Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

Understanding plant-soil interactions underpins enhanced sustainability of crop production

The Green Revolution transformed agriculture with high-yielding, stress-resistant varieties. However, the urgent need for more sustainable agricultural development presents new challenges: increasing crop yield, improving nutritional quality, and enhancing resource-use efficiency. Soil plays a vital role in crop-production systems and ecosystem services, providing water, nutrients, and physical anchorage for crop growth. Despite advancements in plant and soil sciences, our understanding of belowground plant-soil interactions, which impact both crop performance and soil health, remains limited. Here, we argue that a lack of understanding of these plant-soil interactions hinders sustainable crop production. We propose that targeted engineering of crops and soils can provide a fresh approach to achieve higher yields, more efficient sustainable crop production, and improved soil health.

Multi-trait association mapping for phosphorous efficiency reveals flexible root architectures in sorghum

BACKGROUND

On tropical regions, phosphorus (P) fixation onto aluminum and iron oxides in soil clays restricts P diffusion from the soil to the root surface, limiting crop yields. While increased root surface area favors P uptake under low-P availability, the relationship between the three-dimensional arrangement of the root system and P efficiency remains elusive. Here, we simultaneously assessed allelic effects of loci associated with a variety of root and P efficiency traits, in addition to grain yield under low-P availability, using multi-trait genome-wide association. We also set out to establish the relationship between root architectural traits assessed in hydroponics and in a low-P soil. Our goal was to better understand the influence of root morphology and architecture in sorghum performance under low-P availability.

RESULT

In general, the same alleles of associated SNPs increased root and P efficiency traits including grain yield in a low-P soil. We found that sorghum P efficiency relies on pleiotropic loci affecting root traits, which enhance grain yield under low-P availability. Root systems with enhanced surface area stemming from lateral root proliferation mostly up to 40 cm soil depth are important for sorghum adaptation to low-P soils, indicating that differences in root morphology leading to enhanced P uptake occur exactly in the soil layer where P is found at the highest concentration.

CONCLUSION

Integrated QTLs detected in different mapping populations now provide a comprehensive molecular genetic framework for P efficiency studies in sorghum. This indicated extensive conservation of P efficiency QTL across populations and emphasized the terminal portion of chromosome 3 as an important region for P efficiency in sorghum. Increases in root surface area via enhancement of lateral root development is a relevant trait for sorghum low-P soil adaptation, impacting the overall architecture of the sorghum root system. In turn, particularly concerning the critical trait for water and nutrient uptake, root surface area, root system development in deeper soil layers does not occur at the expense of shallow rooting, which may be a key reason leading to the distinctive sorghum adaptation to tropical soils with multiple abiotic stresses including low P availability and drought.

Enigmatic role of auxin response factors in plant growth and stress tolerance

Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.

Hydrotropism mechanisms and their interplay with gravitropism

Plants partly optimize their water recruitment from the growth medium by directing root growth toward a moisture source, a phenomenon termed hydrotropism. The default mechanism of downward growth, termed gravitropism, often functions to counteract hydrotropism when the water-potential gradient deviates from the gravity vector. This review addresses the identity of the root sites in which hydrotropism-regulating factors function to attenuate gravitropism and the interplay between these various factors. In this context, the function of hormones, including auxin, abscisic acid, and cytokinins, as well as secondary messengers, calcium ions, and reactive oxygen species in the conflict between these two opposing tropisms is discussed. We have assembled the available data on the effects of various chemicals and genetic backgrounds on both gravitropism and hydrotropism, to provide an up-to-date perspective on the interactions that dictate the orientation of root tip growth. We specify the relevant open questions for future research. Broadening our understanding of root mechanisms of water recruitment holds great potential for providing advanced approaches and technologies that can improve crop plant performance under less-than-optimal conditions, in light of predicted frequent and prolonged drought periods due to global climate change.

Defying gravity: WEEP promotes negative gravitropism in peach trees by establishing asymmetric auxin gradients

Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The peach (Prunus persica) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Little is known about the function of WEEP despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.

Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots

The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.

The OsEIL1-OsWOX11 transcription factor module controls rice crown root development in response to soil compaction

Optimizing the root architecture of crops is an effective strategy for improving crop yields. Soil compaction is a serious global problem that limits crop productivity by restricting root growth, but the underlying molecular mechanisms are largely unclear. Here, we show that ethylene stimulates rice (Oryza sativa) crown root development in response to soil compaction. First, we demonstrate that compacted soil promotes ethylene production and the accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) in rice roots, stimulating crown root primordia initiation and development, thereby increasing crown root number in lower stem nodes. Through transcriptome profiling and molecular analyses, we reveal that OsEIL1 directly activates the expression of WUSCHEL-RELATED HOMEOBOX 11 (OsWOX11), an activator of crown root emergence and growth, and that OsWOX11 mutations delay crown root development, thus impairing the plant's response to ethylene and soil compaction. Genetic analysis demonstrates that OsWOX11 functions downstream of OsEIL1. In summary, our results demonstrate that the OsEIL1-OsWOX11 module regulates ethylene action during crown root development in response to soil compaction, providing a strategy for the genetic modification of crop root architecture and grain agronomic traits.

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.

Convolutional neural networks combined with conventional filtering to semantically segment plant roots in rapidly scanned X-ray computed tomography volumes with high noise levels

BACKGROUND

X-ray computed tomography (CT) is a powerful tool for measuring plant root growth in soil. However, a rapid scan with larger pots, which is required for throughput-prioritized crop breeding, results in high noise levels, low resolution, and blurred root segments in the CT volumes. Moreover, while plant root segmentation is essential for root quantification, detailed conditional studies on segmenting noisy root segments are scarce. The present study aimed to investigate the effects of scanning time and deep learning-based restoration of image quality on semantic segmentation of blurry rice (Oryza sativa) root segments in CT volumes.

RESULTS

VoxResNet, a convolutional neural network-based voxel-wise residual network, was used as the segmentation model. The training efficiency of the model was compared using CT volumes obtained at scan times of 33, 66, 150, 300, and 600 s. The learning efficiencies of the samples were similar, except for scan times of 33 and 66 s. In addition, The noise levels of predicted volumes differd among scanning conditions, indicating that the noise level of a scan time ≥ 150 s does not affect the model training efficiency. Conventional filtering methods, such as median filtering and edge detection, increased the training efficiency by approximately 10% under any conditions. However, the training efficiency of 33 and 66 s-scanned samples remained relatively low. We concluded that scan time must be at least 150 s to not affect segmentation. Finally, we constructed a semantic segmentation model for 150 s-scanned CT volumes, for which the Dice loss reached 0.093. This model could not predict the lateral roots, which were not included in the training data. This limitation will be addressed by preparing appropriate training data.

CONCLUSIONS

A semantic segmentation model can be constructed even with rapidly scanned CT volumes with high noise levels. Given that scanning times ≥ 150 s did not affect the segmentation results, this technique holds promise for rapid and low-dose scanning. This study offers insights into images other than CT volumes with high noise levels that are challenging to determine when annotating.

Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.)

Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.

Deep learning-based association analysis of root image data and cucumber yield

The root system is important for the absorption of water and nutrients by plants. Cultivating and selecting a root system architecture (RSA) with good adaptability and ultrahigh productivity have become the primary goals of agricultural improvement. Exploring the correlation between the RSA and crop yield is important for cultivating crop varieties with high-stress resistance and productivity. In this study, 277 cucumber varieties were collected for root system image analysis and yield using germination plates and greenhouse cultivation. Deep learning tools were used to train ResNet50 and U-Net models for image classification and segmentation of seedlings and to perform quality inspection and productivity prediction of cucumber seedling root system images. The results showed that U-Net can automatically extract cucumber root systems with high quality (F1_score ≥ 0.95), and the trained ResNet50 can predict cucumber yield grade through seedling root system image, with the highest F1_score reaching 0.86 using 10-day-old seedlings. The root angle had the strongest correlation with yield, and the shallow- and steep-angle frequencies had significant positive and negative correlations with yield, respectively. RSA and nutrient absorption jointly affected the production capacity of cucumber plants. The germination plate planting method and automated root system segmentation model used in this study are convenient for high-throughput phenotypic (HTP) research on root systems. Moreover, using seedling root system images to predict yield grade provides a new method for rapidly breeding high-yield RSA in crops such as cucumbers.

A newly evolved rice-specific gene JAUP1 regulates jasmonate biosynthesis and signalling to promote root development and multi-stress tolerance

Root architecture and function are critical for plants to secure water and nutrient supply from the soil, but environmental stresses alter root development. The phytohormone jasmonic acid (JA) regulates plant growth and responses to wounding and other stresses, but its role in root development for adaptation to environmental challenges had not been well investigated. We discovered a novel JA Upregulated Protein 1 gene (JAUP1) that has recently evolved in rice and is specific to modern rice accessions. JAUP1 regulates a self-perpetuating feed-forward loop to activate the expression of genes involved in JA biosynthesis and signalling that confers tolerance to abiotic stresses and regulates auxin-dependent root development. Ectopic expression of JAUP1 alleviates abscisic acid- and salt-mediated suppression of lateral root (LR) growth. JAUP1 is primarily expressed in the root cap and epidermal cells (EPCs) that protect the meristematic stem cells and emerging LRs. Wound-activated JA/JAUP1 signalling promotes crosstalk between the root cap of LR and parental root EPCs, as well as induces cell wall remodelling in EPCs overlaying the emerging LR, thereby facilitating LR emergence even under ABA-suppressive conditions. Elevated expression of JAUP1 in transgenic rice or natural rice accessions enhances abiotic stress tolerance and reduces grain yield loss under a limited water supply. We reveal a hitherto unappreciated role for wound-induced JA in LR development under abiotic stress and suggest that JAUP1 can be used in biotechnology and as a molecular marker for breeding rice adapted to extreme environmental challenges and for the conservation of water resources.

Not so hidden anymore: Advances and challenges in understanding root growth under water deficits

Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.

Regulatory networks in plant responses to drought and cold stress

Drought and cold represent distinct types of abiotic stress, each initiating unique primary signaling pathways in response to dehydration and temperature changes, respectively. However, a convergence at the gene regulatory level is observed where a common set of stress-responsive genes is activated to mitigate the impacts of both stresses. In this review, we explore these intricate regulatory networks, illustrating how plants coordinate distinct stress signals into a collective transcriptional strategy. We delve into the molecular mechanisms of stress perception, stress signaling, and the activation of gene regulatory pathways, with a focus on insights gained from model species. By elucidating both the shared and distinct aspects of plant responses to drought and cold, we provide insight into the adaptive strategies of plants, paving the way for the engineering of stress-resilient crop varieties that can withstand a changing climate.

Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.

Genomic basis determining root system architecture in maize

KEY MESSAGE

A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.

Fast and Efficient Root Phenotyping via Pose Estimation

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.

Rhizosphere engineering for soil carbon sequestration

The rhizosphere is the central hotspot of water and nutrient uptake by plants, rhizodeposition, microbial activities, and plant-soil-microbial interactions. The plasticity of plants offers possibilities to engineer the rhizosphere to mitigate climate change. We define rhizosphere engineering as targeted manipulation of plants, soil, microorganisms, and management to shift rhizosphere processes for specific aims [e.g., carbon (C) sequestration]. The rhizosphere components can be engineered by agronomic, physical, chemical, biological, and genomic approaches. These approaches increase plant productivity with a special focus on C inputs belowground, increase microbial necromass production, protect organic compounds and necromass by aggregation, and decrease C losses. Finally, we outline multifunctional options for rhizosphere engineering: how to boost C sequestration, increase soil health, and mitigate global change effects.

Root system architecture change in response to waterlogging stress in a 448 global collection of rapeseeds (Brassica napus L.)

MAIN CONCLUSIONS

A novel image-based screening method for precisely identifying genotypic variations in rapeseed RSA under waterlogging stress was developed. Five key root traits were confirmed as good indicators of waterlogging and might be employed in breeding, particularly when using the MFVW approach. Waterlogging is a vital environmental factor that has detrimental effects on the growth and development of rapeseed (Brassica napus L.). Plant roots suffer from hypoxia under waterlogging, which ultimately confers yield penalty. Therefore, it is crucially important to understand the genetic variation of root system architecture (RSA) in response to waterlogging stress to guide the selection of new tolerant cultivars with favorable roots. This research was conducted to investigate RSA traits using image-based screening techniques to better understand how RSA changes over time during waterlogging at the seedling stage. First, we performed a t-test by comparing the relative root trait value between four tolerant and four sensitive accessions. The most important root characteristics associated with waterlogging tolerance at 12 h are total root length (TRL), total root surface area (TRSA), total root volume (TRV), total number of tips (TNT), and total number of forks (TNF). The root structures of 448 rapeseed accessions with or without waterlogging showed notable genetic diversity, and all traits were generally restrained under waterlogging conditions, except for the total root average diameter. Additionally, according to the evaluation and integration analysis of 448 accessions, we identified that five traits, TRL, TRSA, TRV, TNT, and TNF, were the most reliable traits for screening waterlogging-tolerant accessions. Using analysis of the membership function value (MFVW) and D-value of the five selected traits, 25 extremely waterlogging-tolerant materials were screened out. Waterlogging significantly reduced RSA, inhibiting root growth compared to the control. Additionally, waterlogging increased lipid peroxidation, accompanied by a decrease in the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). This study effectively improves our understanding of the response of RSA to waterlogging. The image-based screening method developed in this study provides a new scientific guidance for quickly examining the basic RSA changes and precisely predicting waterlogging-tolerant rapeseed germplasms, thus expanding the genetic diversity of waterlogging-tolerant rapeseed germplasm available for breeding.

A double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice

Drought stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of drought resistance in rice. Here, through a genome-wide association study, we reveal that natural variations in DROUGHT RESISTANCE GENE 9 (DRG9), encoding a double-stranded RNA (dsRNA) binding protein, contribute to drought resistance. Under drought stress, DRG9 condenses into stress granules (SGs) through liquid-liquid phase separation via a crucial α-helix. DRG9 recruits the mRNAs of OsNCED4, a key gene for the biosynthesis of abscisic acid, into SGs and protects them from degradation. In drought-resistant DRG9 allele, natural variations in the coding region, causing an amino acid substitution (G267F) within the zinc finger domain, increase DRG9's binding ability to OsNCED4 mRNA and enhance drought resistance. Introgression of the drought-resistant DRG9 allele into the elite rice Huanghuazhan significantly improves its drought resistance. Thus, our study underscores the role of a dsRNA-binding protein in drought resistance and its promising value in breeding drought-resistant rice.

Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant

The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.

Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.

Complex plant responses to drought and heat stress under climate change

Global climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development and reproduction, and previous studies have revealed how these stresses induce plant responses at physiological and molecular levels. Here, we provide a comprehensive overview of current knowledge concerning how drought, heat, and combinations of these stress conditions affect the status of plants, including crops, by affecting factors such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, and molecular signaling mechanisms. We further discuss stress-responsive regulatory factors such as transcription factors and signaling factors, which play critical roles in adaptation to both drought and heat stress conditions and potentially function as 'hubs' in drought and/or heat stress responses. Additionally, we present recent findings based on forward genetic approaches that reveal natural variations in agricultural crops that play critical roles in agricultural traits under drought and/or heat conditions. Finally, we provide an overview of the application of decades of study results to actual agricultural fields as a strategy to increase drought and/or heat stress tolerance. This review summarizes our current understanding of plant responses to drought, heat, and combinations of these stress conditions.

How plants sense and respond to osmotic stress

Drought is one of the most serious abiotic stresses to land plants. Plants sense and respond to drought stress to survive under water deficiency. Scientists have studied how plants sense drought stress, or osmotic stress caused by drought, ever since Charles Darwin, and gradually obtained clues about osmotic stress sensing and signaling in plants. Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level, including changes in turgor, cell wall stiffness and integrity, membrane tension, and cell fluid volume, and plants may sense some of these stimuli and trigger downstream responses. In this review, we emphasized water potential and movements in organisms, compared putative signal inputs in cell wall-containing and cell wall-free organisms, prospected how plants sense changes in turgor, membrane tension, and cell fluid volume under osmotic stress according to advances in plants, animals, yeasts, and bacteria, summarized multilevel biochemical and physiological signal outputs, such as plasma membrane nanodomain formation, membrane water permeability, root hydrotropism, root halotropism, Casparian strip and suberin lamellae, and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors. We also discussed the core scientific questions, provided perspective about the future directions in this field, and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

Understanding role of roots in plant response to drought: Way forward to climate-resilient crops

Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high-throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought-resilient cultivars.

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.

Grass lignin: biosynthesis, biological roles, and industrial applications

Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.

Genetic regulation of the root angle in cereals

The root angle plays a critical role in efficiently capturing nutrients and water from different soil layers. Steeper root angles enable access to mobile water and nitrogen from deeper soil layers, whereas shallow root angles facilitate the capture of immobile phosphorus from the topsoil. Thus, understanding the genetic regulation of the root angle is crucial for breeding crop varieties that can efficiently capture resources and enhance yield. Moreover, this understanding can contribute to developing varieties that effectively sequester carbon in deeper soil layers, supporting global carbon mitigation efforts. Here we review and consolidate significant recent discoveries regarding the molecular components controlling root angle in cereal crop species and outline the remaining research gaps in this field.

Combined GWAS and eGWAS reveals the genetic basis underlying drought tolerance in emmer wheat (Triticum turgidum L.)

Drought is one of the major environmental constraints for wheat production world-wide. As the progenitor and genetic reservoir of common wheat, emmer wheat is considered as an invaluable gene pool for breeding drought-tolerant wheat. Combining GWAS and eGWAS analysis of 107 accessions, we identified 86 QTLs, 105 462 eQTLs as well as 68 eQTL hotspots associating with drought tolerance (DT) in emmer wheat. A complex regulatory network composed of 185 upstream regulator and 2432 downstream drought-responsive candidates was developed, of which TtOTS1 was found to play a negative effect in determining DT through affecting root development. This study sheds light on revealing the genetic basis underlying DT, which will provide the indispensable genes and germplasm resources for elite drought tolerance wheat improvement and breeding.

Choreographing root architecture and rhizosphere interactions through synthetic biology

Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

Morpho-Anatomical Modulation of Seminal Roots in Response to Water Deficit in Durum Wheat (Triticum turgidum var. durum)

The productivity of durum wheat in Mediterranean regions is greatly reduced by water deficits that vary in intensity and time of occurrence. The development of more tolerant cultivars is the main solution for fighting these stresses, but this requires prior study of their mechanisms. The involvement of the root system in drought avoidance is of major importance. It is in this context that the present work attempts to establish the impact of morpho-anatomical remodeling of seminal roots on dehydration avoidance at the javelina stage in five durum wheat genotypes grown under three water regimes, 100%, 60% and 30% of field capacity (FC). In the last two treatments, which were applied by stopping irrigation, moisture was concentrated mainly in the depths of the substrate cylinders and was accompanied by greater root elongation compared with the control. The elongation reached rates of 20 and 22% in the ACSAD 1231 genotype and 12 and 13% in the Waha genotype, in the 60% FC and 30% FC treatments respectively. The seminal roots anatomy was also modified by water deficit in all genotypes but to different degrees. The diameter of vessels in the late metaxylem vessels was reduced, reaching 17.3 and 48.2% in the Waha genotype in the 60% FC and 30% FC treatments, respectively. The water deficit also increased the number of vessels in the early metaxylem, while reducing the diameter of its conducting vessels. ACSAD 1361 and Langlois genotypes stood out with the highest rates of diameter reduction. The morpho-anatomical transformations of the roots contributed effectively to the plants' absorption of water and, consequently, to the maintenance of a fairly high relative water content, approaching 80%.

Do DEEPER ROOTING 1 Homologs Regulate the Lateral Root Slope Angle in Cucumber (Cucumis sativus)?

The architecture of the root system is fundamental to plant productivity. The rate of root growth, the density of lateral roots, and the spatial structure of lateral and adventitious roots determine the developmental plasticity of the root system in response to changes in environmental conditions. One of the genes involved in the regulation of the slope angle of lateral roots is DEEPER ROOTING 1 (DRO1). Its orthologs and paralogs have been identified in rice, Arabidopsis, and several other species. However, nothing is known about the formation of the slope angle of lateral roots in species with the initiation of lateral root primordia within the parental root meristem. To address this knowledge gap, we identified orthologs and paralogs of the DRO1 gene in cucumber (Cucumis sativus) using a phylogenetic analysis of IGT protein family members. Differences in the transcriptional response of CsDRO1, CsDRO1-LIKE1 (CsDRO1L1), and CsDRO1-LIKE2 (CsDRO1L2) to exogenous auxin were analyzed. The results showed that only CsDRO1L1 is auxin-responsive. An analysis of promoter-reporter fusions demonstrated that the CsDRO1, CsDRO1L1, and CsDRO1L2 genes were expressed in the meristem in cell files of the central cylinder, endodermis, and cortex; the three genes displayed different expression patterns in cucumber roots with only partial overlap. A knockout of individual CsDRO1, CsDRO1L1, and CsDRO1L2 genes was performed via CRISPR/Cas9 gene editing. Our study suggests that the knockout of individual genes does not affect the slope angle formation during lateral root primordia development in the cucumber parental root.

The crucial role of lateral root angle in enhancing drought resilience in cotton

Introduction

Plant responses to drought stress are influenced by various factors, including the lateral root angle (LRA), stomatal regulation, canopy temperature, transpiration rate and yield. However, there is a lack of research that quantifies their interactions, especially among different cotton varieties.

Methods

This experiment included two water treatments: well-watered (75 ± 5% soil relative water content) and drought stress (50 ± 5% soil relative water content) starting from the three-leaf growth stage.

Results

The results revealed that different LRA varieties show genetic variation under drought stress. Among them, varieties with smaller root angles show greater drought tolerance. Varieties with smaller LRAs had significantly increased stomatal opening by 15% to 43%, transpiration rate by 61.24% and 62.00%, aboveground biomass by 54% to 64%, and increased seed cotton yield by 76% to 79%, and decreased canopy temperature by 9% to 12% under drought stress compared to the larger LRAs. Varieties with smaller LRAs had less yield loss under drought stress, which may be due to enhanced access to deeper soil water, compensating for heightened stomatal opening and elevated transpiration rates. The increase in transpiration rate promotes heat dissipation from leaves, thereby reducing leaf temperature and protecting leaves from damage.

Discussion

Demonstrating the advantages conferred by the development of a smaller LRA under drought stress conditions holds value in enhancing cotton's resilience and promoting its sustainable adaptation to abiotic stressors.

Effect of a QTL on wheat chromosome 5B associated with enhanced root dry mass on transpiration and nitrogen uptake under contrasting drought scenarios in wheat

BACKGROUND

A sufficient nitrogen supply is crucial for high-quality wheat yields. However, the use of nitrogen fertilization can also negatively influence ecosystems due to leaching or volatile atmospheric emissions. Drought events, increasingly prevalent in many crop production areas, significantly impact nitrogen uptake. Breeding more efficient wheat varieties is necessary to achieve acceptable yields with limited nitrogen and water. Crop root systems play a crucial role as the primary organ for absorbing water and nutrients. To investigate the impact of an enhanced root system on nitrogen and water use efficiency in wheat under various irrigation conditions, this study conducted two experiments using precision phenotyping platforms for controlled drought stress treatment. Experiment 1 involved four contrasting winter wheat genotypes. It included the Chinese variety Ning0604, carrying a quantitative trait locus (QTL) on chromosome 5B associated with a higher root dry biomass, and three elite German varieties, Elixer, Genius, and Leandrus. Experiment 2 compared near-isogenic lines (NIL) of the three elite varieties, each containing introgressions of the QTL on chromosome 5B linked to root dry mass. In both experiments, nitrogen partitioning was tracked via isotope discrimination after fertilization with 5 Atom % 15N-labeled KNO3-.

RESULTS

In experiment 1 the quantification by 15N isotope discrimination revealed significantly (p < 0.05) higher nitrogen derived from fertilizer in the root organ for Ning0604 than those of the three German varieties. In experiment 2, two out of three NILs showed a significantly (p < 0.05) higher uptake of N derived from fertilizer than their respective recipient line under well-watered conditions. Furthermore, significantly lower transpiration rates (p < 0.1) were observed in one NIL compared to its respective recipient.

CONCLUSIONS

The combination of the DroughtSpotter facility coupled with 15N tracer-based tracking of N uptake and remobilization extends the insight into the impact of genetically altered root biomass on wheat NUE and WUE under different water availability scenarios. The study shows the potential for how a modified genetic constitution of the locus on wheat chromosome 5B can reduce transpiration and enhance N uptake. The dependence of the observations on the recipient and water availability suggests a need for further research to investigate the interaction with genetic background traits.

Potential of rice tillering for sustainable food production

Tillering, also known as shoot branching, is a fundamental trait for cereal crops such as rice to produce sufficient panicle numbers. Effective tillering that guarantees successful panicle production is essential for achieving high crop yields. Recent advances in molecular biology have revealed the mechanisms underlying rice tillering; however, in rice breeding and cultivation, there remain limited genes or alleles suitable for effective tillering and high yields. A recently identified quantitative trait locus (QTL) called MORE PANICLES 3 (MP3) has been cloned as a single gene and shown to promote tillering and to moderately increase panicle number. This gene is an ortholog of the maize domestication gene TB1, and it has the potential to increase grain yield under ongoing climate change and in nutrient-poor environments. This review reconsiders the potential and importance of tillering for sustainable food production. Thus, I provide an overview of rice tiller development and the currently understood molecular mechanisms that underly it, focusing primarily on the biosynthesis and signaling of strigolactones, effective QTLs, and the importance of MP3 (TB1). The possible future benefits in using promising QTLs such as MP3 to explore agronomic solutions under ongoing climate change and in nutrient-poor environments are also highlighted.

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.

Ethylene Modulates Rice Root Plasticity under Abiotic Stresses

Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.

Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways

KEY MESSAGE

Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle

BACKGROUND

Plants adjust their growth orientations primarily in response to light and gravity signals. Considering that the gravity vector is fixed and the angle of light incidence is constantly changing, plants must somehow integrate these signals to establish organ orientation, commonly referred to as gravitropic set-point angle (GSA). The IGT gene family contains known regulators of GSA, including the gene clades LAZY, DEEPER ROOTING (DRO), and TILLER ANGLE CONTROL (TAC).

RESULTS

Here, we investigated the influence of light on different aspects of GSA phenotypes in LAZY and DRO mutants, as well as the influence of known light signaling pathways on IGT gene expression. Phenotypic analysis revealed that LAZY and DRO genes are collectively required for changes in the angle of shoot branch tip and root growth in response to light. Single lazy1 mutant branch tips turn upward in the absence of light and in low light, similar to wild-type, and mimic triple and quadruple IGT mutants in constant light and high-light conditions, while triple and quadruple IGT/LAZY mutants show little to no response to changing light regimes. Further, the expression of IGT/LAZY genes is differentially influenced by daylength, circadian clock, and light signaling.

CONCLUSIONS

Collectively, the data show that differential expression of LAZY and DRO genes are required to enable plants to alter organ angles in response to light-mediated signals.

Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture

A central goal of biology is to understand how genetic variation produces phenotypic variation, which has been described as a genotype to phenotype (G to P) map. The plant form is continuously shaped by intrinsic developmental and extrinsic environmental inputs, and therefore plant phenomes are highly multivariate and require comprehensive approaches to fully quantify. Yet a common assumption in plant phenotyping efforts is that a few pre-selected measurements can adequately describe the relevant phenome space. Our poor understanding of the genetic basis of root system architecture is at least partially a result of this incongruence. Root systems are complex 3D structures that are most often studied as 2D representations measured with relatively simple univariate traits. In prior work, we showed that persistent homology, a topological data analysis method that does not pre-suppose the salient features of the data, could expand the phenotypic trait space and identify new G to P relations from a commonly used 2D root phenotyping platform. Here we extend the work to entire 3D root system architectures of maize seedlings from a mapping population that was designed to understand the genetic basis of maize-nitrogen relations. Using a panel of 84 univariate traits, persistent homology methods developed for 3D branching, and multivariate vectors of the collective trait space, we found that each method captures distinct information about root system variation as evidenced by the majority of non-overlapping QTL, and hence that root phenotypic trait space is not easily exhausted. The work offers a data-driven method for assessing 3D root structure and highlights the importance of non-canonical phenotypes for more accurate representations of the G to P map.

Root architecture and rhizosphere-microbe interactions

Plant roots fulfil crucial tasks during a plant's life. As roots encounter very diverse conditions while exploring the soil for resources, their growth and development must be responsive to changes in the rhizosphere, resulting in root architectures that are tailor-made for all prevailing circumstances. Using multi-disciplinary approaches, we are gaining more intricate insights into the regulatory mechanisms directing root system architecture. This Special Issue provides insights into our advancement of knowledge on different aspects of root development and identifies opportunities for future research.

Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum

Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.

Aluminium stress-induced modulation of root gravitropism in pea (Pisum sativum) via auxin signalling

Aluminium (Al) toxicity stands out as a primary cause of crop failure in acidic soils. The root gravity setpoint angle (GSA), one of the important traits of the root system architecture (RSA), plays a pivotal role in enabling plants to adapt to abiotic stress. This study explored the correlation between GSA and Al stress using hydroponic culture with pea (Pisum sativum) plants. The findings revealed that under Al stress, GSA increased in newly developed lateral roots. Notably, this response remained consistent regardless of the treatment duration, extending for at least 3 days during the experiment. Furthermore, exposure to Al led to a reduction in both the size and quantity of starch granules, pivotal components linked to gravity perception. The accumulation of auxin in root transition zone increased. This variation was mirrored in the expression of genes linked to granule formation and auxin efflux, particularly those in the PIN-formed family. This developmental framework suggested a unique role for the root gravitropic response that hinges on starch granules and auxin transport, acting as mediators in the modulation of GSA under Al stress. Exogenous application of indole-3-acetic acid (IAA) and the auxin efflux inhibitor N-1-naphthylphthalamic acid (NPA) had an impact on the root gravitropic response to Al stress. The outcomes indicate that Al stress inhibited polar auxin transport and starch granule formation, the two processes crucial for gravitropism. This impairment led to an elevation in GSA and a reconfiguration of RSA. This study introduces a novel perspective on how plant roots react to Al toxicity, culminating in RSA modification in the context of acidic soil with elevated Al concentrations.

Nitraria sibirica adapts to long-term soil water deficit by reducing photosynthesis, stimulating antioxidant systems, and accumulating osmoregulators

Amid climate change and shifts in precipitation patterns, drought conditions are expanding worldwide. Drought stress severely threatens plant growth in arid and semi-arid regions, wherein shrubs play a crucial role in maintaining ecological stability. Despite its ecological significance, studies are lacking on how Nitraria sibirica adapts to long-term drought stress. Therefore, in this study, to elucidate the mechanism of drought stress adaptation in N. sibirica, we analysed morphological, physiological, and transcriptional characteristics of plants in two soil habitats: riparian (moist) and desert (arid). The results showed that in desert soils, as soil water content decreased, leaf thickness increased, while plant height and leaf area decreased. Physiologically, photosynthesis decreased; soluble sugar, starch, proline, and hydrogen peroxide content increased significantly; while soluble proteins decreased significantly. Additionally, membrane lipid peroxidation products and antioxidant enzyme activities significantly increased under drought stress. Then, Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis identified 313 key genes, which were considered the most significantly enriched in the photosynthesis and photosynthetic antenna protein pathways. Further, we found that the proteins encoding photosystem II (PsbP, PsbQ, PsbR, PsbY, and Psb27), photosystem I (PsaD, PsaF, PsaG, PsaH, PsaK, and PsaO), photosynthetic electron transport (PetF), and light-trapping antenna proteins were significantly downregulated under drought stress. Taken together, these results suggest that N. sibirica adapts to long-term drought conditions by suppressing photosynthesis, activating antioxidant systems, and recruiting osmoregulators. This study provides a basis for elucidating the growth mechanisms of N. sibirica under long-term drought stress conditions.

Genetic Signature Controlling Root System Architecture in Diverse Spring Wheat Germplasm

Roots are the main sensing organ, initiating multiple signaling pathways in response to abiotic factors, including nutrients, drought, and salt stress. A focus on improving the root system architecture is a key strategy to mitigate these stresses in wheat crop. In the present study, a diversity panel comprising indigenous landraces and historical cultivars from Pakistan was characterized for the root system architecture (RSA) and important loci were identified using a genome-wide association study (GWAS). RSA of the diversity panel was characterized 30 days after sowing in brunch tubes, and root images were taken. A high-throughput root imaging analysis using Rhizovision software was performed by setting the scale to extract the eight RSA traits and four plant biomass-related traits. GWAS identified 323 association signals for 12 root and biomass traits present on all wheat chromosomes, while the most important and reliable genetic loci (based on pleotropic loci and candidate genes) were identified on chromosomes 2A, 2B, 5A, 5D, 6A, 7B, and 7D for RSA. SNP annotation and transcriptome profiling identified nine candidate genes regulating the RSA and plant biomass traits, including ROOTLESS WITH UNDETECTABLE MERISTEM1, MYB TRANSCRIPTION FACTOR4, BRASSINOSTEROID INSENSITIVE1, SLENDER RICE1, AUXIN-RESPONSIVE FACTOR25, SCARECROW, NARROW LEAF2, PIN-FORMED1 AND PHOSPHATE TRANSCRIPTION FACTOR1. This study provided pre-breeding information for deep-rooting genotypes and associated markers that will accelerate the incorporation of such traits in breeding.

Nitrogen fertilization application strategies improve yield of the rice cultivars with different yield types by regulating phytohormones

Rice (Oryza sativa L.) is the most important food crop worldwide, and its sustainable development is essential to ensure global food security. Panicle morphological and physiological characteristics plays an important role in rice yield formation. However, under different nitrogen (N) fertilization strategies, it is not clear whether the morphological and physiological state of panicles at panicle development stage affects the formation of yield. To understand how the panicle differentiation and development, and grain yield are affected by the N fertilization strategies, and clarify the relationship between related traits and yield in the process of panicle development in different cultivars. In this study consisted of no N fertilizer and four N fertilization strategies, a panicle weight type (PWT) rice cultivar, Dongfu 114 (DF114) and a panicle number type (PNT) rice cultivar, Longdao 11 (LD11) were grown in the field. The results showed that N fertilization strategies could improve the nitrogen use efficiency and yield of rice, but the response of different rice varieties to N fertilizer strategies was different. Different from the DF114, the further increase of panicle N fertilizer ratio could not further improve the yield of LD11, and the highest grain yield of DF114 and LD11 was obtained under N4 and N3 conditions, respectively. In addition, this study found that N fertilizer strategies can affect the content of phytohormones in rice at the panicle differentiation stage, and then regulate the differentiation and development of rice panicles to affect yield. It is of great significance to optimize the application mode of N fertilizer according to the characteristics of varieties to improve rice yield and ensure food security.

Enhancing climate change resilience in agricultural crops

Climate change threatens global food and nutritional security through negative effects on crop growth and agricultural productivity. Many countries have adopted ambitious climate change mitigation and adaptation targets that will exacerbate the problem, as they require significant changes in current agri-food systems. In this review, we provide a roadmap for improved crop production that encompasses the effective transfer of current knowledge into plant breeding and crop management strategies that will underpin sustainable agriculture intensification and climate resilience. We identify the main problem areas and highlight outstanding questions and potential solutions that can be applied to mitigate the impacts of climate change on crop growth and productivity. Although translation of scientific advances into crop production lags far behind current scientific knowledge and technology, we consider that a holistic approach, combining disciplines in collaborative efforts, can drive better connections between research, policy, and the needs of society.