Alongside biosynthesis and transport, inactivation regulates indole-3-acetic acid (IAA) concentration, a compound with numerous functions in plant development. The main inactive IAA metabolites are oxidised forms and ester- or amide-linked conjugates. DIOXYGENASE FOR AUXIN OXIDATION1 (DAO1) and DAO2, 2-oxoglutarate and iron-dependent dioxygenases, contribute to IAA oxidative inactivation with group II GRETCHEN HAGEN3 (GH3) IAA-amido synthetases, while UDP-glycosyltransferases (UGTs) conjugate IAA to sugars. To study IAA inactivation routes, we generated combinatorial Arabidopsis mutants between all group II GH3s (gh3oct) and DAO1 or DAO2, and between DAOs and the main UGTs. In vivo [13C6]IAA feeding experiments traced exogenously applied IAA's metabolic fate, supporting the main IAA inactivation pathway where DAOs act downstream of GH3s. Results from these experiments also indicated UGT-mediated IAA glycosylation is more important than previously assumed for modulating IAA levels and plant development. Our metabolic and transcriptomic data revealed that gh3oct may still retain some GH3 activity, explaining previously reported phenotypic inconsistencies. Our data additionally suggest that unidentified metabolic activities might play a role in IAA overproducing plants, and that premature downregulation of flowering time regulators like FLOWERING LOCUS C (FLC) likely underlies early flowering of gh3oct and gh3oct dao1-6 plants.

Modern crop breeding and seed certification agencies ignore the known spatial heterogeneity of soils and develop cultivars to thrive in a ‘one-size-fits-all’ soil environment. Neglecting the evolving dynamics of soils substantially undermines the capacity of new genotypes to deliver optimal yield and stress resilience, and requires urgent consideration in future plant breeding programmes.

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.

Plant processes regulating the quantity and quality of soil organic carbon inputs such as photosynthesis, above- and below-ground plant growth, and root exudation are integral to our understanding of soil carbon dynamics. However, based on a bibliometric analysis including more than 55 000 scientific papers, we found that plant physiology has been severely underrepresented in global soil organic carbon research. Less than 10 % of peer-reviewed soil organic carbon research published in the last century addressed plant physiological processes relevant to soil carbon inputs. Similarly, plant physiology was overlooked by the overwhelming majority (>90 %) of the peer-reviewed literature investigating linkages between soil organic carbon, climate change, and land use and land management. These findings show that our understanding of both soil carbon dynamics and the carbon sequestration potential of terrestrial ecosystems is largely built on research that neglects the fundamental processes underlying organic carbon inputs. We maintain that the active engagement of plant scientists in soil carbon research is imperative for shedding light on this blind spot. Long-term interdisciplinary research will be essential for developing a comprehensive perspective of soil carbon dynamics and informing and designing effective policies that support soil carbon sequestration.

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.

Agricultural intensification coupled with changing climate are causing soils to become increasingly vulnerable to stresses such as drought, soil erosion, and compaction. The mechanisms by which roots detect and respond to soil stresses remain poorly understood. Recent breakthroughs show that roots release volatile and soluble hormone signals into the surrounding soil, then monitor their levels to sense soil stresses. Our review discusses how hormones can act 'outside the plant' as 'rhizocrine' signals that function to improve plant resilience to different soil stresses. We also propose a novel signalling paradigm which we term 'root RADAR' where 'rhizocrine' levels change in soil in response to environmental stresses, feeding back to roots and triggering adaptive responses.

Soil stresses impact crop yields, presenting global agricultural challenges. Soil compaction triggers root length reduction and radial expansion driven by the plant hormone ethylene. We report how ethylene controls cell wall properties to promote root radial expansion. We demonstrate how soil compaction stress, via ethylene, upregulates Auxin Response Factor1 in the root cortex, which represses Cellulose Synthase (CESA) genes. CESA repression drives radial expansion of root cortical cells by modifying the thickness and mechanics of their cell walls, which result in a "stiff epidermis-soft cortex" contrast. Our research thus connects ethylene signaling with root mechanics via cell wall strength, and reveals how dynamic regulation of cellulose synthesis crucially controls root growth in compacted soil. ### Competing Interest Statement The authors have declared no competing interest.

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.

Auxin-mediated root gravitropism critically determines root angle, a key trait that underpins root system architecture (RSA). Auxin response factors (ARFs) regulate this process, but their downstream targets and functions remain unclear. We demonstrate that OsARF12 and OsARF25 induce cell wall thickness in epidermal cells of the lower side of the root, positioning auxin as a "break" of these cells during gravistimulation by directly regulating Increased Leaf Angle1 (OsILA1) through a dual set of auxin response elements. Our study therefore establishes a direct link between auxin transcriptional signaling and cell wall fortification, driving the differential cell elongation required for root gravitropism and angle.

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.

Enhancing drought resistance through the manipulation of root system architecture (RSA) in crops represents a crucial strategy for addressing food insecurity challenges. Abscisic acid (ABA) plays important roles in drought tolerance; yet, its molecular mechanisms in regulating RSA, especially in cereal crops, remain unclear. In this study, we report a new mechanism whereby ABA mediates local auxin biosynthesis to regulate root gravitropic response, thereby controlling the alteration of RSA in response to drought in cereal crops. Under drought conditions, wild-type (WT) plants displayed a steep root angle compared with normal conditions, while ABA biosynthetic mutants (mhz4, mhz5, osaba1, and osaba2) showed a significantly shallower crown root angle. Gravitropic assays revealed that ABA biosynthetic mutants have reduced gravitropic responses compared with WT plants. Hormone profiling analysis indicated that the mhz5 mutant has reduced auxin levels in root tips, and exogenous auxin (naphthaleneacetic acid [NAA]) application restored its root gravitropic defects. Consistently, auxin reporter analysis in mhz5 showed a reduced auxin gradient formation in root epidermis during gravitropic bending response compared with WT plants. Furthermore, NAA, rather than ABA, was able to rescue the compromised gravitropic response in the auxin biosynthetic mutant mhz10-1/tryptophan amino transferase2 (ostar2). Additionally, the maize ABA biosynthetic mutant viviparous5 (vp5) also showed gravitropic defects and a shallower seminal root angle than WT plants, which were restored by external auxin treatment. Collectively, we suggest that ABA-induced auxin synthesis governs the root gravitropic machinery, thereby influencing root angle in rice, maize, and possibly other cereal crops.

Land plants thrive in soils showing vastly different properties and environmental stresses1. Root systems can adapt to contrasting soil conditions and stresses, yet how their responses are programmed at the individual cell scale remains unclear. Using single-cell RNA sequencing and spatial transcriptomic approaches, we showed major expression changes in outer root cell types when comparing the single-cell transcriptomes of rice roots grown in gel versus soil conditions. These tissue-specific transcriptional responses are related to nutrient homeostasis, cell wall integrity and defence in response to heterogeneous soil versus homogeneous gel growth conditions. We also demonstrate how the model soil stress, termed compaction, triggers expression changes in cell wall remodelling and barrier formation in outer and inner root tissues, regulated by abscisic acid released from phloem cells. Our study reveals how root tissues communicate and adapt to contrasting soil conditions at single-cell resolution.

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.

Bovine tuberculosis (bTB) is a major disease of cattle in the UK, placing a significant economic burden on the taxpayer. The causative agent, Mycobacterium bovis, has a wide host range, including the European badger (Meles meles). While badgers have been implicated in the transmission and maintenance of infection in cattle in areas of endemic disease, their role at the edge of the endemic area is poorly understood. Here we present data on the prevalence of infection in badgers collected along the southern edge of England’s bTB epidemic. Stakeholders across five counties (Oxfordshire, Berkshire, Buckinghamshire, Hampshire, and East Sussex) submitted found-dead badgers for post-mortem examination and testing by bacterial culture. The overall prevalence, as confirmed by whole genome sequencing, was 6.5% (28/428), ranging between 1.1% (1/88) in Hampshire and 13.0% (14/108) in Oxfordshire. The commonest M. bovis clade in badgers was B6-62, which was predominant in 4/5 counties. B6-62 was also the commonest clade found in cattle and was detected in all counties except East Sussex where, although absent from the cattle population, it was detected in local badgers. This study highlights the co-incidence of infection in badgers and cattle in parts of the southern edge area consistent with localised clustering of infection in both species.

Plants grow complex root systems to extract unevenly distributed resources from soils. Spatial differences in soil moisture are perceived by root tips, leading to the patterning of new root branches toward available water in a process called hydropatterning. Little is known about hydropatterning behavior and its genetic basis in crop plants. Here, we developed an assay to measure hydropatterning in maize and revealed substantial differences between tropical/subtropical and temperate maize breeding germplasm that likely resulted from divergent selection. Genetic analysis of hydropatterning confirmed the regulatory role of auxin and revealed that the gaseous hormone ethylene locally inhibits root branching from air-exposed tissues. Our results demonstrate how distinct signaling pathways translate spatial patterns of water availability to developmental programs that determine root architecture.

Rice (Oryza sativa L.) is a staple food for more than half of the world’s population, but its yields are increasingly threatened by environmental problems, including soil compaction. This problem limits root growth which limits water and nutrient foraging capacity thus reduces productivity due to, restricted diffusion of ethylene, a key plant hormone playing an important role in exacerbating these effects. Elevated ethylene levels in compacted soils can further inhibit root development. However, rice varieties that are less sensitive to ethylene may have an advantage as they exhibit better root growth and resource utilization under such conditions. In this study, 220 diverse rice accessions were analyzed to uncover the genetic factors that influence root length reduction (RLR) in response to ethylene. Genome-wide association studies (GWAS) identified a significant QTL on chromosome 10, named qRLR10, associated with ethylene response. Within this region, 20 candidate genes were identified, with three F-box genes namely Os10g0124700, Os10g0126600 and Os10g0128200 showing a strong correlation with RLR variations. These genes are involved in protein degradation, root development and hormone signaling, indicating their possible role in regulating ethylene sensitivity. The results suggest that rice varieties with lower ethylene sensitivity may have better root growth in compacted soils, making them ideal targets for breeding programs aimed at improving resilience to harsh environmental conditions. These results underscore the critical role of ethylene in rice root development and provide valuable insights for future rice improvement strategies aimed at mitigating the effects of soil compaction.

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning.

AbstractReactive oxygen species (ROS) function as key signals in plants to enable adaptation to environmental stresses. Plant roots respond to transient water stress by temporarily ceasing branching using the acclimative response xerobranching1. In this study, we report that a rapid ROS burst regulates Xerobranching by inducing multimerization of auxin repressor protein IAA3/SHY2. Mutations in specific cysteine residues in IAA3/SHY2 disrupt redox-mediated multimerization and interaction with co-repressor TPL, but not with auxin response partner ARF7 and auxin receptor TIR1. ROS-mediated oligomerization of IAA3/SHY2 is required for efficient ARF mediated target gene repression during Xerobranching and lateral root emergence. We demonstrate that AUX/IAA proteins vary in their redox mediated multimerization, revealing a new auxin response regulatory mechanism that directly connects ROS sensing to auxin signalling. Our study reveals how ROS, auxin and water stress intersect to shape acclimative responses in plant roots and maintain their phenotypic plasticity.

Auxin plays a pivotal role in plant development by activating AUXIN RESPONSE FACTORs (ARFs). Under low auxin levels, ARF activity is inhibited by interacting with Aux/IAAs. Aux/IAAs are degraded when the cellular auxin concentration increases, causing the release of ARF inhibition. Here, we show that levels of the ARF5/MONOPTEROS (MP) protein are regulated in a cell-type-specific and isoform-dependent manner. We find that the stability of MP isoforms is differentially controlled depending on the auxin level. The canonical MP isoform is degraded by the proteasome in root tissues with low auxin levels. While auxin sharpens the MP localization domain in roots, it does not do so in ovules or embryos. Our research highlights a mechanism for providing spatial control of auxin signaling capacity. Together with recent advances in understanding the tissue-specific expression and post-transcriptional modification of auxin signaling components, these results provide insights into understanding how auxin can elicit so many distinct responses.

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A. E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, by whole-genome re-sequencing of 827 Watkins landraces and 208 modern cultivars and in-depth field evaluation spanning a decade. We found that modern cultivars are derived from two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium-based haplotypes and association genetics analyses link Watkins genomes to the thousands of identified high-resolution quantitative trait loci and significant marker-trait associations. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritized quantitative trait loci in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilizing genetic diversity in crop improvement to achieve sustainable food security.