed an implementation of the functional-structural plant/soil model – OpenSimRoot, for pearl millet in typical sub-Sahelian soil and environmental conditions. Root architectural, anatomical, and physiological parameters were measured using a popular pearl millet variety (Souna 3) and implemented in the model. The above-ground biomass and root length density predicted by the model were similar to data from field trials. The utility of different root phenes was then evaluated for improved phosphorus uptake and plant growth in P deficient soils. Doubled root hair length and density, shallower root angle (-15°) and doubled long lateral root density were found to improve plant growth by 76%, 33% and 33% respectively under low P conditions. Moreover, these phenes showed synergism when combined in silico and led to optimal biomass production in low P supply conditions that resulted in a 75% loss of biomass in the reference variety. Our study suggests that these phenotypes could be targeted to improve biomass production in pearl millet and consequently its yield in low-P availability conditions.

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modeling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including genome-wide association study and quantitative trait loci (QTL) approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding gene PgGRXC9 as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homolog AtROXY19 revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.

BackgroundRoot hairs are single-celled projections on root surfaces, critical for water and nutrient uptake. Here, we describe the first short root hair mutant in wheat (Triticum aestivum L.), identified in a mutagenized population and termed here short root hair 1 (srh1).ResultsWhile the srh1 mutant can initiate root hair bulges, lack of subsequent extension results in very short root hairs. Due to its semi-dominant nature, heterozygous lines displayed intermediate root hair lengths compared to wild-type. Bulked segregant analysis in a BC1F3 segregating population genotyped via exome capture sequencing localized the genetic control of this mutant to a region on the long arm of chromosome 3A. Via RNA sequencing and bioinformatic analysis, we identified two promising candidate genes. The first was a respiratory burst oxidase homolog (RBOH) encoding gene TaNOX3-A, orthologous to RBOH genes controlling root hair elongation in rice (OsNOX3) and maize (ZmRTH5), that carries a missense mutation in a conserved region of the predicted protein. RBOHs are membrane bound proteins that produce reactive oxygen species (ROS) which trigger cell wall extensibility, allowing subsequent root hair elongation. Notably, reduced ROS levels were observed in srh1 root hair bulges compared to wild-type. The second candidate was the calreticulin-3 encoding gene TaCRT3-A, located within the wider srh1 interval and whose expression was significantly downregulated in srh1 root tissues.ConclusionsThe identification of a major effect gene controlling wheat root hair morphology provides an entry point for future optimization of root hair architecture best suited to future agricultural environments.

Pearl millet is a key cereal for food security in drylands but its yield is strongly impacted by drought. We investigated how root anatomical traits contribute to mitigating the effects of vegetative drought stress in pearl millet. We examined associations between root anatomical traits and agronomical performance in a pearl millet diversity panel under irrigated and vegetative drought stress treatments in field trials. The impact of associated anatomical traits on transpiration was assessed using subpanels grown in different soil within a greenhouse. In the field, total metaxylem area was positively correlated with grain weight and its maintenance under drought. In the greenhouse, genotypes with larger metaxylem area grown in sandy soil exhibited a consumerist water use strategy under irrigation, which shifted to a conservative strategy under drought. Water savings was mediated by transpiration restriction under high evaporative demand. This mechanism was dependent on soil hydraulics as it was not observed in peat soil with higher hydraulic conductivity upon soil drying. We propose that water savings under drought, mediated by large metaxylem area and its interaction with soil hydraulics, help mitigate vegetative drought stress. Our findings highlight the role of soil hydraulic properties in shaping plant hydraulics and drought tolerance. ### Competing Interest Statement The authors have declared no competing interest.

Organ loss occurs frequently during plant and animal evolution. Sometimes, non-functional organs are retained through evolution. Vestigial organs are defined as genetically determined structures that have lost their ancestral (or salient) function.1,2,3 Duckweeds, an aquatic monocot family, exhibit both these characteristics. They possess a uniquely simple body plan, variably across five genera, two of which are rootless. Due to the existence of closely related species with a wide diversity in rooting strategies, duckweed roots represent a powerful system for investigating vestigiality. To explore this, we employed a panel of physiological, ionomic, and transcriptomic analyses, with the main goal of elucidating the extent of vestigiality in duckweed roots. We uncovered a progressive reduction in root anatomy as genera diverge and revealed that the root has lost its salient ancestral function as an organ required for supplying nutrients to the plant. Accompanying this, nutrient transporter expression patterns have lost the stereotypical root biased localization observed in other plant species. While other examples of organ loss such as limbs in reptiles4 or eyes in cavefish5 frequently display a binary of presence/absence, duckweeds provide a unique snapshot of an organ with varying degrees of vestigialization in closely related neighbors and thus provide a unique resource for exploration of how organs behave at different stages along the process of loss.

Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.

The role of root phenes in nitrogen (N) acquisition and biomass production was evaluated in 10 contrasting natural accessions of Arabidopsis thaliana L. Seedlings were grown on vertical agar plates with two different nitrate supplies. The low N treatment increased the root to shoot biomass ratio and promoted the proliferation of lateral roots and root hairs. The cost of a larger root system did not impact shoot biomass. Greater biomass production could be achieved through increased root length or through specific root hair characteristics. A greater number of root hairs may provide a low-resistance pathway under elevated N conditions, while root hair length may enhance root zone exploration under low N conditions. The variability of N uptake and the expression levels of genes encoding nitrate transporters were measured. A positive correlation was found between root system size and high-affinity nitrate uptake, emphasizing the benefits of an exploratory root organ in N acquisition. The expression levels of NRT1.2/NPF4.6, NRT2.2, and NRT1.5/NPF7.3 negatively correlated with some root morphological traits. Such basic knowledge in Arabidopsis demonstrates the importance of root phenes to improve N acquisition and paves the way to design eudicot ideotypes.

The challenges of securing future food security will require deployment of innovative technologies to accelerate crop production. Plant phenotyping methods have advanced significantly, spanning low-cost hand-held devices to large-scale satellite imaging. Field-based phenotyping aims to capture plant response to the environment, generating data that can be used to inform breeding and selection requirements. This in turn requires access to multiple representative locations and capacities for collecting useful information. In this paper we identify the current challenges in access to field phenotyping in multiple locations in Europe based on stakeholder feedback. We present a map of current infrastructure and propose opportunities for greater integration of existing facilities for meeting different user requirements. We also review the currently available technology and data requirements for effective multi-location field phenotyping and provide recommendations for ensuring future access and co-ordination. Taken together we provide an overview of the current status of European field phenotyping capabilities and provides a roadmap for their future use to support crop improvement. This provides a wider framework for the analysis and planning of field phenotyping activities for crop improvement worldwide.

Root system architecture (RSA) is important in optimizing the use of nitrogen. High-throughput phenotyping techniques may be used to study root system architecture traits under controlled environments. A root pheno-typing platform, consisting of germination paper-based pouch and wick coupled with image analysis, was used to characterize root seedling traits in 30 landrace-derived bread wheat genotypes and the bread wheat parent Paragon under hydroponic high N (HN) and low N (LN) conditions. In addition, two glasshouse experiments under HN and LN conditions were carried out to measure whole plant performance including flag-leaf photo-synthetic rate, N uptake and biomass per plant for 13 wheat genotypes of which eight were common with those in the root phenotyping hydroponic experiment. There were significant differences in RSA traits between ge-notypes for seminal root number per plant, lateral root number per plant, seminal root length per plant and seminal root angle, with transgressive segregation for landrace-derived lines above the elite parental cultivar Paragon under HN and LN conditions. In the glasshouse experiments, genetic variation in flag-leaf photosynthesis rate was found in landrace-derived genotypes in the range 25.9-33.3 mu mol m- 2 s- 1 under HN and in N uptake in the ranges 0.37-0.48 g N plant-1and 0.21-0.30 g plant-1 under HN and LN conditions, respectively (P < 0.05), with transgressive segregation above Paragon. Plant Nitrogen Nutrition Index also showed transgressive segre-gation in the landrace-derived lines above Paragon under HN and LN conditions. Greater maximum root depth and more lateral roots per plant in the hydroponic screen were each correlated with increased biomass per plant under LN conditions. Results from this study demonstrated genetic variation for seedling RSA traits in landrace-derived lines above the elite parental cultivar Paragon, which potentially could be utilized to improve N-use efficiency in breeding programmes.

Duckweeds are morphologically simplified, free floating aquatic monocots comprising both rooted and rootless genera. This has led to the idea that roots in these species may be vestigial, but empirical evidence supporting this is lacking. Here we show that duckweed roots are no longer required for their ancestral role of nutrient uptake. Comparative analyses of nearly all rooted duckweed species revealed a highly reduced anatomy, with greater simplification in the more recently diverged genus Lemna . A series of root excision experiments demonstrated that roots are dispensable for normal growth in Spirodela polyrhiza and Lemna minor . Furthermore, ionomic analyses of fronds in these two species showed little difference in the elemental composition of plants in rooted versus root-excised samples. In comparison, another free-floating member of the Araceae, Pistia stratiotes , which colonized the aquatic environment independently of duckweeds, has retained a more complex root anatomy. Whilst Pistia roots were not absolutely required for growth, their removal inhibited plant growth and resulted in a broad change in the mineral profile of aerial tissues. Collectively, these observations suggest that duckweeds and Pistia may be different stages along a trajectory towards root vestigialization Given this, along with the striking diversity of root phenotypes, culminating in total loss in the most derived species, we propose that duckweed roots are a powerful system with which to understand organ loss and vestigiality.One sentence summary Through their adaption to the aquatic environment, duckweed roots have progressively become structurally reduced making them an ideal plant model with which to study vestigiality.

The root system architecture (RSA) of a crop has a profound effect on the uptake of nutrients and consequently the potential yield. However, little is known about the genetic basis of RSA and resource adaptive responses in wheat (Triticum aestivum L.). Here, a high-throughput germination paper-based plant phenotyping system was used to identify seedling traits in a wheat doubled haploid mapping population, Savannah×Rialto. Significant genotypic and nitrate-N treatment variation was found across the population for seedling traits with distinct trait grouping for root size-related traits and root distribution-related traits. Quantitative trait locus (QTL) analysis identified a total of 59 seedling trait QTLs. Across two nitrate treatments, 27 root QTLs were specific to the nitrate treatment. Transcriptomic analyses for one of the QTLs on chromosome 2D, which was found under low nitrate conditions, revealed gene enrichment in N-related biological processes and 28 differentially expressed genes with possible involvement in a root angle response. Together, these findings provide genetic insight into root system architecture and plant adaptive responses to nitrate, as well as targets that could help improve N capture in wheat.