Root hair formation in rice (Oryza sativa L.) differs between root types and is altered in artificial growth conditions

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.

The effect of root hairs on root water uptake is determined by root-soil contact and root hair shrinkage

The effect of root hairs on water uptake remains controversial. In particular, the key root hair and soil parameters that determine their importance have been elusive. We grew maize plants (Zea mays) in microcosms and scanned them using synchrotron-based X-ray computed microtomography. By means of image-based modelling, we investigated the parameters determining the effectiveness of root hairs in root water uptake. We explicitly accounted for rhizosphere features (e.g. root-soil contact and pore structure) and took root hair shrinkage of dehydrated root hairs into consideration. Our model suggests that > 85% of the variance in root water uptake is explained by the hair-induced increase in root-soil contact. In dry soil conditions, root hair shrinkage reduces the impact of hairs substantially. We conclude that the effectiveness of root hairs on root water uptake is determined by the hair-induced increase in root-soil contact and root hair shrinkage. Although the latter clearly reduces the effect of hairs on water uptake, our model still indicated facilitation of water uptake by root hairs at soil matric potentials from -1 to -0.1 MPa. Our findings provide new avenues towards a mechanistic understanding of the role of root hairs on water uptake.

Do roots need a good haircut for water uptake?

This article is a Commentary on Duddek et al. (2023), 240: 2484–2497.

Novel QTL for Lateral Root Density and Length Improve Phosphorus Uptake in Rice (Oryza sativa L.)

The rice root system consists of two types of lateral roots, indeterminate larger L-types capable of further branching, and determinate, short, unbranched S-types. L-type laterals correspond to the typical lateral roots of cereals whereas S-type laterals are unique to rice. Both types contribute to nutrient and water uptake and genotypic variation for density and length of these laterals could be exploited in rice improvement to enhance adaptations to nutrient and water-limited environments. Our objectives were to determine how best to screen for lateral root density and length and to identify markers linked to genotypic variation for these traits. Using different growing media showed that screening in nutrient solution exposed genotypic variation for S-type and L-type density, but only the lateral roots of soil-grown plants varied for their lengths. A QTL mapping population developed from parents contrasting for lateral root traits was grown in a low-P field, roots were sampled, scanned and density and length of lateral roots measured. One QTL each was detected for L-type density (LDC), S-type density on crown root (SDC), S-type density on L-type (SDL), S-type length on L-type (SLL), and crown root number (RNO). The QTL for LDC on chromosome 5 had a major effect, accounting for 46% of the phenotypic variation. This strong positive effect was confirmed in additional field experiments, showing that lines with the donor parent allele at qLDC5 had 50% higher LDC. Investigating the contribution of lateral root traits to P uptake using stepwise regressions indicated LDC and RNO were most influential, followed by SDL. Simulating effects of root trait differences conferred by the main QTL in a P uptake model confirmed that qLDC5 was most effective in improving P uptake followed by qRNO9 for RNO and qSDL9 for S-type lateral density on L-type laterals. Pyramiding qLDC5 with qRNO9 and qSDL9 would be possible given that trade-offs between traits were not detected. Phenotypic selection for the RNO trait during variety development would be feasible, however, the costs of doing so reliably for lateral root density traits is prohibitive and markers identified here therefore provide the first opportunity to incorporate such traits into a breeding program.

Phenotypes and Molecular Mechanisms Underlying the Root Response to Phosphate Deprivation in Plants

Phosphorus (P) is an essential macronutrient for plant growth. The roots are the main organ for nutrient and water absorption in plants, and they adapt to low-P soils by altering their architecture for enhancing absorption of inorganic phosphate (Pi). This review summarizes the physiological and molecular mechanisms underlying the developmental responses of roots to Pi starvation, including the primary root, lateral root, root hair, and root growth angle, in the dicot model plant Arabidopsis thaliana and the monocot model plant rice (Oryza sativa). The importance of different root traits and genes for breeding P-efficient roots in rice varieties for Pi-deficient soils are also discussed, which we hope will benefit the genetic improvement of Pi uptake, Pi-use efficiency, and crop yields.

Comparative Transcriptome Analysis Reveals the Interaction of Sugar and Hormone Metabolism Involved in the Root Hair Morphogenesis of the Endangered Fir Abies beshanzuensis

Abies beshanzuensis, an extremely rare and critically endangered plant with only three wild adult trees globally, is strongly mycorrhizal-dependent, leading to difficulties in protection and artificial breeding without symbiosis. Root hair morphogenesis plays an important role in the survival of mycorrhizal symbionts. Due to the lack of an effective genome and transcriptome of A. beshanzuensis, the molecular signals involved in the root hair development remain unknown, which hinders its endangered mechanism analysis and protection. Herein, transcriptomes of radicles with root hair (RH1) and without root hair (RH0) from A. beshanzuensis in vitro plantlets were primarily established. Functional annotation and differentially expressed gene (DEG) analysis showed that the two phenotypes have highly differentially expressed gene clusters. Transcriptome divergence identified hormone and sugar signaling primarily involved in root hair morphogenesis of A. beshanzuensis. Weighted correlation network analysis (WGCNA) coupled with quantitative real-time PCR (qRT-PCR) found that two hormone-sucrose-root hair modules were linked by IAA17, and SUS was positioned in the center of the regulation network, co-expressed with SRK2E in hormone transduction and key genes related to root hair morphogenesis. Our results contribute to better understanding of the molecular mechanisms of root hair development and offer new insights into deciphering the survival mechanism of A. beshanzuensis and other endangered species, utilizing root hair as a compensatory strategy instead of poor mycorrhizal growth.

Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation

BACKGROUND

Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus, indica, temperate japonica, and tropical japonica). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.

RESULTS

We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and Arabidopsis.

CONCLUSIONS

Root hair length and density are quantitative traits with complex and independent genetic control in rice. The genomic regions described here could be used as the basis for QTL development and further analysis of the genetic control of root hair length and density. We present a list of candidate genes involved in root hair formation and growth in rice, many of which have not been previously identified as having a relation to root hair growth. Since little is known about root hair growth in grasses, these provide a guide for further research and crop improvement.

Wheat heat shock factor TaHsfA2d contributes to plant responses to phosphate deficiency

Phosphate (Pi) availability has become a major constraint limiting crop growth and production. Heat shock factors (Hsfs) play important roles in mediating plant resistance to various environmental stresses, including heat, drought and salinity. However, whether members of the Hsf family are involved in the transcriptional regulation of plant responses to Pi insufficiency has not been reported. Here, we identified that TaHsfA2d, a member of the heat shock factor family, was strongly repressed by Pi deficiency. Overexpressing TaHsfA2d-4A in Arabidopsis results in significantly enhanced sensitivity to Pi deficiency, evidenced by increased anthocyanin content, decreased proliferation and elongation of lateral roots, and reduced Pi uptake. Furthermore, RNA-seq analyses showed that TaHsfA2d-4A functions through up-regulation of a number of genes involved in stress responses and flavonoid biosynthesis. Collectively, these results provide evidence that TaHsfA2d participates in the regulation of Pi deficiency stress, and that TaHsfA2d could serve as a valuable gene for genetic modification of crop tolerance to Pi starvation.

ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17

Background

The auxin indole-3-acetic acid (IAA) is a type of endogenous plant hormone with a low concentration in plants, but it plays an important role in their growth and development. The AUX/IAA gene family was found to be an early sensitive auxin gene with a complicated way of regulating growth and development in plants. The regulation of root growth and development by AUX/IAA family genes has been reported in Arabidopsis, rice and maize.

Results

In this study, subcellular localization indicated that ZmIAA1-ZmIAA6 primarily played a role in the nucleus. A thermogram analysis showed that AUX/IAA genes were highly expressed in the roots, which was also confirmed by the maize tissue expression patterns. In maize overexpressing ZmIAA5, the length of the main root, the number of lateral roots, and the stalk height at the seedling stage were significantly increased compared with those of the wild type, while the EMS mutant zmiaa5 was significantly reduced. The total number of roots and the dry weight of maize overexpressing ZmIAA5 at the mature stage were also significantly increased compared with those of the wild type, while those of the mutant zmiaa5 was significantly reduced. Yeast one-hybrid experiments showed that ZmTCP15/16/17 could specifically bind to the ZmIAA5 promoter region. Bimolecular fluorescence complementation and yeast two-hybridization indicated an interaction between ZmIAA5 and ZmARF5.

Conclusions

Taken together, the results of this study indicate that ZmIAA5 regulates maize root growth and development by interacting with ZmARF5 under the specific binding of ZmTCP15/16/17.

Building soil sustainability from root-soil interface traits

Great potential exists to harness plant traits at the root-soil interface, mainly rhizodeposition and root hairs, to 'build' soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.

Genome Editing Targets for Improving Nutrient Use Efficiency and Nutrient Stress Adaptation

In recent years, the development of RNA-guided genome editing (CRISPR-Cas9 technology) has revolutionized plant genome editing. Under nutrient deficiency conditions, different transcription factors and regulatory gene networks work together to maintain nutrient homeostasis. Improvement in the use efficiency of nitrogen (N), phosphorus (P) and potassium (K) is essential to ensure sustainable yield with enhanced quality and tolerance to stresses. This review outlines potential targets suitable for genome editing for understanding and improving nutrient use (NtUE) efficiency and nutrient stress tolerance. The different genome editing strategies for employing crucial negative and positive regulators are also described. Negative regulators of nutrient signalling are the potential targets for genome editing, that may improve nutrient uptake and stress signalling under resource-poor conditions. The promoter engineering by CRISPR/dead (d) Cas9 (dCas9) cytosine and adenine base editing and prime editing is a successful strategy to generate precise changes. CRISPR/dCas9 system also offers the added advantage of exploiting transcriptional activators/repressors for overexpression of genes of interest in a targeted manner. CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) are variants of CRISPR in which a dCas9 dependent transcription activation or interference is achieved. dCas9-SunTag system can be employed to engineer targeted gene activation and DNA methylation in plants. The development of nutrient use efficient plants through CRISPR-Cas technology will enhance the pace of genetic improvement for nutrient stress tolerance of crops and improve the sustainability of agriculture.

Abandoned agriculture soil can be recultivated by promoting biological phosphorus fertility when amended with nano-rock phosphate and suitable bacterial inoculant

In semi-arid regions, post-restoration vegetation recovery on abandoned agricultural lands often fails due to inherently low organic matter content and poor soil fertility conditions, including phosphorus (P). As such, amending these soils with controlled release P fertilizer, especially with suitable P solubilizing bacteria (PSB) may promote plant growth and productivity by stimulating biological P fertility. To this aim, a pot study was performed to evaluate the agronomic potential of maize and soil biological P pools, using encapsulated (ENRP) and non-encapsulated (NRP) nano-rock phosphate as the P fertilizer source, on reclaimed agricultural soil in the presence and absence of PSB inoculant. The experiment was setup following a 3 × 2 factorial arrangement with four replicates. Without PSB, NRP treatment showed marginal positive effects on plant growth, P nutrition and P use efficiency (PUE) compared to control treatment. Although larger gains with NRP treatment were more noticeable under PSB inoculation, ENRP was the most convenient slow-release P fertilizer, increasing plant growth, P nutrition and grain yield compared to all treatments. Importantly, PSB inoculation with ENRP resulted in significantly higher increase in soil CaCl2-P (8.91 mg P kg soil-1), citrate-P (26.98 mg P kg soil-1), enzyme-P (18.98 mg P kg soil-1), resin-P (11.41 mg P kg soil-1), and microbial-P (18.94 mg P kg soil-1), when compared to all treatment combinations. Although a decrease in soil HCl-P content was observed with both types of P fertilizer, significant differences were found only with PSB inoculation. A significant increase in soil biological P pools could be due to the higher specific area and crystalline structure of nano materials, providing increased number of active sites for PSB activity in the presence of biobased encapsulated shell. Furthermore, the increase in PSB abundance, higher root carboxylate secretions, and decreased rhizosphere pH in response to nano-structured P fertilizer, implies greater extension of rhizosphere promoting greater P mobilization and/or solubilization, particularly under PSB inoculated conditions. We conclude that cropping potential of abandoned agricultural lands can be enhanced by the use of nano-rock phosphate in combination with PSB inoculant, establishing a favorable micro-environment for higher plant growth and biochemical P fertility.

Integrated root phenotypes for improved rice performance under low nitrogen availability

Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional-structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L-type and S-type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct-seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct-seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.

Rice increases phosphorus uptake in strongly sorbing soils by intra-root facilitation

Upland rice (Oryza sativa) is adapted to strongly phosphorus (P) sorbing soils. The mechanisms underlying P acquisition, however, are not well understood, and models typically underestimate uptake. This complicates root ideotype development and trait-based selection for further improvement. We present a novel model, which correctly simulates the P uptake by a P-efficient rice genotype measured over 48 days of growth. The model represents root morphology at the local rhizosphere scale, including root hairs and fine S-type laterals. It simulates fast- and slowly reacting soil P and the P-solubilizing effect of root-induced pH changes in the soil. Simulations predict that the zone of pH changes and P solubilization around a root spreads further into the soil than the zone of P depletion. A root needs to place laterals outside its depletion- but inside its solubilization zone to maximize P uptake. S-type laterals, which are short but hairy, appear to be the key root structures to achieve that. Thus, thicker roots facilitate the P uptake by fine lateral roots. Uptake can be enhanced through longer root hairs and greater root length density but was less sensitive to total root length and root class proportions.

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15)

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

Significance of root hairs in developing stress-resilient plants for sustainable crop production

Root hairs represent a beneficial agronomic trait to potentially reduce fertilizer and irrigation inputs. Over the past decades, research in the plant model Arabidopsis thaliana has provided insights into root hair development, the underlying genetic framework and the integration of environmental cues within this framework. Recent years have seen a paradigm shift, where studies are now highlighting conservation and diversification of root hair developmental programs in other plant species and the agronomic relevance of root hairs in a wider ecological context. In this review, we specifically discuss the molecular evolution of the RSL (RHD Six-Like) pathway that controls root hair development and growth in land plants. We also discuss how root hairs contribute to plant performance as an active physiological rooting structure by performing resource acquisition, providing anchorage and constructing the rhizosphere with desirable physical, chemical and biological properties. Finally, we outline future research directions that can help achieve the potential of root hairs in developing sustainable agroecosystems.

Leaf phosphorus fractionation in rice to understand internal phosphorus-use efficiency

BACKGROUND AND AIMS

Phosphorus (P) availability is often limiting for rice (Oryza sativa) production. Improving internal P-use efficiency (PUE) is crucial to sustainable food production, particularly in low-input systems. A critical aspect of PUE in plants, and one that remains poorly understood, is the investment of leaf P in different chemical P fractions (nucleic acid-P, lipid-P, inorganic-P, metabolite-P and residual-P). The overarching objective of this study was to understand how these key P fractions influence PUE.

METHODS

Three high-PUE and two low-PUE rice genotypes were grown in hydroponics with contrasting P supplies. We measured PUE, total P, P fractions, photosynthesis and biomass.

KEY RESULTS

Low investment in lipid-P was strongly associated with increased photosynthetic PUE (PPUE), achieved by reducing total leaf P concentration while maintaining rapid photosynthetic rates. All low-P plants exhibited a low investment in inorganic-P and lipid-P, but not nucleic acid-P. In addition, whole-plant PUE was strongly associated with reduced total P concentration, increased biomass and increased preferential allocation of resources to the youngest mature leaves.

CONCLUSIONS

Lipid remodelling has been shown in rice before, but we show for the first time that reduced lipid-P investment improves PUE in rice without reducing photosynthesis. This presents a novel pathway for increasing PUE by targeting varieties with reduced lipid-P investment. This will benefit rice production in low-P soils and in areas where fertilizer use is limited, improving global food security by reducing P fertilizer demands and food production costs.

Breeding rice for a changing climate by improving adaptations to water saving technologies

Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.

Root hair phenotypes influence nitrogen acquisition in maize

BACKGROUND AND AIMS

The utility of root hairs for nitrogen (N) acquisition is poorly understood.

METHODS

We explored the utility of root hairs for N acquisition in the functional-structural model SimRoot and with maize genotypes with variable root hair length (RHL) in greenhouse and field environments.

KEY RESULTS

Simulation results indicate that long, dense root hairs can improve N acquisition under varying N availability. In the greenhouse, ammonium availability had no effect on RHL and low nitrate availability increased RHL, while in the field low N reduced RHL. Longer RHL was associated with 216 % increase in biomass and 237 % increase in plant N content under low-N conditions in the greenhouse and a 250 % increase in biomass and 200 % increase in plant N content in the field compared with short-RHL phenotypes. In a low-N field environment, genotypes with long RHL had 267 % greater yield than those with short RHL. We speculate that long root hairs improve N capture by increased root surface area and expanded soil exploration beyond the N depletion zone surrounding the root surface.

CONCLUSIONS

We conclude that root hairs play an important role in N acquisition. We suggest that root hairs merit consideration as a breeding target for improved N acquisition in maize and other crops.

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

Soil textures rather than root hairs dominate water uptake and soil-plant hydraulics under drought

Although the role of root hairs (RHs) in nutrient uptake is well documented, their role in water uptake and drought tolerance remains controversial. Maize (Zea mays) wild-type and its hair-defective mutant (Mut; roothairless 3) were grown in two contrasting soil textures (sand and loam). We used a root pressure chamber to measure the relation between transpiration rate (E) and leaf xylem water potential (ψleaf_x) during soil drying. Our hypotheses were: (1) RHs extend root-soil contact and reduce the ψleaf_x decline at high E in dry soils; (2) the impact of RHs is more pronounced in sand; and (3) Muts partly compensate for lacking RHs by producing longer and/or thicker roots. The ψleaf_x(E) relation was linear in wet conditions and became nonlinear as the soils dried. This nonlinearity occurred more abruptly and at less negative matric potentials in sand (ca. -10 kPa) than in loam (ca. -100 kPa). At more negative soil matric potentials, soil hydraulic conductance became smaller than root hydraulic conductance in both soils. Both genotypes exhibited 1.7 times longer roots in loam, but 1.6 times thicker roots in sand. No differences were observed in the ψleaf_x(E) relation and active root length between the two genotypes. In maize, RHs had a minor contribution to soil-plant hydraulics in both soils and their putative role in water uptake was smaller than that reported for barley (Hordeum vulgare). These results suggest that the role of RHs cannot be easily generalized across species and soil textures affect the response of root hydraulics to soil drying.

Genome-wide association study reveals the genetic architecture of root hair length in maize

Background

Root hair, a special type of tubular-shaped cell, outgrows from root epidermal cell and plays important roles in the acquisition of nutrients and water, as well as interactions with biotic and abiotic stress. Although many genes involved in root hair development have been identified, genetic basis of natural variation in root hair growth has never been explored.

Results

Here, we utilized a maize association panel including 281 inbred lines with tropical, subtropical, and temperate origins to decipher the phenotypic diversity and genetic basis of root hair length. We demonstrated significant associations of root hair length with many metabolic pathways and other agronomic traits. Combining root hair phenotypes with 1.25 million single nucleotide polymorphisms (SNPs) via genome-wide association study (GWAS) revealed several candidate genes implicated in cellular signaling, polar growth, disease resistance and various metabolic pathways.

Conclusions

These results illustrate the genetic basis of root hair length in maize, offering a list of candidate genes predictably contributing to root hair growth, which are invaluable resource for the future functional investigation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07961-z.

Heterogeneous nutrient supply promotes maize growth and phosphorus acquisition: additive and compensatory effects of lateral roots and root hairs

BACKGROUND AND AIMS

Root proliferation is a response to a heterogeneous nutrient distribution. However, the growth of root hairs in response to heterogeneous nutrients and the relationship between root hairs and lateral roots remain unclear. This study aims to understand the effects of heterogeneous nutrients on root hair growth and the trade-off between root hairs and lateral roots in phosphorus (P) acquisition.

METHODS

Near-isogenic maize lines, the B73 wild type (WT) and the rth3 root hairless mutant, were grown in rhizoboxes with uniform or localized supply of 40 (low) or 140 (high) mg P kg-1 soil.

RESULTS

Both WT and rth3 had nearly two-fold greater shoot biomass and P content under local than uniform treatment at low P. Significant root proliferation was observed in both WT and rth3 in the nutrient patch, with the WT accompanied by an obvious increase (from 0.7 to 1.2 mm) in root hair length. The root response ratio of rth3 was greater than that of WT at low P, but could not completely compensate for the loss of root hairs. This suggests that plants enhanced P acquisition through complementarity between lateral roots and root hairs, and thus regulated nutrient foraging and shoot growth. The disappearance of WT and rth3 root response differences at high P indicated that the P application reduced the dependence of the plants on specific root traits to obtain nutrients.

CONCLUSIONS

In addition to root proliferation, the root response to a nutrient-rich patch was also accompanied by root hair elongation. The genotypes without root hairs increased their investment in lateral roots in a nutrient-rich patch to compensate for the absence of root hairs, suggesting that plants enhanced nutrient acquisition by regulating the trade-off of complementary root traits.

In situ Root Phenotypes of Cotton Seedlings Under Phosphorus Stress Revealed Through RhizoPot

Phosphorus (P) deficiency is a common challenge in crop production because of its poor mobility through the soil. The root system plays a significant role in P absorption from the soil and is the initial indicator of low P levels. However, the phenotypic dynamics and longevity of cotton roots under P stress remain unknown. In this study, RhizoPot, an improvised in situ root observation device, was used to monitor the dynamics of root phenotypes of cotton seedlings under P-deficient (PD) and P-replete (PR) conditions. Low P stress reduced P absorption and accumulation in the roots, leading to low dry weight accumulation. Cotton seedlings responded to low P stress by increasing the number of lateral roots, specific root length, branch density, root length density, and length of root hairs. Additionally, the life span of root hairs was prolonged. Low P stress also reduced the average diameter of roots, promoted root extension, expanded the root coverage area, and increased the range of P acquisition. Principal component analysis revealed that the net root growth rate, root length density, root dry weight, P absorption efficiency, average root hair length, and taproot daily growth significantly influenced the cotton root architecture. Collectively, these results show that low P stress reduces the net growth rate of cotton seedling roots and restricts plant growth. Plants respond to P deficiency by extending the life span of root hairs and increasing specific root length and lateral root branch density. This change in root system architecture improves the adaptability of plants to low P conditions. The findings of this study may guide the selection of cotton varieties with efficient P utilization.

Root hairs are the most important root trait for rhizosheath formation of barley (Hordeum vulgare), maize (Zea mays) and Lotus japonicus (Gifu)

BACKGROUND AND AIMS

Rhizosheaths are defined as the soil adhering to the root system after it is extracted from the ground. Root hairs and mucilage (root exudates) are key root traits involved in rhizosheath formation, but to better understand the mechanisms involved their relative contributions should be distinguished.

METHODS

The ability of three species [barley (Hordeum vulgare), maize (Zea mays) and Lotus japonicus (Gifu)] to form a rhizosheath in a sandy loam soil was compared with that of their root-hairless mutants [bald root barley (brb), maize root hairless 3 (rth3) and root hairless 1 (Ljrhl1)]. Root hair traits (length and density) of wild-type (WT) barley and maize were compared along with exudate adhesiveness of both barley and maize genotypes. Furthermore, root hair traits and exudate adhesiveness from different root types (axile versus lateral) were compared within the cereal species.

KEY RESULTS

Per unit root length, rhizosheath size diminished in the order of barley > L. japonicus > maize in WT plants. Root hairs significantly increased rhizosheath formation of all species (3.9-, 3.2- and 1.8-fold for barley, L. japonicus and maize, respectively) but there was no consistent genotypic effect on exudate adhesiveness in the cereals. While brb exudates were more and rth3 exudates were less adhesive than their respective WTs, maize rth3 bound more soil than barley brb. Although both maize genotypes produced significantly more adhesive exudate than the barley genotypes, root hair development of WT barley was more extensive than that of WT maize. Thus, the greater density of longer root hairs in WT barley bound more soil than WT maize. Root type did not seem to affect rhizosheath formation, unless these types differed in root length.

CONCLUSIONS

When root hairs were present, greater root hair development better facilitated rhizosheath formation than root exudate adhesiveness. However, when root hairs were absent root exudate adhesiveness was a more dominant trait.

Does half a millimetre matter? Root hairs for yield stability. A commentary on 'Significance of root hairs for plant performance under contrasting field conditions and water deficit'

This article comments on:

M. Marin, D. S. Feeney, L. K. Brown, M. Naveed, S. Ruiz, N. Koebernick, A. G. Bengough, P. D. Hallett, T. Roose, J. Puértolas, I. C. Dodd and T. S. George, Significance of root hairs for plant performance under contrasting field conditions and water deficit, Annals of Botany, Volume 128, Issue 1, 30 June 2021, Pages 3–18, 10.1093/aob/mcaa181

Significance of root hairs for plant performance under contrasting field conditions and water deficit

BACKGROUND AND AIMS

Previous laboratory studies have suggested selection for root hair traits in future crop breeding to improve resource use efficiency and stress tolerance. However, data on the interplay between root hairs and open-field systems, under contrasting soils and climate conditions, are limited. As such, this study aims to experimentally elucidate some of the impacts that root hairs have on plant performance on a field scale.

METHODS

A field experiment was set up in Scotland for two consecutive years, under contrasting climate conditions and different soil textures (i.e. clay loam vs. sandy loam). Five barley (Hordeum vulgare) genotypes exhibiting variation in root hair length and density were used in the study. Root hair length, density and rhizosheath weight were measured at several growth stages, as well as shoot biomass, plant water status, shoot phosphorus (P) accumulation and grain yield.

KEY RESULTS

Measurements of root hair density, length and its correlation with rhizosheath weight highlighted trait robustness in the field under variable environmental conditions, although significant variations were found between soil textures as the growing season progressed. Root hairs did not confer a notable advantage to barley under optimal conditions, but under soil water deficit root hairs enhanced plant water status and stress tolerance resulting in a less negative leaf water potential and lower leaf abscisic acid concentration, while promoting shoot P accumulation. Furthermore, the presence of root hairs did not decrease yield under optimal conditions, while root hairs enhanced yield stability under drought.

CONCLUSIONS

Selecting for beneficial root hair traits can enhance yield stability without diminishing yield potential, overcoming the breeder's dilemma of trying to simultaneously enhance both productivity and resilience. Therefore, the maintenance or enhancement of root hairs can represent a key trait for breeding the next generation of crops for improved drought tolerance in relation to climate change.

Abscisic Acid Mediates Drought-Enhanced Rhizosheath Formation in Tomato

The rhizosheath, commonly defined as soil adhering to the root surface, may confer drought tolerance in various crop species by enhancing access to water and nutrients under drying stress conditions. Since the role of phytohormones in establishing this trait remains largely unexplored, we investigated the role of ABA in rhizosheath formation of wild-type (WT) and ABA-deficient (notabilis, not) tomatoes. Both genotypes had similar rhizosheath weight, root length, and root ABA concentration in well-watered soil. Drying stress treatment decreased root length similarly in both genotypes, but substantially increased root ABA concentration and rhizosheath weight of WT plants, indicating an important role for ABA in rhizosheath formation. Neither genotype nor drying stress treatment affected root hair length, but drying stress treatment decreased root hair density of not. Under drying stress conditions, root hair length was positively correlated with rhizosheath weight in both genotypes, while root hair density was positively correlated with rhizosheath weight in well-watered not plants. Root transcriptome analysis revealed that drought stress increased the expression of ABA-responsive transcription factors, such as AP2-like ER TF, alongside other drought-regulatory genes associated with ABA (ABA 8'-hydroxylase and protein phosphatase 2C). Thus, root ABA status modulated the expression of specific gene expression pathways. Taken together, drought-induced rhizosheath enhancement was ABA-dependent, but independent of root hair length.

Wheat root systems as a breeding target for climate resilience

In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.

Synergy between a shallow root system with a DRO1 homologue and localized P application improves P uptake of lowland rice

Improved phosphorus (P) use efficiency for crop production is needed, given the depletion of phosphorus ore deposits, and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has been little understood. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots after placing P near the roots at transplanting (P-dipping). The experiment identified that the P-dipping created an available P hotspot at the plant base of the soil surface layer where the qsor1-NIL had the greatest root biomass and root surface area despite no genotyipic differences in total values, whereby the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The superior surface root development of qsor1-NIL could have facilitated P uptakes from the P hotspot, implying that P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.

Cost-Benefit Analysis of the Upland-Rice Root Architecture in Relation to Phosphate: 3D Simulations Highlight the Importance of S-Type Lateral Roots for Reducing the Pay-Off Time

The rice root system develops a large number of nodal roots from which two types of lateral roots branch out, large L-types and fine S-types, the latter being unique to the species. All roots including S-types are covered by root hairs. To what extent these fine structures contribute to phosphate (P) uptake under P deficiency was investigated using a novel 3-D root growth model that treats root hairs as individual structures with their own Michaelis-Menten uptake kinetics. Model simulations indicated that nodal roots contribute most to P uptake followed by L-type lateral roots and S-type laterals and root hairs. This is due to the much larger root surface area of thicker nodal roots. This thickness, however, also meant that the investment in terms of P needed for producing nodal roots was very large. Simulations relating P costs and time needed to recover that cost through P uptake suggest that producing nodal roots represents a considerable burden to a P-starved plant, with more than 20 times longer pay-off time compared to S-type laterals and root hairs. We estimated that the P cost of these fine root structures is low enough to be recovered within a day of their formation. These results expose a dilemma in terms of optimizing root system architecture to overcome P deficiency: P uptake could be maximized by developing more nodal root tissue, but when P is growth-limiting, adding more nodal root tissue represents an inefficient use of the limiting factor P. In order to improve adaption to P deficiency in rice breeding two complementary strategies seem to exist: (1) decreasing the cost or pay-off time of nodal roots and (2) increase the biomass allocation to S-type roots and root hairs. To what extent genotypic variation exists within the rice gene pool for either strategy should be investigated.

A functional-structural model of upland rice root systems reveals the importance of laterals and growing root tips for phosphate uptake from wet and dry soils

BACKGROUND AND AIMS

Upland rice is often grown where water and phosphorus (P) are limited. To better understand the interaction between water and P availability, functional-structural models that mechanistically represent small-scale nutrient gradients and water dynamics in the rhizosphere are needed.

METHODS

Rice was grown in large columns using a P-deficient soil at three P supplies in the topsoil (deficient, sub-optimal and non-limiting) in combination with two water regimes (field capacity vs. drying periods). Root system characteristics, such as nodal root number, lateral types, interbranch distance, root diameters and the distribution of biomass with depth, as well as water and P uptake, were measured. Based on the observed root data, 3-D root systems were reconstructed by calibrating the structural architecure model CRootBox for each scenario. Water flow and P transport in the soil to each of the individual root segments of the generated 3-D root architectures were simulated using a multiscale flow and transport model. Total water and P uptake were then computed by adding up the uptake by all the root segments.

KEY RESULTS

Measurements showed that root architecture was significantly affected by the treatments. The moist, high P scenario had 2.8 times the root mass, double the number of nodal roots and more S-type laterals than the dry, low P scenario. Likewise, measured plant P uptake increased >3-fold by increasing P and water supply. However, drying periods reduced P uptake at high but not at low P supply. Simulation results adequately predicted P uptake in all scenarios when the Michaelis-Menten constant (Km) was corrected for diffusion limitation. They showed that the key drivers for P uptake are the different types of laterals (i.e. S- and L-type) and growing root tips. The L-type laterals become more important for overall water and P uptake than the S-type laterals in the dry scenarios. This is true across all the P treatments, but the effect is more pronounced as the P availability decreases.

CONCLUSIONS

This functional-structural model can predict the function of specific rice roots in terms of P and water uptake under different P and water supplies, when the structure of the root system is known. A future challenge is to predict how the structure root systems responds to nutrient and water availability.

P-dipping of rice seedlings increases applied P use efficiency in high P-fixing soils

Applied phosphorus (P) use efficiency is generally low due to the low mobility of P in soil and its affinity to form insoluble complexes. Localized P application nearby the root zone is a potential approach to overcome this issue in crop production. However, the interaction with soil conditions is little understood, which results in less effective application of this approach. Using root-box experiments and changing P-retention capacity of soils, we revealed that applied P use efficiency of rice can be substantially improved by dipping seedlings in P-enriched slurry at transplanting (P-dipping) even in highly P-fixing soils. Spatial analysis of soluble P in soils indicated that P-dipping creates a P hotspot because the P-enriched slurry is transferred with seedling roots. The P hotspot could have induced vigorous surface root and facilitated further P uptake from the spot. In contrast, the effect of conventional P incorporation depended on P-retention capacity of soils; no increases in soluble P content in soils or plant P uptakes were observed when P-retention capacity was high. Our finding of significant interaction between localized P application and a specific soil property should help improving applied P use efficiency and achieving sustainable rice production against depleting P fertilizer resources.

Moderate water stress in rice induces rhizosheath formation associated with abscisic acid and auxin responses

The rhizosheath is known to be beneficial for drought resistance in many plants, but the regulation of rhizosheath formation in rice plants is unclear. Here, we investigate rhizosheath formation in different rice varieties and root hair mutants. Our results showed that moderate water stress in rice induced rhizosheath formation. The soil porosity and water content were higher in the rice rhizosheath than in the rice bulk soil under moderate water stress. Additionally, rhizosheath formation in short root hair mutants was lower than in wild-type rice under moderate water stress. Moreover, transcriptomic results indicated that abscisic acid (ABA) and auxin were involved in root and root hair responses in rhizosheath formation. Further, blocking ABA and auxin pathways in wild type and in rhl1-1, the shortest root hair mutant, rhizosheath formation and root hair length were significantly decreased under moderate water stress. However, wild type plants maintained a higher root ABA content, root basipetal auxin transport, root hair length, and amount of rhizosheath than did rhl1-1. Our results suggest that moderate water stress in rice induces rhizosheath formation by modulating the ABA and auxin responses to regulate root and root hair growth, which may be used to breed rice varieties resistant to drought.

Energy costs of salt tolerance in crop plants

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H⁺ -ATPase also is a critical component. One proposed leak, that of Na⁺ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na⁺ and Cl^- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.

Estimating the importance of maize root hairs in low phosphorus conditions and under drought

BACKGROUND AND AIMS

Root hairs are single-cell extensions of the epidermis that face into the soil and increase the root-soil contact surface. Root hairs enlarge the rhizosphere radially and are very important for taking up water and sparingly soluble nutrients, such as the poorly soil-mobile phosphate. In order to quantify the importance of root hairs for maize, a mutant and the corresponding wild type were compared.

METHODS

The rth2 maize mutant with very short root hairs was assayed for growth and phosphorus (P) acquisition in a slightly alkaline soil with low P and limited water supply in the absence of mycorrhization and with ample P supply.

KEY RESULTS

Root and shoot growth was additively impaired under P deficiency and drought. Internal P concentrations declined with reduced water and P supply, whereas micronutrients (iron, zinc) were little affected. The very short root hairs in rth2 did not affect internal P concentrations, but the P content of juvenile plants was halved under combined stress. The rth2 plants had more fine roots and increased specific root length, but P mobilization traits (root organic carbon and phosphatase exudation) differed little.

CONCLUSIONS

The results confirm the importance of root hairs for maize P uptake and content, but not for internal P concentrations. Furthermore, the performance of root hair mutants may be biased by secondary effects, such as altered root growth.

Lateral Roots: Random Diversity in Adversity

Lateral roots are essential for soil foraging and uptake of minerals and water. They feature a large morphological diversity that results from divergent primordia or root growth and development patterns. Besides a structured diversity, resulting from the hierarchical and developmental organization of root systems, there exists a random diversity, occurring between roots of similar age, of the same hierarchical order, and exposed to uniform conditions. The physiological bases and functional consequences of this random diversity are largely ignored. Here we review the evidence for such random diversity throughout the plant kingdom, present innovative approaches based on statistical modeling to account for such diversity, and set the list of its potential benefits in front of a variable and unpredictable soil environment.

Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress

The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%-14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

Rice H2A.Z negatively regulates genes responsive to nutrient starvation but promotes expression of key housekeeping genes

The H2A.Z histone variant plays a role in the modulation of environmental responses, but the nature of the associated mechanisms remains enigmatic. We investigated global H2A.Z deposition and transcriptomic changes in rice (Oryza sativa) upon exposure to phosphate (Pi) deficiency and in response to RNAi knockdown of OsARP6, which encodes a key component of the H2A.Z exchange complex. Both Pi deficiency and OsARP6-knockdown resulted in similar, profound effects on global H2A.Z distribution. H2A.Z in the gene body of stress-responsive genes was negatively correlated with gene expression, and this was more apparent in response to Pi deficiency. In contrast, the role of H2A.Z at the transcription start site (TSS) was more context dependent, acting as a repressor of some stress-responsive genes, but an activator of some genes with housekeeping functions. This was especially evident upon OsARP6-knockdown, which resulted in down-regulation of a number of genes linked to chloroplast function that contained decreases in H2A.Z at the TSS. Consistently, OsARP6-RNAi plants exhibited lower chlorophyll content relative to the wild-type. Our results demonstrate that gene body-localized H2A.Z plays a prominent role in repressing stress-responsive genes under non-inductive conditions, whereas H2A.Z at the TSS functions as a positive or negative regulator of transcription.

Measurement of micro-scale soil deformation around roots using four-dimensional synchrotron tomography and image correlation

This study applied time lapse (four-dimensional) synchrotron X-ray computed tomography to observe micro-scale interactions between plant roots and soil. Functionally contrasting maize root tips were repeatedly imaged during ingress into soil columns of varying water content and compaction. This yielded sequences of three-dimensional densiometric data, representing time-resolved geometric soil and root configurations at the micronmetre scale. These data were used as inputs for two full-field kinematic quantification methods, which enabled the analysis of three-dimensional soil deformation around elongating roots. Discrete object tracking was used to track rigid mineral grains, while continuum digital volume correlation was used to track grey-level patterns within local sub-volumes. These techniques both allowed full-field soil displacements to be quantified at an intra-rhizosphere spatial sampling scale of less than 300 µm. Significant differences in deformation mechanisms were identified around different phenotypes under different soil conditions. A uniquely strong contrast was observed between intact and de-capped roots grown in dry, compacted soil. This provides evidence that functional traits of the root cap significantly reduce the amount of soil disturbance per unit of root elongation, with this effect being particularly significant in drier soil.

Fungal Disease Prevention in Seedlings of Rice (Oryza sativa) and Other Grasses by Growth-Promoting Seed-Associated Endophytic Bacteria from Invasive Phragmites australis

Non-cultivated plants carry microbial endophytes that may be used to enhance development and disease resistance of crop species where growth-promoting and protective microbes may have been lost. During seedling establishment, seedlings may be infected by several fungal pathogens that are seed or soil borne. Several species of Fusarium, Pythium and other water moulds cause seed rots during germination. Fusarium blights of seedlings are also very common and significantly affect seedling development. In the present study we screened nine endophytic bacteria isolated from the seeds of invasive Phragmites australis by inoculating onto rice, Bermuda grass (Cynodon dactylon), or annual bluegrass (Poa annua) seeds to evaluate plant growth promotion and protection from disease caused by Fusarium oxysporum. We found that three bacteria belonging to genus Pseudomonas spp. (SLB4-P. fluorescens, SLB6-Pseudomonas sp. and SY1-Pseudomonas sp.) promoted seedling development, including enhancement of root and shoot growth, and stimulation of root hair formation. These bacteria were also found to increase phosphate solubilization in in vitro experiments. Pseudomonas sp. (SY1) significantly protected grass seedlings from Fusarium infection. In co-culture experiments, strain SY1 strongly inhibited fungal pathogens with 85.71% growth inhibition of F. oxysporum, 86.33% growth inhibition of Curvularia sp. and 82.14% growth inhibition of Alternaria sp. Seedlings previously treated with bacteria were found much less infected by F. oxysporum in comparison to non-treated controls. On microscopic observation we found that bacteria appeared to degrade fungal mycelia actively. Metabolite products of strain SY1 in agar were also found to inhibit fungal growth on nutrient media. Pseudomonas sp. (SY1) was found to produce antifungal volatiles. Polymerase chain reaction (PCR) amplification using specific primers for pyrrolnitirin synthesis and HCN (hydrogen cyanide) production suggested presence of genes for both compounds in the genome of SY1. HCN was detected in cultures of SY1. We conclude that microbes from non-cultivated plants may provide disease protection and promote growth of crop plants.

An Explicit Structural Model of Root Hair and Soil Interactions Parameterised by Synchrotron X-ray Computed Tomography

The rhizosphere is a zone of fundamental importance for understanding the dynamics of nutrient acquisition by plant roots. The canonical difficulty of experimentally investigating the rhizosphere led long ago to the adoption of mathematical models, the most sophisticated of which now incorporate explicit representations of root hairs and rhizosphere soil. Mathematical upscaling regimes, such as homogenisation, offer the possibility of incorporating into larger-scale models the important mechanistic processes occurring at the rhizosphere scale. However, we lack concrete descriptions of all the features required to fully parameterise models at the rhizosphere scale. By combining synchrotron X-ray computed tomography (SRXCT) and a novel root growth assay, we derive a three-dimensional description of rhizosphere soil structure suitable for use in multi-scale modelling frameworks. We describe an approach to mitigate sub-optimal root hair detection via structural root hair growth modelling. The growth model is explicitly parameterised with SRXCT data and simulates three-dimensional root hair ideotypes in silico, which are suitable for both ideotypic analysis and parameterisation of 3D geometry in mathematical models. The study considers different hypothetical conditions governing root hair interactions with soil matrices, with their respective effects on hair morphology being compared between idealised and image-derived soil/root geometries. The studies in idealised geometries suggest that packing arrangement of soil affects hair tortuosity more than the particle diameter. Results in field-derived soil suggest that hair access to poorly mobile nutrients is particularly sensitive to the physical interaction between the growing hairs and the phase of the soil in which soil water is present (i.e. the hydrated textural phase). The general trends in fluid-coincident hair length with distance from the root, and their dependence on hair/soil interaction mechanisms, are conserved across Cartesian and cylindrical geometries.

SIZ1-mediated SUMOylation during phosphate homeostasis in plants: Looking beyond the tip of the iceberg

Availability of phosphate (Pi) is often limited in rhizospheres in different agroclimatic zones and adversely affects growth and development of plants. To circumvent this impasse, there is an urgent need and global consensus to develop Pi use efficient crops. To achieve this goal, it is essential to identify the molecular entities that exert regulatory influences on the sensing and signaling cascade governing Pi homeostasis. SIZ1 encodes a small ubiquitin-like modifier (SUMO E3) ligase, and plays a pivotal role in the post-translational SUMOylation of proteins. In this review, we discuss the reverse genetics approach conventionally used for providing circumstantial evidence towards the regulatory influences of SIZ1 on several morphophysiological and molecular traits that govern Pi homeostasis in taxonomically diverse Arabidopsis thaliana (Arabidopsis) and Oryza sativa (rice) model species. However, the efforts have been rather modest in identifying SUMO protein targets that play key roles in the maintenance of Pi homeostasis in these model plants contrary to the plethora of them now known in lower organisms and animals. Therefore, to predict the SIZ1-mediated SUMOylome involved in Pi homeostasis, the state-of-the-art high-throughput technologies often used for animals thus provide an attractive paradigm towards achieving the long-term goal of developing Pi use efficient crops.

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.

Analysis of aneuploid lines of bread wheat to map chromosomal locations of genes controlling root hair length

Background and Aims

Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Genetic stocks of the wheat cultivar 'Chinese Spring' were used to map genes that control root hair length.

Methods

Aneuploid stocks of 'Chinese Spring' were screened using a rapid method based on rhizosheath size and then selected lines were assayed for root hair length to identify chromosomes harbouring genes controlling root hair length. A series of lines with various fractional deletions of candidate chromosomes were then screened to map the root hair loci more accurately. A line with a deletion in chromosome 5A was analysed with a 90 000 single nucleotide polymorphism (SNP) array. The phosphorus acquisition efficiency (PAE) of one deletion line was compared with that of euploid 'Chinese Spring' by growing the seedlings in pots at low and luxury phosphorus supplies.

Key Results

Chromosomes 1A, 1D and 5A were found to harbour genes controlling root hair length. The 90 000 SNP array identified two candidate genes controlling root hair length located on chromosome 5A. The line with a deletion in chromosome 5A had root hairs that were approx. 20 % shorter than euploid 'Chinese Spring', but this was insufficient to reduce its PAE.

Conclusions

A rapid screen for rhizosheath size enabled chromosomal regions controlling root hair length to be mapped in the wheat cultivar 'Chinese Spring' and subsequent analysis with an SNP array identified candidate genes controlling root hair length. The difference in root hair length between euploid 'Chinese Spring' and a deletion line identified in the rapid screen was still apparent, albeit attenuated, when the seedlings were grown on a fully fertilized soil.

Roles, Regulation, and Agricultural Application of Plant Phosphate Transporters

Phosphorus (P) is an essential mineral nutrient for plant growth and development. Low availability of inorganic phosphate (orthophosphate; Pi) in soil seriously restricts the crop production, while excessive fertilization has caused environmental pollution. Pi acquisition and homeostasis depend on transport processes controlled Pi transporters, which are grouped into five families so far: PHT1, PHT2, PHT3, PHT4, and PHT5. This review summarizes the current understanding on plant PHT families, including phylogenetic analysis, function, and regulation. The potential application of Pi transporters and the related regulatory factors for developing genetically modified crops with high phosphorus use efficiency (PUE) are also discussed in this review. At last, we provide some potential strategies for developing high PUE crops under salt or drought stress conditions, which can be valuable for improving crop yields challenged by global scarcity of water resources and increasing soil salinization.