Poonam Mehra

Single-cell and spatial transcriptomics are transforming our ability to understand how crop roots respond to soil stress by resolving gene expression at cellular resolution within intact tissues. This is particularly important because roots grow in heterogeneous soil environments, where physical structure, mechanical impedance, water availability, and nutrient distribution vary at fine spatial and temporal scales. Such complexity generates dynamic and localized stress signals that cannot be captured by bulk transcriptomics. The logic of applying these approaches lies in linking soil structure and stress gradients to cell-specific transcriptional responses that ultimately regulate root growth. While recent advances have enabled single-cell atlases in several crop species and emerging spatial transcriptomic datasets, most studies have been conducted under simplified conditions (e.g. gels, hydroponics, artificial chemical treatments), only few studies are adopting soil stresses. Despite this progress, major gaps remain, including the need for true in-situ spatial maps in intact agriculture soil systems, integration with temporal dynamics of root growth, and coupling transcriptional data with local measurements of water status, mechanical stress, gaseous diffusion, microbial assembly and nutrient gradients. Addressing these challenges will be essential to capture the full complexity of root responses and to translate cell-level transcriptional dynamics under realistic soil stress conditions.

Vascular plants rapidly coordinate root and shoot responses to water stress. Abscisic acid (ABA) mediates these adaptations; however, it remains unclear which cells produce ABA, whether ABA synthesis shifts during stress, and whether ABA movement is required for its adaptive functions. Here, we map ABA biosynthesis at cellular resolution in Arabidopsis and report that water-stress adaptive responses in roots and shoots require movement of ABA and its precursor AB-aldehyde from vascular tissues to target cells. We suggest that ABA accumulation arises from two parallel routes: (i) ABA synthesized in the vasculature via ABA2 and AAO3, then moving to guard cells, and (ii) phloem-derived AB-aldehyde being converted to ABA in the epidermis or bundle sheath by AAO1 and AAO2. Finally, we predict that tightly packed cells beneath leaf veins facilitate efficient ABA delivery to guard cells, an anatomical arrangement that has enabled angiosperms to evolve the use of ABA to rapidly close stomata.

Reactive oxygen species (ROS) function as key signals in plant adaptation to environmental stresses, such as drought. Roots respond to transient water unavailability by temporarily ceasing branching through the acclimative response xerobranching. In this study, we report how a xerobranching stimulus triggers rapid changes of ROS levels in root nuclei, triggering redox-dependent multimerization of the auxin repressor protein IAA3. Mutations in specific cysteine residues of IAA3 disrupt redox-mediated multimerization and interaction with co-repressor TPL, thereby attenuating IAA3-mediated target gene repression. Other AUX/IAA proteins also vary in their redox-mediated multimerization, which reveals a regulatory mechanism that connects dynamic changes in cellular redox status to auxin signaling. Our study reveals how ROS, auxin, and water availability intersect and shape root adaptive responses, thereby maintaining phenotypic plasticity in plants.

The emergence of molecular biology, along with the use of Arabidopsis thaliana as a model organism, has significantly enhanced our understanding of plant development. Research on Arabidopsis has led to the identification of key regulatory genes involved in various developmental processes. In the past decade, advances in genome sequencing and the decoding of numerous plant genomes have enabled the application of these findings from Arabidopsis to crop species. In this review, leading plant scientists summarize historical insights gained from arabidopsis studies and highlight their implications for crop development, with the aim of inspiring further research in these promising new areas.

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.

Water stress presents a critical challenge affecting plant growth and agricultural productivity, with drought alone causing substantial yield losses. Roots serve as the primary site for water uptake, enabling plants to detect water stress by sensing changes in soil moisture levels. This initial perception prompts roots to initiate a spectrum of adaptive responses at morphological, anatomical, and biochemical levels. In addition to coping with severe water stress conditions such as drought, roots also respond to microscale variations in water availability within the rhizosphere as they navigate through soil, exhibiting responses such as hydrotropism, xerobranching, and hydropatterning. These adaptive responses are orchestrated by dynamic and sophisticated sensing and signalling mechanisms mediated by plant hormones at the cellular level. This review explores recent advances in our understanding of root responses to water stress, emphasizing the hormonal mechanisms underpinning these adaptations. Furthermore, it outlines future perspectives aimed at enhancing crop resilience to water stress through improved understanding and manipulation of root–water interactions.

Phosphate (Pi) deficiency leads to the induction of purple acid phosphatases (PAPs) in plants, which dephosphorylates organic phosphorus complexes in the rhizosphere and intracellular compartments to release Pi. In this study, we demonstrate that OsPAP3b belongs to group III low molecular weight PAP, and is low Pi responsive, preferentially in roots. The expression of OsPAP3b is negatively regulated with Pi re-supply. Interestingly, OsPAP3b was found to be dual localized to the nucleus and secretome. Furthermore, OsPAP3b is transcriptionally regulated by OsPHR2 as substantiated by DNA-protein binding assay. Through in-vitro biochemical assays, we further demonstrate that OsPAP3b is a functional acid phosphatase with broad substrate specificity. Overexpression of OsPAP3b in rice led to increased secreted APase activity and improved mineralization of organic P sources, reflected in better growth of transgenics compared to wild type when grown on organic P as exogenous P substrate. Under Pi deprivation, OsPAP3b knockdown and knockout lines showed no significant changes in total P content and dry biomass. However, the expression of other phosphate starvation-induced (PSI) genes and the levels of metabolites were found to be altered in the overexpression and knockdown lines. In addition, in-vitro pull-down assay revealed multiple putative interacting proteins of OsPAP3b. Our data collectively suggest that OsPAP3b can aid in organic P utilization in rice. The APase isoforms behavior and nuclear localization indicate its additional role, possibly in stress signaling. Considering its important roles, OsPAP3b could be a potential target for improving low Pi adaptation in rice.

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.