Root phenotypes for improved nutrient capture: an underexploited opportunity for global agriculture

Optimizing Root Phenotypes for Compacted Soils: Enhancing Root-Soil-Microbe Interactions

Soil compaction impedes root growth, reduces crop yields, and threatens global food security and sustainable agriculture. Addressing this challenge requires a comprehensive understanding of root-soil interactions in compacted environments. This review examines key root traits-architectural, anatomical, biochemical, and biomechanical-that enhance plant resilience in compacted soils. We discuss how these traits influence root penetration and the formation of more favorable soil pore structures, which are crucial for alleviating compaction stress. Additionally, we explore the molecular mechanisms underlying root adaptation, identifying key genetic and biochemical factors that contribute to stress-tolerant root phenotypes. The review emphasizes the role of root-microbe interactions in boosting root adaptability under compaction. By integrating these insights, we propose a framework for breeding crops with resilient root systems that thrive in high soil strength, supporting sustainable agricultural practices essential for food security amidst environmental challenges.

Synergistic Optimisation of Root Hydraulic Architecture Enhances Drought Tolerance in Cotton

Optimising the root hydraulic architecture, which is defined by the integration of morphological and hydraulic traits, plays a crucial role in enhancing the drought tolerance of crops. However, the mechanisms by which root hydraulic architecture coordinates structural and functional adaptations under drought remain unclear. In this study, we used paper-based cultured 13 cotton cultivars under no-stressed and drought-stressed conditions, and identified a drought-tolerant (Guoxin 02) and a drought-sensitive (Ji 228) cultivar. The drought-tolerant cultivar exhibited enhanced root hydraulic conductance (Lpr) through increased lateral root length and number, reduced lateral root tip angle, and lower root width/depth ratio. Anatomically, drought tolerance was associated with narrower xylem vessels to limit axial conductance (Kx) and reduced cortex cell layers to increase radial hydraulic conductance (Kox), thereby balancing hydraulic efficiency and embolism resistance. Despite lower Kx, the high root hydraulic conductance (Kroot) in the drought-tolerant cultivar was maintained by lateral root proliferation, demonstrating a synergistic interplay between morphology and hydraulics. These findings highlight the plasticity of root hydraulic architecture as a key target for breeding drought-resilient cotton.

Enhancing Crop Nitrogen Efficiency: The Role of Mixed Nitrate and Ammonium Supply in Plant Growth and Development

Nitrogen fertilizers play a critical role in enhancing crop yields; however, excessive application has resulted in significant environmental challenges, including water contamination and increased greenhouse gas emissions. Therefore, improving nitrogen use efficiency is essential for sustainable agriculture. This review based on a systematic search of Web of Science and CNKI for peer-reviewed studies on maize nitrogen efficiency published between 1945 and 2024 (excluding conference abstracts), this review presents the first multiscale synthesis demonstrating how balanced nitrate-ammonium nutrition coordinates N-C metabolism and phytohormone signaling to boost nitrogen use efficiency and stimulate maize growth, with supporting evidence from other crops. By integrating results from hydroponic and field experiments, the review evaluates the influence of mixed nitrogen sources on nitrogen uptake, root morphology, photosynthesis, carbon metabolism, and hormone signaling. Findings indicate that optimal NO3-:NH4+ ratios improve nitrogen absorption through enhanced root development and activation of specific nitrogen transporters. Additionally, mixed nitrogen nutrition increases photosynthetic efficiency, promotes carbon assimilation, reduces energy expenditure, and stimulates auxin-mediated growth. This review shows that balanced nitrate-ammonium co-application synergistically enhances crop nitrogen-use efficiency and yield, provides a theoretical basis for high-efficiency nitrogen-fertilizer development, and helps alleviate environmental pressures, advance sustainable agriculture, and secure food and ecosystem safety. Its efficacy, however, is modulated by soil type, climate, and genotypic variation, necessitating systematic validation and application optimization in future research.

A CLE14 Signalling Cascade Promotes Arabidopsis Root Hair Elongation

The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED(CLE) peptides play crucial roles in plentiful plant developmental and adaptive processes. In this study, we demonstrate that Arabidopsis CLE14 acts as a critical regulator of root hair elongation. Compared to the wild-type (WT) plant, CRISPR/Cas9-generated cle14-cr mutants exhibit reduced root hair length, whereas overexpression of CLE14 promotes root hair elongation. In consistence, the synthetic CLE14 peptide also facilitates root hair elongation. However, CLE14 peptide-induced root hair elongation is significantly compromised in clv2 and crn mutants, suggesting the requirement of CLV2 and CRN proteins in CLE14-mediated root hair growth. Genetic and pharmacological evidence further indicates that ethylene acts downstream of CLE14-CLV2/CRN module to regulate root hair elongation. Additionally, CLE14 peptide upregulates the expression level of RHD6 and RSL4 via EIN3 and EIL1, the key transcription factors in ethylene signalling. Subsequently, RSL4 acts downstream of RHD6 to trigger hydrogen peroxide (H2O2) and nitric oxide (NO) accumulation by upregulating the expression of H2O2 and NO biosynthesis-related genes, ultimately driving root hair elongation. Collectively, our findings elucidate the signalling components underlying CLE14-mediated root hair elongation.

Multiple layers of regulators emerge in the network controlling lateral root organogenesis

Lateral root (LR) formation is a postembryonic organogenesis process that is crucial for plant root system development and adaptation to heterogenous soil environments. Since the early 1990s, a wealth of experimental data on arabidopsis (Arabidopsis thaliana) has helped reveal the LR formation regulatory network, in which dynamic auxin distribution and transcriptional cascades direct root cells through their organogenesis pathway. Some parts of this network appear conserved across diverse plant species or distinct developmental contexts. Recently, our knowledge of this process dramatically expanded thanks to technical advances, from single cell profiling to whole-root system phenotyping. Interestingly, new players are now emerging in this network, such as fatty acids and reactive oxygen species (ROS), transforming our knowledge of this hidden half of plant biology.

Root Hair Development Is Suppressed by Long-Term Mild Heat Through Down-Regulation of RHD6 and RHD6-like Genes

Roots located in the upper soil layers are prone to experiencing high temperatures. Despite their importance for water and nutrient absorption, little is known about the effect of high temperature on root hairs. Here, we found that exposure of Arabidopsis thaliana seedlings to long-term mild heat suppressed root hair initiation. Epidermal patterning of hair and non-hair cells was maintained, as observed with GL2- and CPC-based marker genes, and the suppression was independent of the activity of GL2 and its upstream regulators. Instead, we found that expression of downstream RHD6 and RHD6-like bHLH transcription factor genes RSL2 and RSL4 was reduced and that overexpression of RHD6 via an inducible transgene or ethylene treatment maintained the transcriptional expression of RSL2 and RSL4 and fully rescued the root hair phenotype. We conclude that GL2-independent downregulation of RHD6 and its homologues mediates the inhibition in root hair initiation under long-term mild heat stress. This finding may contribute to the development of strategies for improving plant performance under high temperature.

A systematic review to identify target genes that modulate root system architecture in response to abiotic stress

The exposure of plant roots to soil-related stresses, including drought, high temperatures, salinization, and nutrient deficiency, is on the rise due to climate change caused by human activities. A systematic literature review was conducted, which revealed evidence for conserved genes that modulate root system architecture under specific stress conditions. A collection of Arabidopsis thaliana mutants displaying a root phenotype distinct from the wild type is available in The Arabidopsis Information Resource database. Gene expression data was gathered for specific genes in response to selected abiotic stress treatments. K-means clustering, and fold change analyses identified 118 genes that were upregulated and 185 genes that were downregulated. A dedicated phenotyping approach was used to ascertain that lack of nutrients induced the transition from a 'steep, cheap, and deep' root morphotype to a 'topsoil foraging' root morphotype in the Columbia- 0 reference genotype. The anticipated role of ISOPENTENYLTRANSFERASE 3, LIPOXYGENASE 1, and WEE1 KINASE HOMOLOG as negative regulators of root growth in response to multiple stress signals was assayed. Further research with the candidate genes identified in this study may reveal promising targets for crop improvement.

Nutrient limitations on photosynthesis: from individual to combinational stresses

Liebig's law of the minimum states that increasing photosynthetic productivity on nutrient-impoverished soils depends on addressing the most limiting nutrient. Research has identified the roles of different mineral nutrients in photosynthetic processes. However, diffusional and biochemical regulation of photosynthesis both feature patterns of cumulative effects that jointly determine photosynthetic capacity. More importantly, responses to multiple nutrient stresses are not simply additive and require a comprehensive understanding of how these stresses interact and impact photosynthetic performance. In this review we highlight key macroelements for photosynthesis - nitrogen, phosphorus, potassium, and magnesium - focusing on their unique functions and interactions in regulating carbon fixation under multiple nutrient deficiencies, with the goal of enhancing crop productivity through balanced nutrient applications.

Effects of Ecosystem Recovery Types on Soil Phosphorus Bioavailability, Roles of Plant and Microbial Diversity: A Meta-Analysis

Strategies for restoring degraded ecosystems vary widely in the levels of human intervention. It has commonly been assumed that recovery with artificial inputs would be quicker and more efficient. However, is this truly the situation? We conducted a meta-analysis to evaluate the differences and applicability between ecological restoration and ecological rehabilitation. Relationships between soil phosphorus content, plant diversity, and soil microbial diversity were analyzed using 463 valid experimental data points collected from 72 publications. The results indicated that in grassland ecosystems, ecological restoration outperformed rehabilitation by 35%, 68%, 38%, and 48% in belowground biomass, community coverage, plant richness, and Shannon diversity, respectively. In forests, rehabilitation trailed behind restoration by 58%, 26%, and 92% in belowground biomass, Simpson diversity, and bacterial Shannon diversity. Furthermore, there was minimal difference in the recovery mode among different fungal and bacterial phyla. Rehabilitation demonstrated lower stability and efficiency in long-term phosphorus cycling compared to restoration. Overall, ecological restoration offers more stable and efficient long-term phosphorus cycling, thereby questioning the effectiveness of ecological rehabilitation for sustainable ecosystem recovery, especially for species diversity and phosphorus cycling.

Phenotyping, genome-wide dissection, and prediction of maize root architecture for temperate adaptability

Root System Architecture (RSA) plays an essential role in influencing maize yield by enhancing anchorage and nutrient uptake. Analyzing maize RSA dynamics holds potential for ideotype-based breeding and prediction, given the limited understanding of the genetic basis of RSA in maize. Here, we obtained 16 root morphology-related traits (R-traits), 7 weight-related traits (W-traits), and 108 slice-related microphenotypic traits (S-traits) from the meristem, elongation, and mature zones by cross-sectioning primary, crown, and lateral roots from 316 maize lines. Significant differences were observed in some root traits between tropical/subtropical and temperate lines, such as primary and total root diameters, root lengths, and root area. Additionally, root anatomy data were integrated with genome-wide association study (GWAS) to elucidate the genetic architecture of complex root traits. GWAS identified 809 genes associated with R-traits, 261 genes linked to W-traits, and 2577 key genes related to 108 slice-related traits. We confirm the function of a candidate gene, fucosyltransferase5 (FUT5), in regulating root development and heat tolerance in maize. The different FUT5 haplotypes found in tropical/subtropical and temperate lines are associated with primary root features and hold promising applications in molecular breeding. Furthermore, we performed machine learning prediction models of RSA using root slice traits, achieving high prediction accuracy. Collectively, our study offers a valuable tool for dissecting the genetic architecture of RSA, along with resources and predictive models beneficial for molecular design breeding and genetic enhancement.

Ultra-Tiny Scale Topographical Cues Direct Arabidopsis Root Growth and Development

Plant growth involves intricate processes, including cell division, expansion, and tissue organization, necessitating innovative technologies that emulate native cell-microenvironment interactions. Herein, we introduce ultra-tiny topographical cues (e.g., patterned micro/nanoscale substrates) that mimic micronanofiber structures found in the plant cell wall. We cultured Arabidopsis on unique cell wall-inspired ultra-tiny cues within specialized chambers that positively influenced various physiological aspects compared to a flat surface. Specifically, we observed bidirectional behavior, favoring maximum primary root growth and thickness on sparse features (e.g., 5 μm) and induced predominant anisotropic root alignment on dense features (e.g., 400-800 nm), with alignment decreasing monotonically as the feature size increased. Additionally, RNA sequencing revealed distinct molecular mechanisms underlying Arabidopsis root growth dynamics in response to these ultra-tiny cues, demonstrating modulation of specific genes involved in root development. Collectively, our findings highlight the potential of ultra-tiny cues to modulate gene expression and plant growth dynamics, offering innovative approaches to enhance agricultural productivity sustainably through feature-size-dependent interactions.

Field plants strategically regulate water uptake from different soil depths by spatiotemporally adjusting their radial root hydraulic conductivity

Plants modify their root hydraulics to maintain water status and strategically use soil water, but how they achieve this in the field conditions remains elusive. We developed a method to measure and calculate daily root water uptake, root water potential, and radial root water permeability at different depths in a wheat (Triticum aestivum L.) field and a permanent grassland dominated by ryegrass (Lolium perenne L.). During the drying processes, both plant systems reduced the radial water permeability of their shallow roots to limit topsoil water uptake, while increasing the radial water permeability of their roots in the subsoil to enhance water extraction. Conversely, after the topsoil was rewetted, both plant systems increased the radial water permeability of their shallow roots to enhance water extraction, while reducing the radial water permeability of their roots in the subsoil to limit water uptake. Root water uptake in the subsoil was more influenced by the topsoil water than by the subsoil water. The topsoil water serves both as a resource and a signal, coordinating optimal water uptake from different soil depths. These findings have important implications for understanding how plants cope with periodic water stress in the field and for screening drought-tolerant crop varieties.

Effects of N and P Fertilization on Soil N-Cycling Microbial Community Structure in White Clover Grasslands

Although nitrifying and N-fixing functional gene microbes play a crucial role in regulating ecosystem nitrogen (N) cycling, understanding of how N and phosphorus (P) fertilization affect their community structure remains limited. N fertilizer levels were set to simulate N deposition and combined with different P fertilizer levels, to explore the soil-root-shoot physiological indexes, and the response of community structure of N-fixing and nitrifying microorganisms that caused changes in the N cycle of the system to fertilization. The results showed that N and P fertilization significantly decreased soil N pool (NH4+-N, NO3--N, IN), the concentrations of shoot TN, root TP, root OC, and root biomass, and slowed down soil N flux (net ammoniation rate, net nitrification rate, and net N mineralization rate). This effect was more pronounced under NP fertilization compared to single N or P fertilization. Short-term N and P fertilization had little effect on AOA and AOB. Anaeromyxobacter is a dominant genus of diazotrophs, and its relative abundance was significantly improved by N fertilization. Fertilization significantly increased Geobacter, but significantly decreased the relative abundance of Zoogloea, Rhizobium, and Azohydromonas. Root biomass and TP, soil NH4+-N, OC, and AP changed by fertilization were the main factors affecting N-fixing microorganisms. This study showed that in addition to soil N, soil OC and P changes caused by fertilization were also important factors affecting the N-cycling microbial community structure. Later relevant studies should also consider the effect of fertilization duration, environmental temperature, soil base condition, etc.

Interacting effects of crop domestication and soil resources on leaf and root functional traits

MAIN CONCLUSION

Domestication altered wheat leaf functional trait expression, and soil amendments altered root trait expression. These alterations shape crop suitability to stressed environments, and informs variety selection for agronomic conditions. Crop traits have been altered through domestication, resulting in syndromes that assist modern crops in contending with environmental constraints. Yet, we have limited understanding of how domestication has shaped the ability of crops to alter leaf and root functional traits for optimal performance under contemporary agronomic conditions, such as water limitation and organic amendments. We used a greenhouse pot experiment that included a wild progenitor of wheat (Aegilops tauschii), three domesticated wheat (Triticum aestivum) varieties (Watkins, Red Fife and Marquis), and three modern wheat varieties (developed from 1969 to 2016) to assess the effects of domestication on crop functional traits under water limitation and under organic and inorganic soil amendments, and to evaluate how this trait expression moderates rhizosphere soil conditions. Leaf functional trait expression varied significantly across wheat domestication classes, with these differences being almost independent of soil amendment or watering treatments. The wild progenitor expressed resource conservative leaf trait values, with low water use efficiency and stomatal conductance. Root trait expression was influenced by both soil amendment and watering treatment, with all wheat lineages expressing acquisitive traits, e.g., higher specific root length and lower root diameter, under organic amendments. Soil amendments and watering treatments impacted rhizosphere conditions, including microbial diversity and acid phosphatase activity, and domestication class impacted fungal diversity. Broadly, domestication altered the expression of wheat leaf functional traits, and soil amendments altered the expression of wheat root functional traits. These alterations in trait expression and rhizosphere soil response shape crop suitability to drought-prone or nutrient stressed environments, and should be considered when selecting varieties for hybridization for contemporary agronomic conditions.

Enhancing Sorghum Growth: Influence of Arbuscular Mycorrhizal Fungi and Sorgoleone

The low availability of phosphorus (P) in soil is one of the main constraints on crop production. Plants have developed several strategies to increase P use efficiency, including modifications in root morphology, the exudation of different compounds, and associations with microorganisms such as arbuscular mycorrhizal fungi (AMF). This study aimed to investigate the effect of sorgoleone compound on AMF colonization and its subsequent impact on P uptake, rhizosphere microbiota, and sorghum growth. The experiment was conducted in a greenhouse using the sorghum genotype P9401, known for low sorgoleone production. Three doses of purified sorgoleone (20 μM, 40 μM, and 80 μM) were added to low-P soil and plants were harvested after 45 days. Treatments included inoculation with the arbuscular mycorrhizal fungi Rhizophagus clarus and a negative control without inoculum. The addition of 40 and 80 μM of sorgoleone did not significantly increase mycorrhization. However, treatment with 20 μM sorgoleone combined with R. clarus inoculation significantly increased total sorghum biomass by 1.6-fold (p ≤ 0.05) compared to the non-inoculated treatment. AMF inoculation influenced only AMF colonization and the fungal microbiota, without affecting the bacterial community, whereas sorgoleone showed no effect on either. The activities of acid and alkaline phosphatases in the rhizospheric soil did not differ significantly among the treatments. Furthermore, the sorghum genes CYP71AM1, associated with sorgoleone biosynthesis, and Sb02g009880, Sb06g002560, Sb06g002540, and Sb03g029970 (related to phosphate transport induced by mycorrhiza) were significantly upregulated (p ≤ 0.05) in fine roots under these conditions. The 20 μM concentration of sorgoleone can enhance AMF colonization in sorghum and promote plant growth under low-P conditions, without significantly altering the microbiota.

Co-inoculation of Trichoderma viride with Azospirillum brasilense could suppress the development of Harpophora maydis-infected maize in Egypt

Plant diseases caused by fungal pathogens are responsible for severe damage to strategic crops worldwide. Late wilt disease (LWD) is a vascular disease that occurs late in maize development. Harpophora maydis, the causative agent of maize LWD, is responsible for significant economic losses in Egypt. Therefore, the aim of this study was to control LWD of maize using an alternative approach to reduce the use of chemical pesticides. A combination of Trichoderma viride, a fungal biocontrol agent, and Azospirillum brasilense, a bacterial endophytic plant growth promoter, was applied in vitro and in planta. T. viride showed high mycoparasitic potential against H. maydis via various antagonistic activities, including the production of lytic enzymes, secondary metabolites, volatile compounds, and siderophores. A. brasilense and T. viride filtrates were also shown to suppress H. maydis growth, in addition to their ability to produce gibberellic and indole acetic acids. A significant change in the metabolites secreted by T. viride was observed using GC/MS in the presence of H. maydis. A field experiment was conducted on susceptible and resistant hybrids of maize to evaluate the antagonistic activity of T. viride combined with A. brasilense on LWD incidence as well as plant growth promotion under field conditions. The data revealed a significant decrease in both disease incidence and severity in maize plants treated with T. viride and/or A. brasilense. Further, there was a noticeable increase in all plant growth and yield parameters. An anatomical examination of the control and inoculated maize roots was also reflective of plant responses under biotic stress. Taken together, the obtained results provide successful eco-friendly management strategies against LWD in maize.

Deciphering the Genetic Basis of Sugar Cane (Saccharum spontaneum L) Root System and Related Traits under Nitrogen Stress through the Integration of Genome-Wide Association Studies and RNA-seq

Nitrogen (N) is an essential element for plant growth and development. Identifying functional gene loci associated with nitrogen absorption and utilization in sugar cane can facilitate the development of nutrient-efficient sugar cane varieties. In this study, sugar cane seedlings were subjected to normal and low nitrogen stress treatments within a hydroponic system for the identification of candidate genes related to six root-associated traits using a diversity population of 297 accessions. A total of 262 single nucleotide polymorphisms were found to be significantly associated with the mutation, including 30 stable or pleiotropic loci. The integration of genome-wide association studies and differential gene analysis from RNA sequencing (RNA-seq) identified five key candidate genes. Overexpression of one of them, ScMYB-CC gene, in Arabidopsis significantly affected root growth and development. In summary, the findings of this study provide valuable genetic resources for the breeding of nitrogen-efficient sugar cane varieties.

Multi-scale phenotyping of senescence-related changes in roots of rapeseed in response to nitrate limitation

Root senescence remains largely unexplored. In this study, the time-course of the morphological, metabolic, and proteomic changes occurring with root aging were investigated, providing a comprehensive picture of the root senescence program. We found novel senescence-related markers for the characterization of the developmental stage of root tissues. The rapeseed root system is unique in that it consists of the taproot and lateral roots. Our study confirmed that the taproot, which transiently accumulates large quantities of starch and proteins, is specifically dedicated to nutrient storage and remobilization, while the lateral roots are mainly dedicated to nutrient uptake. Proteomic data from the taproot and lateral roots highlighted the different senescence-related events that control nutrient remobilization and nutrient uptake capacities. Both the proteome and enzyme activities revealed senescence-induced proteases and nucleotide catabolic enzymes that deserve attention as they may play important roles in nutrient remobilization efficiency in rapeseed roots. Taking advantage of publicly available transcriptomic and proteomic data on senescent Arabidopsis leaves, we provide a novel lists of senescence-related proteins specific or common to root organs and/or leaves.

Ammonium Polyphosphate Promotes Maize Growth and Phosphorus Uptake by Altering Root Properties

Phosphorus (P) is an essential nutrient for maize growth, significantly affecting both yield and quality. Despite the typically high concentration of available P in black soils, the efficiency of crop uptake and utilization remains relatively low. This study aimed to evaluate the effects of different P fertilizers on maize yield, root growth parameters, and P use efficiency to identify strategies for optimizing P management in black soil regions. Field experiment results indicated that the combination of ammonium polyphosphate (APP) with other P fertilizers led to variations in yield and P fertilizer absorption efficiency. Various P fertilizers were tested, including diammonium phosphate (DAP), ammonium polyphosphate (APP), fused calcium magnesium phosphate (FCMP), a combination of DAP and FCMP (DAP+FCMP), and a control with no phosphate (CK). The results indicated that P application significantly increased maize yield, with APP (171.8 g/plant) outperforming other P application treatments. Different P fertilizer types significantly affect soil P content and the composition of P fractions. APP significantly increased both the total P (TP) and the proportion of inorganic P (Pi). Furthermore, APP application significantly improved root length (RL), surface area (SAR), and root activity (RA) compared to CK, leading to enhanced nutrient absorption. APP also significantly increased P uptake and utilization (REp, FPp, AEp, PHI, and PAC). In summary, by optimizing plant biomass and P uptake, APP can directly and indirectly influence maize yield. Improving rhizosphere properties through the selection of suitable fertilizer types can enhance fertilizer use efficiency and increase maize production.

Environmental factors drive latitudinal patterns of fine-root architectures of 96 xerophytic species in the dry valleys of Southwest China

Fine-root architecture is critical feature reflecting root explorative and exploitative strategies for soil resources and soil space occupancy. Yet, studies on the variation of fine-root architecture across different species are scare and little work has been done to integrate the potential drivers on these variations along a biogeographical gradient in arid ecosystems. We measured root branching intensity, topological index, and root branching ratios as well as morphological traits (root diameter and length) in dry valley along a 1000 km latitudinal gradient. Influence of phylogeny, environmental factors on fine-root architecture and trade-offs among root traits were evaluated. With increasing latitude, the topological index and second to third root order branching ratio decreased, whereas first-to-second branching ratio increased. Root branching intensity was associated with short and thin fine roots, but has no significant latitudinal pattern. As a whole, soil microbial biomass was the most important driver in the variation of root branching intensity, and soil texture was the strongest predictor of topological index. Additionally, mean annual temperature was an important factor influencing first-to-second branching ratio. Our results suggest variations in fine-root architectures were more dependent on environmental variables than phylogeny, signifying that fine-root architecture is sensitive to environmental variations.

Effect of fertility levels and stress mitigating chemicals on nutrient content, uptake, intercropping advantage and competition effect in cowpea-baby corn intercropping

The primary goal of this study was to analyze how various row ratios of intercrops, in conjunction with different fertilizer levels with spray of two stress mitigating chemical, affect nutrient content, land productivity, and economic viability during Summer season. Furthermore, we aimed to explore the competitive dynamics within legume/cereal intercropping systems. Hence, A field experiment at Agriculture University, Kota, during the summers of 2019 and 2020, investigated different cowpea + baby corn intercropping system's intercropping indices, nutrient dynamics, uptake, and post-harvest soil nutrient balance under varying recommended fertilizer levels and foliar spray of stress mitigating chemicals. Using a split-split plot design replicated four times, the experiment involved thirty treatment combinations, including five intercropping techniques viz. Sole cowpea, sole baby corn, cowpea + baby corn 2:1, cowpea + baby corn 3:1, cowpea + baby corn 4:1 in the main plot, three fertility levels viz. 100 %, 125 % and 150 % recommended dose of fertilizer (RDF) in subplots, and two stress mitigation chemicals; CaCl2 0.5 % and KNO3 1% in sub-subplots. The findings revealed notable trends, including nitrogen (N) and (P) content in cowpea seeds and straw, baby corn cobs and fodder, as well as enhanced land-equivalent ratio (LER) and monetary advantage index (MAI) within the cowpea + baby corn 2:1 row ratio. However, despite these advantages, total N and P uptake were markedly higher in sole crops. Notably, sole cowpea demonstrated the highest actual N and P balance and lowest was under sole baby corn. Among the fertility levels, the 150 % RDF level exhibited the most favorable outcomes across various parameters, including LER, MAI, NP content, and uptake in both crops. Additionally, higher fertility levels correlated with increased apparent and actual soil nutrient balances. While, among stress mitigation chemicals, CaCl2 0.5 % resulted in significantly heightened N and P uptake. Hence, to optimize intercropping dynamics and maintain soil nutrient balance, it is advisable to intensify cowpea cultivation along with baby corn in a 2:1 row ratio, utilizing 150 % RDF is beneficial. Additionally, alleviating higher temperature stress during the summer season can be achieved by applying a 0.5 % solution CaCl2 through spraying at the flowering and pod development stages of cowpea.

NIN-LIKE PROTEIN3.2 inhibits repressor Aux/IAA14 expression and enhances root biomass in maize seedlings under low nitrogen

Plants generally enhance their root growth in the form of greater biomass and/or root length to boost nutrient uptake in response to short-term low nitrogen (LN). However, the underlying mechanisms of short-term LN-mediated root growth remain largely elusive. Our genome-wide association study, haplotype analysis, and phenotyping of transgenic plants showed that the crucial nitrate signaling component NIN-LIKE PROTEIN3.2 (ZmNLP3.2), a positive regulator of root biomass, is associated with natural variations in root biomass of maize (Zea mays L.) seedlings under LN. The monocot-specific gene AUXIN/INDOLE-3-ACETIC ACID14 (ZmAux/IAA14) exhibited opposite expression patterns to ZmNLP3.2 in ZmNLP3.2 knockout and overexpression lines, suggesting that ZmNLP3.2 hampers ZmAux/IAA14 transcription. Importantly, ZmAux/IAA14 knockout seedlings showed a greater root dry weight (RDW), whereas ZmAux/IAA14 overexpression reduced RDW under LN compared with wild-type plants, indicating that ZmAux/IAA14 negatively regulates the RDW of LN-grown seedlings. Moreover, in vitro and vivo assays indicated that AUXIN RESPONSE FACTOR19 (ZmARF19) binds to and transcriptionally activates ZmAux/IAA14, which was weakened by the ZmNLP3.2-ZmARF19 interaction. The zmnlp3.2 ZmAux/IAA14-OE seedlings exhibited further reduced RDW compared with ZmAux/IAA14 overexpression lines when subjected to LN treatment, corroborating the ZmNLP3.2-ZmAux/IAA14 interaction. Thus, our study reveals a ZmNLP3.2-ZmARF19-ZmAux/IAA14 module regulating root biomass in response to nitrogen limitation in maize.

Automated seminal root angle measurement with corrective annotation

Measuring seminal root angle is an important aspect of root phenotyping, yet automated methods are lacking. We introduce SeminalRootAngle, a novel open-source automated method that measures seminal root angles from images. To ensure our method is flexible and user-friendly we build on an established corrective annotation training method for image segmentation. We tested SeminalRootAngle on a heterogeneous dataset of 662 spring barley rhizobox images, which presented challenges in terms of image clarity and root obstruction. Validation of our new automated pipeline against manual measurements yielded a Pearson correlation coefficient of 0.71. We also measure inter-annotator agreement, obtaining a Pearson correlation coefficient of 0.68, indicating that our new pipeline provides similar root angle measurement accuracy to manual approaches. We use our new SeminalRootAngle tool to identify single nucleotide polymorphisms (SNPs) significantly associated with angle and length, shedding light on the genetic basis of root architecture.

Linking root cell wall width with plant functioning under drought conditions

This article comments on:

Sidhu JS, Lopez-Valdivia I, Strock CF, Schneider HM, Lynch JP. 2024. Cortical parenchyma wall width regulates root metabolic cost and maize performance under suboptimal water availability. Journal of Experimental Botany 75, https://doi.org/10.1093/jxb/erae191.

Cortical parenchyma wall width regulates root metabolic cost and maize performance under suboptimal water availability

We describe how increased root cortical parenchyma wall width (CPW) can improve tolerance to drought stress in maize by reducing the metabolic costs of soil exploration. Significant variation (1.0-5.0 µm) for CPW was observed in maize germplasm. The functional-structural model RootSlice predicts that increasing CPW from 2 µm to 4 µm is associated with a ~15% reduction in root cortical cytoplasmic volume, respiration rate, and nitrogen content. Analysis of genotypes with contrasting CPW grown with and without water stress in the field confirms that increased CPW is correlated with an ~32-42% decrease in root respiration. Under water stress in the field, increased CPW is correlated with 125% increased stomatal conductance, 325% increased leaf CO2 assimilation rate, 73-78% increased shoot biomass, and 92-108% increased yield. CPW was correlated with leaf mesophyll midrib parenchyma wall width, indicating pleiotropy. Genome-wide association study analysis identified candidate genes underlying CPW. OpenSimRoot modeling predicts that a reduction in root respiration due to increased CPW would also benefit maize growth under suboptimal nitrogen, which requires empirical testing. We propose CPW as a new phene that has utility under edaphic stress meriting further investigation.

Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots

KEY MESSAGE

We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe. Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (n = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38-0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.

Integrating GWAS with a gene co-expression network better prioritizes candidate genes associated with root metaxylem phenes in maize

Root metaxylems are phenotypically diverse structures whose function is particularly important under drought stress. Significant research has dissected the genetic machinery underlying metaxylem phenotypes in dicots, but that of monocots are relatively underexplored. In maize (Zea mays), a robust pipeline integrated a genome-wide association study (GWAS) of root metaxylem phenes under well-watered and water-stress conditions with a gene co-expression network to prioritize the strongest gene candidates. We identified 244 candidate genes by GWAS, of which 103 reside in gene co-expression modules most relevant to xylem development. Several candidate genes may be involved in biosynthetic processes related to the cell wall, hormone signaling, oxidative stress responses, and drought responses. Of those, six gene candidates were detected in multiple root metaxylem phenes in both well-watered and water-stress conditions. We posit that candidate genes that are more essential to network function based on gene co-expression (i.e., hubs or bottlenecks) should be prioritized and classify 33 essential genes for further investigation. Our study demonstrates a new strategy for identifying promising gene candidates and presents several gene candidates that may enhance our understanding of vascular development and responses to drought in cereals.

Postponed Application of Phosphorus and Potassium Fertilizers Mitigates the Damage of Late Spring Coldness by Improving Winter Wheat Root Physiology

Late spring coldness (LSC) is the main limiting factor threatening wheat yield and quality stability. Optimal nutrient management is beneficial in mitigating the harms of LSC by improving wheat root physiology. This study proposed a nutrient management strategy that postponed the application of phosphorus (P) and potassium (K), effectively strengthening wheat's defense against LSC. This experiment used the winter cultivar "Yannong19" (YN 19) as plant material for two consecutive years (2021-2022 and 2022-2023). Two fertilizer treatments were used: traditional P and K fertilizers application (R1: base fertilizer: jointing fertilizer = 10:0) and postponed P and K fertilizers application (R2: base fertilizer: jointing fertilizer = 5:5); wheat plants at the anther connective formation stage shifted to temperature-controlled phytotrons for normal (T0, 11 °C/4 h) and low temperatures (T1, 4 °C/4 h; T2, -4 °C/4 h) as treatments of LSC. The results showed that under low temperature (LT) treatment, compared with R1, the R2 treatment increased the concentrations of osmotic adjustment substances (soluble sugars and soluble protein contents by 6.2-8.7% and 3.0-8.9%), enhanced activities of antioxidant enzymes (superoxide dismutase, peroxidase and catalase activities by 2.2-9.1%, 6.2-9.7% and 4.2-8.4%), balanced the hormone concentrations (increased IAA and GA3 contents by 2.8-17.5% and 10.4-14.1% and decreased ABA contents by 7.2-14.3%), and reduced the toxicity (malondialdehyde, hydrogen peroxide content and O2·- production rate by 5.7-12.4%, 17.7-22.8% and 19.1-19.1%) of the cellular membranes. Furthermore, the wheat root physiology in R2 significantly improved as the root surface area and dry weight increased by 5.0-6.6% and 4.7-6.6%, and P and K accumulation increased by 7.4-11.3% and 12.2-15.4% compared to R1, respectively. Overall, the postponed application of P and K fertilizers enhanced the physiological function of the root system, maintained root morphology, and promoted the accumulation of wheat nutrients under the stress of LSC.

Root plasticity versus elasticity - when are responses acclimative?

Spatiotemporal soil heterogeneity and the resulting edaphic stress cycles can be decisive for crop growth. However, our understanding of the acclimative value of root responses to heterogeneous soil conditions remains limited. We outline a framework to evaluate the acclimative value of root responses that distinguishes between stress responses that are persistent and reversible upon stress release, termed 'plasticity' and 'elasticity', respectively. Using energy balances, we provide theoretical evidence that the advantage of plasticity over elasticity increases with the number of edaphic stress cycles and if responses lead to comparatively high energy gains. Our framework provides a conceptual basis for assessing the acclimative value of root responses to soil heterogeneity and can catalyse research on crop adaptations to heterogeneous belowground environments.

Root and rhizosphere traits for enhanced water and nutrients uptake efficiency in dynamic environments

Modern agriculture's goal of improving crop resource acquisition efficiency relies on the intricate relationship between the root system and the soil. Root and rhizosphere traits play a critical role in the efficient use of nutrients and water, especially under dynamic environments. This review emphasizes a holistic perspective, challenging the conventional separation of nutrient and water uptake processes and the necessity for an integrated approach. Anticipating climate change-induced increase in the likelihood of extreme weather events that result in fluctuations in soil moisture and nutrient availability, the study explores the adaptive potential of root and rhizosphere traits to mitigate stress. We emphasize the significance of root and rhizosphere characteristics that enable crops to rapidly respond to varying resource availabilities (i.e. the presence of water and mobile nutrients in the root zone) and their accessibility (i.e. the possibility to transport resources to the root surface). These traits encompass for example root hairs, mucilage and extracellular polymeric substance (EPS) exudation, rhizosheath formation and the expression of nutrient and water transporters. Moreover, we recognize the challenge of balancing carbon investments, especially under stress, where optimized traits must consider carbon-efficient strategies. To advance our understanding, the review calls for well-designed field experiments, recognizing the limitations of controlled environments. Non-destructive methods such as mini rhizotron assessments and in-situ stable isotope techniques, in combination with destructive approaches such as root exudation analysis, are proposed for assessing root and rhizosphere traits. The integration of modeling, experimentation, and plant breeding is essential for developing resilient crop genotypes capable of adapting to evolving resource limitation.

Spatiotemporal patterns of leaf nutrients of wild apples in a wild fruit forest plot in the Ili Valley, China

Malus sieversii, commonly known as wild apples, represents a Tertiary relict plant species and serves as the progenitor of globally cultivated apple varieties. Unfortunately, wild apple populations are facing significant degradation in localized areas due to a myriad of factors. To gain a comprehensive understanding of the nutrient status and spatiotemporal variations of M. sieversii, green leaves were collected in May and July, and the fallen leaves were collected in October. The concentrations of leaf nitrogen (N), phosphorus (P), and potassium (K) were measured, and the stoichiometric ratios as well as nutrient resorption efficiencies were calculated. The study also explored the relative contributions of soil, topographic, and biotic factors to the variation in nutrient traits. The results indicate that as the growing period progressed, the concentrations of N and P in the leaves significantly decreased (P < 0.05), and the concentration of K in October was significantly lower than in May and July. Throughout plant growth, leaf N-P and N-K exhibited hyperallometric relationships, while P-K showed an isometric relationship. Resorption efficiency followed the order of N < P < K (P < 0.05), with all three ratios being less than 1; this indicates that the order of nutrient limitation is K > P > N. The resorption efficiencies were mainly regulated by nutrient concentrations in fallen leaves. A robust spatial dependence was observed in leaf nutrient concentrations during all periods (70.1-97.9% for structural variation), highlighting that structural variation, rather than random factors, dominated the spatial variation. Nutrient resorption efficiencies (NRE, PRE, and KRE) displayed moderate structural variation (30.2-66.8%). The spatial patterns of nutrient traits varied across growth periods, indicating they are influenced by multifactorial elements (in which, soil property showed the highest influence). In conclusion, wild apples manifested differentiated spatiotemporal variability and influencing factors across various leaf nutrient traits. These results provide crucial insights into the spatiotemporal patterns and influencing factors of leaf nutrient traits of M. sieversii at the permanent plot scale for the first time. This work is of great significance for the ecosystem restoration and sustainable management of degrading wild fruit forests.

Terrestrial laser scanning and low magnetic field digitization yield similar architectural coarse root traits for 32-year-old Pinus ponderosa trees

BACKGROUND

Understanding how trees develop their root systems is crucial for the comprehension of how wildland and urban forest ecosystems plastically respond to disturbances such as harvest, fire, and climate change. The interplay between the endogenously determined root traits and the response to environmental stimuli results in tree adaptations to biotic and abiotic factors, influencing stability, carbon allocation, and nutrient uptake. Combining the three-dimensional structure of the root system, with root morphological trait information promotes a robust understanding of root function and adaptation plasticity. Low Magnetic Field Digitization coupled with AMAPmod (botAnique et Modelisation de l'Architecture des Plantes) software has been the best-performing method for describing root system architecture and providing reliable measurements of coarse root traits, but the pace and scale of data collection remain difficult. Instrumentation and applications related to Terrestrial Laser Scanning (TLS) have advanced appreciably, and when coupled with Quantitative Structure Models (QSM), have shown some potential toward robust measurements of tree root systems. Here we compare, we believe for the first time, these two methodologies by analyzing the root system of 32-year-old Pinus ponderosa trees.

RESULTS

In general, at the total root system level and by root-order class, both methods yielded comparable values for the root traits volume, length, and number. QSM for each root trait was highly sensitive to the root size (i.e., input parameter PatchDiam) and models were optimized when discrete PatchDiam ranges were specified for each trait. When examining roots in the four cardinal direction sectors, we observed differences between methodologies for length and number depending on root order but not volume.

CONCLUSIONS

We believe that TLS and QSM could facilitate rapid data collection, perhaps in situ, while providing quantitative accuracy, especially at the total root system level. If more detailed measures of root system architecture are desired, a TLS method would benefit from additional scans at differing perspectives, avoiding gravitational displacement to the extent possible, while subsampling roots by hand to calibrate and validate QSM models. Despite some unresolved logistical challenges, our results suggest that future use of TLS may hold promise for quantifying tree root system architecture in a rapid, replicable manner.

Root phosphatase activity is coordinated with the root conservation gradient across a phosphorus gradient in a lowland tropical forest

Soil phosphorus (P) is a growth-limiting nutrient in tropical ecosystems, driving diverse P-acquisition strategies among plants. Particularly, mining for inorganic P through phosphomonoesterase (PME) activity is essential, given the substantial proportion of organic P in soils. Yet, the relationship between PME activity and other nutrient-acquisition root traits remains unclear. We measured root PME activity and commonly measured root traits, including root diameter, specific root length (SRL), root tissue density (RTD), and nitrogen concentration ([N]) in 18 co-occurring species across soils with varying P availability to better understand trees response to P supply. Root [N] and RTD were inversely related, and that axis was not clearly related to soil P supply. Both traits, however, correlated positively and negatively with PME activity, which responded strongly to P supply. Conversely, root diameter was inversely related to SRL, but this axis was not related to P supply. This pattern suggests that limiting similarity influenced variation along the diameter-SRL axis, explaining local trait diversity. Meanwhile, variation along the root [N]-RTD axis might best reflect environmental filtering. Overall, P availability indicator traits such as PME activity and root hairs only tended to be associated with these axes, highlighting limitations of these axes in describing convergent adaptations at local sites.

Rice breeding for low input agriculture

A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, which are desirable traits for the "steep, cheap, and deep" ideotype. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene coexpression analysis was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies.

Genome-wide association studies of root system architecture traits in a broad collection of Brassica genotypes

The root systems of Brassica species are complex. Eight root system architecture (RSA) traits, including total root length, total root surface area, root average diameter, number of tips, total primary root length, total lateral root length, total tertiary root length, and basal link length, were phenotyped across 379 accessions representing six Brassica species (B. napus, B. juncea, B. carinata, B. oleracea, B. nigra, and B. rapa) using a semi-hydroponic system and image analysis software. The results suggest that, among the assessed species, B. napus and B. oleracea had the most intricate and largest root systems, while B. nigra exhibited the smallest roots. The two species B. juncea and B. carinata shared comparable root system complexity and had root systems with larger root diameters. In addition, 313 of the Brassica accessions were genotyped using a 19K Brassica single nucleotide polymorphism (SNP) array. After filtering by TASSEL 5.0, 6,213 SNP markers, comprising 5,103 markers on the A-genome (covering 302,504 kb) and 1,110 markers on the C-genome (covering 452,764 kb), were selected for genome-wide association studies (GWAS). Two general linear models were tested to identify the genomic regions and SNPs associated with the RSA traits. GWAS identified 79 significant SNP markers associated with the eight RSA traits investigated. These markers were distributed across the 18 chromosomes of B. napus, except for chromosome C06. Sixty-five markers were located on the A-genome, and 14 on the C-genome. Furthermore, the major marker-trait associations (MTAs)/quantitative trait loci (QTLs) associated with root traits were located on chromosomes A02, A03, and A06. Brassica accessions with distinct RSA traits were identified, which could hold functional, adaptive, evolutionary, environmental, pathological, and breeding significance.

The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula

The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root-like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide-coding genes in Medicago truncatula. Five out of fifteen GLV/RGF genes were notably upregulated during nodule organogenesis and were differentially responsive to nitrogen deficiency and auxin treatment. Specifically, the expression of MtGLV9 and MtGLV10 at nodule initiation sites was contingent upon the NODULE INCEPTION transcription factor. Overexpression of these five nodule-induced GLV genes in hairy roots of M. truncatula and application of their synthetic peptide analogues led to a decrease in nodule count by 25-50%. Uniquely, the GOLVEN10 peptide altered the positioning of the first formed lateral root and nodule on the primary root axis, an observation we term 'noduletaxis'; this decreased the length of the lateral organ formation zone on roots. Histological section of roots treated with synthetic GOLVEN10 peptide revealed an increased cell number within the root cortical cell layers without a corresponding increase in cell length, leading to an elongation of the root likely introducing a spatiotemporal delay in organ formation. At the transcription level, the GOLVEN10 peptide suppressed expression of microtubule-related genes and exerted its effects by changing expression of a large subset of Auxin responsive genes. These findings advance our understanding of the molecular mechanisms by which GOLVEN peptides modulate root morphology, nodule ontogeny, and interactions with key transcriptional pathways.

Plant root mechanisms and their effects on carbon and nutrient accumulation in desert ecosystems under changes in land use and climate

Deserts represent key carbon reservoirs, yet as these systems are threatened this has implications for biodiversity and climate change. This review focuses on how these changes affect desert ecosystems, particularly plant root systems and their impact on carbon and mineral nutrient stocks. Desert plants have diverse root architectures shaped by water acquisition strategies, affecting plant biomass and overall carbon and nutrient stocks. Climate change can disrupt desert plant communities, with droughts impacting both shallow and deep-rooted plants as groundwater levels fluctuate. Vegetation management practices, like grazing, significantly influence plant communities, soil composition, root microorganisms, biomass, and nutrient stocks. Shallow-rooted plants are particularly susceptible to climate change and human interference. To safeguard desert ecosystems, understanding root architecture and deep soil layers is crucial. Implementing strategic management practices such as reducing grazing pressure, maintaining moderate harvesting levels, and adopting moderate fertilization can help preserve plant-soil systems. Employing socio-ecological approaches for community restoration enhances carbon and nutrient retention, limits desert expansion, and reduces CO2 emissions. This review underscores the importance of investigating belowground plant processes and their role in shaping desert landscapes, emphasizing the urgent need for a comprehensive understanding of desert ecosystems.

Soil phosphorus transformation and plant uptake driven by phosphate-solubilizing microorganisms

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

Evidence that variation in root anatomy contributes to local adaptation in Mexican native maize

Mexican native maize (Zea mays ssp. mays) is adapted to a wide range of climatic and edaphic conditions. Here, we focus specifically on the potential role of root anatomical variation in this adaptation. Given the investment required to characterize root anatomy, we present a machine-learning approach using environmental descriptors to project trait variation from a relatively small training panel onto a larger panel of genotyped and georeferenced Mexican maize accessions. The resulting models defined potential biologically relevant clines across a complex environment that we used subsequently for genotype-environment association. We found evidence of systematic variation in maize root anatomy across Mexico, notably a prevalence of trait combinations favoring a reduction in axial hydraulic conductance in varieties sourced from cooler, drier highland areas. We discuss our results in the context of previously described water-banking strategies and present candidate genes that are associated with both root anatomical and environmental variation. Our strategy is a refinement of standard environmental genome-wide association analysis that is applicable whenever a training set of georeferenced phenotypic data is available.

Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses

Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.

Trade-offs between root-secreted acid phosphatase and root morphology traits, and their contribution to phosphorus acquisition in Brassica napus

Oilseed rape (Brassica napus) is one of the most important oil crops in the world and shows sensitivity to low phosphorus (P) availability. In many soils, organic P (Po) is the main component of the soil P pool. Po must be mineralised to Pi through phosphatases, and then taken up by plants. However, the relationship between root-secreted acid phosphatases (APase) and root morphology traits, two important P-acquisition strategies in response to P deficiency, is unclear among B. napus genotypes. This study aimed to understand their relationship and how they affect P acquisition, which is crucial for the sustainable utilisation of agricultural P resources. This study showed significant genotypic variations in root-secreted APase activity per unit root fresh weight (SAP) and total root-secreted APase activity per plant (total SAP) among 350 B. napus genotypes. Seed yield was positively correlated with total SAP but not significantly correlated with SAP. Six root traits of 18 B. napus genotypes with contrasting root biomass were compared under normal Pi, low Pi and Po. Genotypes with longer total root length (TRL) reduced SAP, but those with shorter TRL increased SAP under P deficiency. Additionally, TRL was important in P-acquisition under three P treatments, and total SAP was also important in P-acquisition under Po treatment. In conclusion, trade-offs existed between the two P-acquisition strategies among B. napus genotypes under P-deficient conditions. Total SAP was an important root trait under Po conditions. These results might help to breed B. napus with greater P-acquisition ability under low P availability conditions.

Identification of mebendazole as an ethylene signaling activator reveals a role of ethylene signaling in the regulation of lateral root angles

The lateral root angle or gravitropic set-point angle (GSA) is an important trait for root system architecture (RSA) that determines the radial expansion of the root system. The GSA therefore plays a crucial role for the ability of plants to access nutrients and water in the soil. Only a few regulatory pathways and mechanisms that determine GSA are known. These mostly relate to auxin and cytokinin pathways. Here, we report the identification of a small molecule, mebendazole (MBZ), that modulates GSA in Arabidopsis thaliana roots and acts via the activation of ethylene signaling. MBZ directly acts on the serine/threonine protein kinase CTR1, which is a negative regulator of ethylene signaling. Our study not only shows that the ethylene signaling pathway is essential for GSA regulation but also identifies a small molecular modulator of RSA that acts downstream of ethylene receptors and that directly activates ethylene signaling.

IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

Iron reprogrammes the root system architecture by regulating OsWRKY71 in arsenic-stressed rice (Oryza sativa L.)

Iron (Fe) has been critically reported to act as a signal that can be interpreted to activate the molecular mechanisms involved in root developmental processes. Arsenic (As) is a well-known metalloid that restricts the growth and productivity of rice plants by altering their root architecture. Since root system architecture (RSA) under As stress targets WRKY transcription factors (TFs) and their interaction partners, the current investigation was carried out to better understand the Fe-dependent dynamics of RSA and its participation in this process. Here, we analyzed the effects of As and Fe (alone or in combination) exposed to hydroponically grown rice roots of 12-day-old plants. Our research showed that adding As to Fe changed how OsWRKY71 was expressed and improved the morphology and anatomy of the rice roots in Ratna and Lalat varieties. As + Fe treatment also manifested the biochemical parameters. OsWRKY71, revealed an up-regulation (Fe alone and As + Fe conditions) and down-regulation (As stress) in both varieties, in comparison to the controls. The improved root anatomy and root oxidizability indicated the enhanced capability of Lalat over the Ratna variety to induce OsWRKY71 for the better development of RSA during As + Fe treatment. Further, OsWRKY71 has revealed the presence of gibberellin-responsive cis-regulatory elements (GAREs) in its promoter region, indicating the involvement of OsWRKY71 in the gibberellin pathway. Molecular docking revealed that OsWRKY71 and SLR1 (DELLA protein) interact positively, which supports the hypothesis that Fe alters RSA by regulating OsWRKY71 through the gibberellin pathway in As-stressed rice.

Unlocking dynamic root phenotypes for simultaneous enhancement of water and phosphorus uptake

Phosphorus (P) and water are crucial for plant growth, but their availability is challenged by climate change, leading to reduced crop production and global food security. In many agricultural soils, crop productivity is confronted by both water and P limitations. The diminished soil moisture decreases available P due to reduced P diffusion, and inadequate P availability diminishes tissue water status through modifications in stomatal conductance and a decrease in root hydraulic conductance. P and water display contrasting distributions in the soil, with P being concentrated in the topsoil and water in the subsoil. Plants adapt to water- and P-limited environments by efficiently exploring localized resource hotspots of P and water through the adaptation of their root system. Thus, developing cultivars with improved root architecture is crucial for accessing and utilizing P and water from arid and P-deficient soils. To meet this goal, breeding towards multiple advantageous root traits can lead to better cultivars for water- and P-limited environments. This review discusses the interplay of P and water availability and highlights specific root traits that enhance the exploration and exploitation of optimal resource-rich soil strata while reducing metabolic costs. We propose root ideotype models, including 'topsoil foraging', 'subsoil foraging', and 'topsoil/subsoil foraging' for maize (monocot) and common bean (dicot). These models integrate beneficial root traits and guide the development of water- and P-efficient cultivars for challenging environments.

Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet

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.

Root system architecture associated zinc variability in wheat (Triticum aestivum L.)

Root system architecture (RSA) plays a fundamental role in nutrient uptake, including zinc (Zn). Wheat grains are inheritably low in Zn. As Zn is an essential nutrient for plants, improving its uptake will not only improve their growth and yield but also the nutritional quality of staple grains. A rhizobox study followed by a pot study was conducted to evaluate Zn variability with respect to RSA and its impact on grain Zn concentration. The grain Zn content of one hundred wheat varieties was determined and grown in rhizoboxes with differential Zn (no Zn and 0.05 mg L-1 ZnSO4). Seedlings were harvested 12 days after sowing, and root images were taken and analyzed by SmartRoot software. Using principal component analysis, twelve varieties were screened out based on vigorous and weaker RSA with high and low grain Zn content. The screened varieties were grown in pots with (11 mg ZnSO4 kg-1 soil) and without Zn application to the soil. Zinc translocation, localization, and agronomic parameters were recorded after harvesting at maturity. In the rhizobox experiment, 4% and 8% varieties showed higher grain Zn content with vigorous and weaker RSA, respectively, while 45% and 43% varieties had lower grain Zn content with vigorous and weaker RSA. However, the pot experiment revealed that varieties with vigorous root system led to higher grain yield, though the grain Zn concentration were variable, while all varieties with weaker root system had lower yield as well as grain Zn concentration. Zincol-16 revealed the highest Zn concentration (28.07 mg kg-1) and grain weight (47.9 g). Comparatively higher level of Zn was localized in the aleurone layer than in the embryonic region and endosperm. It is concluded that genetic variability exists among wheat varieties for RSA and grain Zn content, with a significant correlation. Therefore, RSA attributes are promising targets for the Zn biofortification breeding program. However, Zn localization in endosperm needs to be further investigated to achieve the goal of reducing Zn malnutrition.

CEP hormones at the nexus of nutrient acquisition and allocation, root development, and plant-microbe interactions

A growing understanding is emerging of the roles of peptide hormones in local and long-distance signalling that coordinates plant growth and development as well as responses to the environment. C-TERMINALLY ENCODED PEPTIDE (CEP) signalling triggered by its interaction with CEP RECEPTOR 1 (CEPR1) is known to play roles in systemic nitrogen (N) demand signalling, legume nodulation, and root system architecture. Recent research provides further insight into how CEP signalling operates, which involves diverse downstream targets and interactions with other hormone pathways. Additionally, there is emerging evidence of CEP signalling playing roles in N allocation, root responses to carbon levels, the uptake of other soil nutrients such as phosphorus and sulfur, root responses to arbuscular mycorrhizal fungi, plant immunity, and reproductive development. These findings suggest that CEP signalling more broadly coordinates growth across the whole plant in response to diverse environmental cues. Moreover, CEP signalling and function appear to be conserved in angiosperms. We review recent advances in CEP biology with a focus on soil nutrient uptake, root system architecture and organogenesis, and roles in plant-microbe interactions. Furthermore, we address knowledge gaps and future directions in this research field.