Root nutrient foraging

Safeguarding the fragile rice–wheat ecosystem of the Indo-Gangetic Plains through bio-priming and bioaugmentation interventions

Managing agrochemicals for crop production always remains a classic challenge for us to maintain the doctrine of sustainability. Intensively cultivated rice–wheat production system without using the organics (organic amendments, manures, biofertilizers) has a tremendous impact on soil characteristics (physical, chemical, and biological), environmental quality (water, air), input use efficiency, ecosystem biodiversity, and nutritional security. Consequently, crop productivity is found to be either decreasing or stagnating. Rice–wheat cropping system is the major agroecosystem in India feeding millions of people, which is widely practiced in the Indo-Gangetic Plains (IGP). Microorganisms as key players in the soil system can restore the degraded ecosystems using a variety of mechanisms. Here, we propose how delivery systems (i.e., the introduction of microbes in seed, soil, and crop through bio-priming and/or bioaugmentation) can help us in eradicating food scarcity and maintaining sustainability without compromising the ecosystem services. Both bio-priming and bioaugmentation are efficient techniques to utilize bio-agents judiciously for successful crop production by enhancing phytohormones, nutrition status, and stress tolerance levels in plants (including mitigating of abiotic stresses and biocontrol of pests/pathogens). However, there are some differences in application methods, and the latter one also includes the aspects of bioremediation or soil detoxification. Overall, we have highlighted different perspectives on applying biological solutions in the IGP to sustain the dominant (rice–wheat) cropping sequence.

Rice plants respond to ammonium stress by adopting a helical root growth pattern

High levels of ammonium nutrition reduce plant growth and different plant species have developed distinct strategies to maximize ammonium acquisition while alleviating ammonium toxicity through modulating root growth. To date, the mechanisms underlying plant tolerance or sensitivity towards ammonium remain unclear. Rice (Oryza sativa) uses ammonium as its main N source. Here we show that ammonium supply restricts rice root elongation and induces a helical growth pattern, which is attributed to root acidification resulting from ammonium uptake. Ammonium-induced low pH triggers the asymmetric distribution of auxin in rice root tips through changes in auxin signaling, thereby inducing a helical growth response. Blocking auxin signaling completely inhibited this root response. In contrast, this root response is not activated in ammonium-treated Arabidopsis. Acidification of Arabidopsis roots leads to the protonation of indole-3-acetic acid and dampening of the intracellular auxin signaling levels that are required for maintaining root growth. Our study suggests a different mode of action by ammonium on the root pattern and auxin response machinery in rice versus Arabidopsis, and the rice-specific helical root response towards ammonium is an expression of the ability of rice to moderate auxin signaling and root growth to utilize ammonium while confronting acidic stress.

Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean (Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach

Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.

The Plant Target of Rapamycin: A Conduc TOR of Nutrition and Metabolism in Photosynthetic Organisms

Living organisms possess many mechanisms to sense nutrients and favorable conditions, which allow them to grow and develop. Photosynthetic organisms are very diverse, from green unicellular algae to multicellular flowering plants, but most of them are sessile and thus unable to escape from the biotic and abiotic stresses they experience. The Target of Rapamycin (TOR) signaling pathway is conserved in all eukaryotes and acts as a central regulatory hub between growth and extrinsic factors, such as nutrients or stress. However, relatively little is known about the regulations and roles of this pathway in plants and algae. Although some features of the TOR pathway seem to have been highly conserved throughout evolution, others clearly differ in plants, perhaps reflecting adaptations to different lifestyles and the rewiring of this primordial signaling module to adapt to specific requirements. Indeed, TOR is involved in plant responses to a vast array of signals including nutrients, hormones, light, stresses or pathogens. In this review, we will summarize recent studies that address the regulations of TOR by nutrients in photosynthetic organisms, and the roles of TOR in controlling important metabolic pathways, highlighting similarities and differences with the other eukaryotes.

Rice NIN-LIKE PROTEIN 1 rapidly responds to nitrogen deficiency and improves yield and nitrogen use efficiency

Nitrogen (N) is indispensable for crop growth and yield, but excessive agricultural application of nitrogenous fertilizers has generated severe environmental problems. A desirable and economical solution to cope with these issues is to improve crop nitrogen use efficiency (NUE). Plant NUE has been a focal point of intensive research worldwide, yet much still has to be learned about its genetic determinants and regulation. Here, we show that rice (Oryza sativa L.) NIN-LIKE PROTEIN 1 (OsNLP1) plays a fundamental role in N utilization. OsNLP1 protein localizes in the nucleus and its transcript level is rapidly induced by N starvation. Overexpression of OsNLP1 improves plant growth, grain yield, and NUE under different N conditions, while knockout of OsNLP1 impairs grain yield and NUE under N-limiting conditions. OsNLP1 regulates nitrate and ammonium utilization by cooperatively orchestrating multiple N uptake and assimilation genes. Chromatin immunoprecipitation and yeast one-hybrid assays showed that OsNLP1 can directly bind to the promoter of these genes to activate their expression. Therefore, our results demonstrate that OsNLP1 is a key regulator of N utilization and represents a potential target for improving NUE and yield in rice.

Characterization on TaMPK14, an MAPK family gene of wheat, in modulating N-starvation response through regulating N uptake and ROS homeostasis

Wheat MAPK gene TaMPK14 is N starvation response and is crucial in modulating plant low-N stress tolerance. Improving plant N use efficiency (NUE) contributes largely to the sustainable crop production worldwide. In this study, TaMPK14, a mitogen-activated protein kinase (MAPK) family gene in T. aestivum, was characterized for the role in mediating N starvation response. TaMPK14 harbors conserved domain/motifs specified by the plant MAPK proteins. In vitro assay for kinase activity of TaMPK14 validated its phosphorylation nature. TaMPK14 transcripts were upregulated in both roots and leaves under low-N treatment; moreover, the expression levels induced by N starvation were gradually restored following the N recovery progression. These results suggested transcriptional response of TaMPK14 upon the low-N stress. Compared with wild type (WT), the TaMPK14 overexpressing lines in N. tabacum displayed improved growth and N accumulation traits under deficient-N treatment, which indicated the crucial roles of the MAPK gene in mediating N starvation response. Additionally, the lines treated by N starvation were shown to be improved on cellular ROS homeostasis, displaying higher antioxidant enzymes (AE) activities and less ROS accumulative amount than WT. The transcripts of nitrate transporter gene NtNRT2.1 and those of AE genes NtSOD1, NtCAT1;2, and NtPOD4 were significantly upregulated in N-deprived TaMPK14 lines; overexpression of them conferred plants enhanced N uptake capacity and AE activities, respectively. Moreover, RNA-seq datasets generated from N-deprived transgenic lines contained numerous differential genes involving modulating various biological process, cellular component, and molecular function. Together, our investigation suggested that TaMPK14 improves plant N starvation response through transcriptional regulation of distinct NRT and AE genes as well as modulation of associated biological processes.

Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants

The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil-based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low-income countries. The rhizobox is large enough (approximately 6000 cm² of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low- and middle-income countries to enhance crop yields and climate resilience sustainably.

Auxin-mediated root branching is determined by the form of available nitrogen

To improve water and nutrient acquisition from the soil, plants can modulate their root system architecture. Despite the importance of changes in root architecture to exploit local nutrient patches occurring in heterogenous soils or after placed fertilization, mechanisms integrating external nutrient signals into the root developmental programme remain poorly understood. Here, we show that local ammonium supply stimulates the accumulation of shoot-derived auxin in the root vasculature and promotes lateral root emergence to build a highly branched root system. Activities of pH and auxin reporters indicate that ammonium uptake mediated by ammonium transporters acidifies the root apoplast, which increases pH-dependent import of protonated auxin into cortical and epidermal cells overlaying lateral root primordia, and subsequently promotes their emergence from the parental root. Thereby, ammonium-induced and H⁺-ATPase-mediated acidification of the apoplast allows auxin to bypass the auxin importers AUX1 and LAX3. In nitrogen-deficient plants, auxin also accumulates in the root vasculature but a more alkaline apoplast leads to retention of auxin in these tissues and prevents lateral root formation. Our study highlights the impact of externally available nitrogen forms on pH-dependent radial auxin mobility and its regulatory function in organ development.

Signaling pathways underlying nitrogen-dependent changes in root system architecture: from model to crop species

Among all essential mineral elements, nitrogen (N) is required in the largest amounts and thus is often a limiting factor for plant growth. N is taken up by plant roots in the form of water-soluble nitrate, ammonium, and, depending on abundance, low-molecular weight organic N. In soils, the availability and composition of these N forms can vary over space and time, which exposes roots to various local N signals that regulate root system architecture in combination with systemic signals reflecting the N nutritional status of the shoot. Uncovering the molecular mechanisms underlying N-dependent signaling provides great potential to optimize root system architecture for the sake of higher N uptake efficiency in crop breeding. In this review, we summarize prominent signaling mechanisms and their underlying molecular players that derive from external N forms or the internal N nutritional status and modulate root development including root hair formation and gravitropism. We also compare the current state of knowledge of these pathways between Arabidopsis and graminaceous plant species.

Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging

Plants can develop root systems with distinct anatomical features and morphological plasticity to forage nutrients distributed heterogeneously in soils. Lateral root proliferation is a typical nutrient-foraging response to a local supply of nitrate, which has been investigated across many plant species. However, the underlying mechanism in maize roots remains largely unknown. Here, we report on identification of a maize truncated MIKC-type MADS-box transcription factor (ZmTMM1) lacking K- and C-domains, expressed preferentially in the lateral root branching zone and induced by the localized supply of nitrate. ZmTMM1 belongs to the AGL17-like MADS-box transcription factor family that contains orthologs of ANR1, a key regulator for root nitrate foraging in Arabidopsis. Ectopic overexpression of ZmTMM1 recovers the defective growth of lateral roots in the Arabidopsis anr1 agl21 double mutant. The local activation of glucocorticoid receptor fusion proteins for ZmTMM1 and an artificially truncated form of AtANR1 without the K- and C-domains stimulates the lateral root growth of the Arabidopsis anr1 agl21 mutant, providing evidence that ZmTMM1 encodes a functional MADS-box that modulates lateral root development. However, no phenotype was observed in ZmTMM1-RNAi transgenic maize lines, suggesting a possible genetic redundancy of ZmTMM1 with other AGL17-like genes in maize. A comparative genome analysis further suggests that a nitrate-inducible transcriptional regulation is probably conserved in both truncated and non-truncated forms of ZmTMM1-like MADS-box transcription factors found in grass species.

Integrating N signals and root growth: the role of nitrate transceptor NRT1.1 in auxin-mediated lateral root development

This article comments on: Maghiaoui A, Bouguyon E, Cuesta C, Perrine-Walker F, Alcon C, Krouk G, Benková E, Nacry P, Gojon A and Bach L. 2020. The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate. Journal of Experimental Botany 71, 4480–4494.

How does nitrogen shape plant architecture?

Plant nitrogen (N), acquired mainly in the form of nitrate and ammonium from soil, dominates growth and development, and high-yield crop production relies heavily on N fertilization. The mechanisms of root adaptation to altered supply of N forms and concentrations have been well characterized and reviewed, while reports concerning the effects of N on the architecture of vegetative and reproductive organs are limited and are widely dispersed in the literature. In this review, we summarize the nitrate and amino acid regulation of shoot branching, flowering, and panicle development, as well as the N regulation of cell division and expansion in shaping plant architecture, mainly in cereal crops. The basic regulatory steps involving the control of plant architecture by the N supply are auxin-, cytokinin-, and strigolactone-controlled cell division in shoot apical meristem and gibberellin-controlled inverse regulation of shoot height and tillering. In addition, transport of amino acids has been shown to be involved in the control of shoot branching. The N supply may alter the timing and duration of the transition from the vegetative to the reproductive growth phase, which in turn may affect cereal crop architecture, particularly the structure of panicles for grain yield. Thus, proper manipulation of N-regulated architecture can increase crop yield and N use efficiency.

The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate

In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule in plant growth, development, and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). Here we show that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing the cell wall remodeling required for overlying tissue separation during LRP emergence. NRT1.1-mediated repression of both TAR2 and LAX3 is suppressed at high nitrate availability, resulting in nitrate induction of the TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously expected in regulating the nitrate response of root system architecture.

The Root Foraging Response under Low Nitrogen Depends on DWARF1-Mediated Brassinosteroid Biosynthesis

Root developmental plasticity enables plants to adapt to limiting or fluctuating nutrient conditions in the soil. When grown under nitrogen (N) deficiency, plants develop a more exploratory root system by increasing primary and lateral root length. However, mechanisms underlying this so-called foraging response remain poorly understood. We performed a genome-wide association study in Arabidopsis (Arabidopsis thaliana) and we show here that noncoding variations of the brassinosteroid (BR) biosynthesis gene DWARF1 (DWF1) lead to variation of the DWF1 transcript level that contributes to natural variation of root elongation under low N. In addition to DWF1, other central BR biosynthesis genes upregulated under low N include CONSTITUTIVE PHOTOMORPHOGENIC DWARF, DWF4, and BRASSINOSTEROID-6-OXIDASE 2 Phenotypic characterization of knockout and knockdown mutants of these genes showed significant reduction of their root elongation response to low N, suggesting a systemic stimulation of BR biosynthesis to promote root elongation. Moreover, we show that low N-induced root elongation is associated with aboveground N content and that overexpression of DWF1 significantly improves plant growth and overall N accumulation. Our study reveals that mild N deficiency induces key genes in BR biosynthesis and that natural variation in BR synthesis contributes to the root foraging response, complementing the impact of enhanced BR signaling observed recently. Furthermore, these results suggest a considerable potential of BR biosynthesis to genetically engineer plants with improved N uptake.

Review: Emerging roles of brassinosteroid in nutrient foraging

Brassinosteroids (BRs) are well-characterized growth hormones that are critical for plant growth, development, and productivity. Genetic and molecular studies have revealed the key components of BR biosynthesis and signaling pathways. The membrane-localized BR signaling receptor, BRASSINOSTEROID INSENSITIVE1 (BRI1) binds directly to its ligand and initiates series of signaling events that led to the activation of BR transcriptional regulators, BRASSINAZOLE RESISTANT1 (BZR1) and BRI1-ETHYL METHANESULFONATE-SUPPRESSOR1 (BES1/BZR2) to regulate the cellular processes. Insights from Arabidopsis research revealed tissue and cell type-specific roles of BR in controlling cell elongation and maintenance of stem cell niche in roots. More recently, BRs have gained much attention in regulating the root growth during nutrient deficiency such as nitrogen, phosphorus, and boron. Differential distribution of nutrients in the rhizosphere alters BR hormone levels and signaling to reprogram spatial distribution of root system architecture (RSA) such as a change in primary root growth, lateral root numbers, length, and angle, root hair formation and elongation. These morpho-physiological changes in RSA are also known as an adaptive root trait or foraging response of the plant. In this review, we highlight the role of BRs in regulating RSA to increase root foraging response during fluctuating nutrient availability.

Plant science's next top models

BACKGROUND

Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models.

SCOPE

Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers.

CONCLUSIONS

Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

CEP receptor signalling controls root system architecture in Arabidopsis and Medicago

Root system architecture (RSA) influences the effectiveness of resources acquisition from soils but the genetic networks that control RSA remain largely unclear. We used rhizoboxes, X-ray computed tomography, grafting, auxin transport measurements and hormone quantification to demonstrate that Arabidopsis and Medicago CEP (C-TERMINALLY ENCODED PEPTIDE)-CEP RECEPTOR signalling controls RSA, the gravitropic set-point angle (GSA) of lateral roots (LRs), auxin levels and auxin transport. We showed that soil-grown Arabidopsis and Medicago CEP receptor mutants have a narrower RSA, which results from a steeper LR GSA. Grafting showed that CEPR1 in the shoot controls GSA. CEP receptor mutants exhibited an increase in rootward auxin transport and elevated shoot auxin levels. Consistently, the application of auxin to wild-type shoots induced a steeper GSA and auxin transport inhibitors counteracted the CEP receptor mutant's steep GSA phenotype. Concordantly, CEP peptides increased GSA and inhibited rootward auxin transport in wild-type but not in CEP receptor mutants. The results indicated that CEP-CEP receptor-dependent signalling outputs in Arabidopsis and Medicago control overall RSA, LR GSA, shoot auxin levels and rootward auxin transport. We propose that manipulating CEP signalling strength or CEP receptor downstream targets may provide means to alter RSA.

Crosstalk between heterotrimeric G protein-coupled signaling pathways and WRKY transcription factors modulating plant responses to suboptimal micronutrient conditions

Nutrient stresses induce foliar chlorosis and growth defects. Here we propose heterotrimeric G proteins as signaling mediators of various nutrient stresses, through meta-analyses of >20 transcriptomic data sets associated with nutrient stresses or G protein mutations. Systematic comparison of transcriptomic data yielded 104 genes regulated by G protein subunits under common nutrient stresses: 69 genes under Gβ subunit (AGB1) control and 35 genes under Gα subunit (GPA1) control. Quantitative real-time PCR experiments validate that several transcription factors and metal transporters changed in expression level under suboptimal iron, zinc, and/or copper concentrations, while being misregulated in the Arabidopsis Gβ-null (agb1) mutant. The agb1 mutant had altered metal ion profiles and exhibited severe growth arrest under zinc stress, and aberrant root waving under iron and zinc stresses, while the Gα-null mutation attenuated leaf chlorosis under iron deficiency in both Arabidopsis and rice. Our transcriptional network analysis inferred computationally that WRKY-family transcription factors mediate the AGB1-dependent nutrient responses. As corroborating evidence of our inference, ectopic expression of WRKY25 or WRKY33 rescued the zinc stress phenotypes and the expression of zinc transporters in the agb1-2 background. These results, together with Gene Ontology analyses, suggest two contrasting roles for G protein-coupled signaling pathways in micronutrient stress responses: one enhancing general stress tolerance and the other modulating ion homeostasis through WRKY transcriptional regulatory networks. In addition, tolerance to iron stress in the rice Gα mutant provides an inroad to improve nutrient stress tolerance of agricultural crops by manipulating G protein signaling.

Distinct non-coding RNAs confer root-dependent sense transgene-induced post-transcriptional gene silencing and nitrogen-dependent post-transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots

High-affinity ammonium uptake in roots mediate by AMT1-type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post-translational controls, an organ-dependent and N-dependent post-transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1-transformed atamt1;1-1 Arabidopsis plants resulted from RDR6-dependent sense transgene-induced post-transcriptional gene silencing (S-PTGS). The siRNAs for S-PTGS may derive from the aberrant RNA, of which the production was co-determined by sequence feature and excessive expression of AtAMT1;1. Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA-targeted hotspots reduced AtAMT1;1-specific siRNAs and overcame S-PTGS in roots. In roots of these lines, however, the steady-state transcript levels of AtAMT1;1 still significantly decreased under conditions of N-sufficiency compared with N-deficiency, confirming a N-dependent post-transcriptional regulatory manner. A crucial role of the 207-bp 3'-end sequence of AtAMT1;1 was further demonstrated by N-dependent accumulation of chimeric-AtAMT1;1 transcript in T-DNA insertion lines and of GFP-tagged chimeric-AtAMT1;1 transcript in transgenic lines. A novel non-coding RNA (ncRNA), which was highly abundant in N-sufficient roots, may target the above-identified 3'-end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site (+1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots.

Flavonols regulate root hair development by modulating accumulation of reactive oxygen species in the root epidermis

Reactive oxygen species (ROS) are signaling molecules produced by tissue-specific respiratory burst oxidase homolog (RBOH) enzymes to drive development. In Arabidopsis thaliana, ROS produced by RBOHC was previously reported to drive root hair elongation. We identified a specific role for one ROS, H₂O₂, in driving root hair initiation and demonstrated that localized synthesis of flavonol antioxidants control the level of H₂O₂ and root hair formation. Root hairs form from trichoblast cells that express RBOHC and have elevated H₂O₂ compared with adjacent atrichoblast cells that do not form root hairs. The flavonol-deficient tt4 mutant has elevated ROS in trichoblasts and elevated frequency of root hair formation compared with the wild type. The increases in ROS and root hairs in tt4 are reversed by genetic or chemical complementation. Auxin-induced root hair initiation and ROS accumulation were reduced in an rbohc mutant and increased in tt4, consistent with flavonols modulating ROS and auxin transport. These results support a model in which localized synthesis of RBOHC and flavonol antioxidants establish patterns of ROS accumulation that drive root hair formation.

Transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root (Camellia sinensis L.)

Free amino acids, including theanine, glutamine and glutamate, contribute greatly to the pleasant taste and multiple health benefits of tea. Amino acids in tea plants are mainly synthesized in roots and transported to new shoots, which are significantly affected by nitrogen (N) level and forms. However, the regulatory amino acid metabolism genes have not been systemically identified in tea plants. Here, we investigated the dynamic changes of free amino acid contents in response to N deficiency and forms in tea plant roots, and systemically identified the genes associated amino acid contents in individual metabolism pathways. Our results showed that glutamate-derived amino acids are the most dynamic in response to various forms of N and N deficiency. We then performed transcriptomic analyses of roots treated with N deficiency and various forms of N, and differentially expressed amino acid metabolic genes in each pathway were identified. The analyses on expression patterns and transcriptional responses of metabolic genes to N treatments provided novel insights for the molecular basis of high accumulation of theanine in tea plant root. These analyses also identified potential regulatory genes in dynamic amino acid metabolism in tea plant root. Furthermore, our findings indicated that the dynamic expression levels of CsGDH, CsAlaDC, CsAspAT, CsSDH, CsPAL, CsSHMT were highly correlated with changes of amino acid contents in their corresponding pathways. Herein, this study provides comprehensive insights into transcriptional regulation of amino acid metabolism in response to nitrogen deficiency and nitrogen forms in tea plant root.

Physiological and Proteomic Dissection of the Responses of Two Contrasting Wheat Genotypes to Nitrogen Deficiency

Nitrogen deficiency usually occurs along with aluminum toxicity in acidic soil, which is one of the major constraints for wheat production worldwide. In order to compare adaptive processes to N deficiency with different Al-tolerant wheat cultivars, we chose Atlas 66 and Scout 66 to comprehensively analyze the physiological responses to N deficiency, coupled with label-free mass spectrometry-based proteomics analysis. Results showed that both cultivars were comparable in most physiological indexes under N deficient conditions. However, the chlorophyll content in Scout 66 was higher than that of Atlas 66 under N deficiency. Further proteomic analysis identified 5592 and 5496 proteins in the leaves of Atlas 66 and Scout 66, respectively, of which 658 and 734 proteins were shown to significantly change in abundance upon N deficiency, respectively. The majority of the differentially expressed proteins were involved in cellular N compound metabolic process, photosynthesis, etc. Moreover, tetrapyrrole synthesis and sulfate assimilation were particularly enriched in Scout 66. Our findings provide evidence towards a better understanding of genotype-dependent responses under N deficiency which could help us to develop N efficient cultivars to various soil types.

The physiological mechanism underlying root elongation in response to nitrogen deficiency in crop plants

In response to low nitrogen stress, multiple hormones together with nitric oxide signaling pathways work synergistically and antagonistically in crop root elongation. Changing root morphology allows plants to adapt to soil nutrient availability. Nitrogen is the most important essential nutrient for plant growth. An important adaptive strategy for crops responding to nitrogen deficiency is root elongation, thereby accessing increased soil space and nitrogen resources. Multiple signaling pathways are involved in this regulatory network, working together to fine-tune root elongation in response to soil nitrogen availability. Based on existing research, we propose a model to explain how different signaling pathways interact to regulate root elongation in response to low nitrogen stress. In response to a low shoot nitrogen status signal, auxin transport from the shoot to the root increases. High auxin levels in the root tip stimulate the production of nitric oxide, which promotes the synthesis of strigolactones to accelerate cell division. In this process, cytokinin, ethylene, and abscisic acid play an antagonistic role, while brassinosteroids and auxin play a synergistic role in regulating root elongation. Further study is required to identify the QTLs, genes, and favorable alleles which control the root elongation response to low nitrogen stress in crops.

A Positive Tropism of Rice Roots toward a Nutrient Source

Plants take up water and nutrients through roots, and uptake efficiency depends on root behavior. Roots recognize the moisture gradient in the soil and grow toward the direction of high moisture. This phenomenon is called hydrotropism, and it contributes to efficient water uptake. As nutrients in soil are also unevenly distributed, it is beneficial for plants to grow their roots in the direction of increasing nutrient concentrations, but such a phenomenon has not been demonstrated. Here, we describe the directional growth of roots in response to a nutrient gradient. Using our assay system, the gradient of a nitrogen nutrient, NH4+, was sufficient to stimulate positive tropic responses of rice lateral roots. This phenomenon is a tropism of plant roots to nutrients; hence, we propose the name 'nutritropism'. As well as other tropisms, differential cell elongation was observed before the elongation zone during nutritropism, but the pattern promoting cell elongation preferentially on the non-stimulated side was opposite to those in root hydrotropism and gravitropism. Our evaluation of the NH4+ gradient suggested that the root tips responded to a sub-micromolar difference in NH4+ concentration on both sides of the root. Hydrotropism, gravitropism and phototropism were described in plants as the 'power of movement' by Charles and Francis Darwin in 1880, and these three tropisms have attracted the attention of plant scientists for more than 130 years. Our discovery of nutritropism represents the fourth 'power of movement' in plants and provides a novel root behavioral property used by plants to acquire nutrients efficiently.

Root architecture traits variation and nitrate-influx responses in diverse wheat genotypes under different external nitrogen concentrations

In order to identify the genetic variations in root system architecture traits and their probable association with high- and low-affinity nitrate transport system, we performed several experiments on a genetically diverse set of wheat genotypes grown under two external nitrogen levels (optimum and limited nitrate conditions) at two growth points of the seedling stage. Further, we also examined the nitrate uptake and its transport under different combinations of nitrate availability in the external media using ¹⁵N-labelled N-source (¹⁵NO₃^-), and gene expression pattern of different high- and low-affinity nitrate transporters. We observed that nitrate starvation invariably increases the total root size in all genotypes. However, the variation of component traits of total root size under nitrate starvation is genotype-specific at both stages. Further, we also observed genotypic variation in both nitrate uptake and translocation depending on the growth stage, external nitrate concentration and growing conditions. The expression of the TaNRT2.1 gene was invariably up-regulated under low external nitrate concentration; however, it gets reduced after a longer period (21 days) of starvation than the early stage (14 days). Among the four NRT1.1 orthologs, TaNPF6.3 and TaNPF6.4 consistently showed higher expression than TaNPF6.1 and TaNPF6.2 at higher nitrate concentration at both the growth stages. TaNPF6.3 and TaNPF6.4 apparently showed a feature of typical low-affinity nitrate transporter gene at higher external nitrate concentration at 14 and 21 days growth stages, respectively. The present study reveals the complex root system of wheat that has genotype-specific N-foraging along with highly coordinated high- and low-affinity nitrate transport systems for nitrate uptake and transport.

Spatial regulation of resource allocation in response to nutritional availability

It is critical for a living organism to appropriately allocate resources among its organs, or within a specific organ, because available resources are generally limited. For example, in response to the nutritional environment of their soil, plants regulate resource allocation in their roots in order to plastically change their root system architecture (RSA) for efficiently absorbing nutrients. However, it is still not understood why and how RSA is adaptively controlled. Therefore, we modeled and investigated the spatial regulation of resource allocation, focusing on RSA in response to nutrient availability, and provided analytical solutions to the optimal strategy in the case of simple fitness functions. We first showed that our model could explain the experimental evidence where root growth is maximized at the optimal nutrient concentration under the homogeneous condition. Next, we extended our model to incorporate the spatial heterogeneity of nutrient availability. This extended model revealed that growth suppression by systemic control is required for adapting to high nutrient conditions, whereas growth promotion by local control is sufficient for adaptation to low-nutrient environments. This evidence predicts that systemic control can be evolved in the presence of excessive amounts of nutrition, consistent with the 'N-supply' systemic signal that is observed experimentally. Furthermore, our model can also explain various experimental results using nitrogen nutrition. Our model provides a theoretical basis for understanding the spatial regulation of adaptive resource allocation in response to nutritional environment.

Exodermis and Endodermis Respond to Nutrient Deficiency in Nutrient-Specific and Localized Manner

The exodermis is a common apoplastic barrier of the outer root cortex, with high environmentally-driven plasticity and a protective function. This study focused on the trade-off between the protective advantages provided by the exodermis and its disadvantageous reduction of cortical membrane surface area accessible by apoplastic route, thus limiting nutrient acquisition from the rhizosphere. We analysed the effect of nutrient deficiency (N, P, K, Mg, Ca, K, Fe) on exodermal and endodermal differentiation in maize. To differentiate systemic and localized effects, nutrient deficiencies were applied in three different approaches: to the root system as a whole, locally to discrete parts, or on one side of a single root. Our study showed that the establishment of the exodermis was enhanced in low-N and low-P plants, but delayed in low-K plants. The split-root cultivation proved that the effect is non-systemic, but locally coordinated for individual roots. Within a single root, localized deficiencies didn't result in an evenly differentiated exodermis, in contrast to other stress factors. The maturation of the endodermis responded in a similar way. In conclusion, N, P, and K deficiencies strongly modulated exodermal differentiation. The response was nutrient specific and integrated local signals of current nutrient availability from the rhizosphere.

Nitrate and Ammonium Affect the Overall Maize Response to Nitrogen Availability by Triggering Specific and Common Transcriptional Signatures in Roots

Nitrogen (N) is an essential macronutrient for crops. Plants have developed several responses to N fluctuations, thus optimizing the root architecture in response to N availability. Nitrate and ammonium are the main inorganic N forms taken up by plants, and act as both nutrients and signals, affecting gene expression and plant development. In this study, RNA-sequencing was applied to gain comprehensive information on the pathways underlying the response of maize root, pre-treated in an N-deprived solution, to the provision of nitrate or ammonium. The analysis of the transcriptome shows that nitrate and ammonium regulate overlapping and distinct pathways, thus leading to different responses. Ammonium activates the response to stress, while nitrate acts as a negative regulator of transmembrane transport. Both the N-source repress genes related to the cytoskeleton and reactive oxygen species detoxification. Moreover, the presence of ammonium induces the accumulation of anthocyanins, while also reducing biomass and chlorophyll and flavonoids accumulation. Furthermore, the later physiological effects of these nutrients were evaluated through the assessment of shoot and root growth, leaf pigment content and the amino acid concentrations in root and shoot, confirming the existence of common and distinct features in response to the two nitrogen forms.

Auxin-dependent control of a plasmodesmal regulator creates a negative feedback loop modulating lateral root emergence

Lateral roots originate from initial cells deep within the main root and must emerge through several overlying layers. Lateral root emergence requires the outgrowth of the new primordium (LRP) to coincide with the timely separation of overlying root cells, a developmental program coordinated by the hormone auxin. Here, we report that in Arabidopsis thaliana roots, auxin controls the spatiotemporal expression of the plasmodesmal regulator PDLP5 in cells overlying LRP, creating a negative feedback loop. PDLP5, which functions to restrict the cell-to-cell movement of signals via plasmodesmata, is induced by auxin in cells overlying LRP in a progressive manner. PDLP5 localizes to plasmodesmata in these cells and negatively impacts organ emergence as well as overall root branching. We present a model, incorporating the spatiotemporal expression of PDLP5 in LRP-overlying cells into known auxin-regulated LRP-overlying cell separation pathways, and speculate how PDLP5 may function to negatively regulate the lateral root emergence process.

Influence of Heterogeneous Karst Microhabitats on the Root Foraging Ability of Chinese Windmill Palm (Trachycarpus fortunei) Seedlings

Chinese windmill palms (Trachycarpus fortunei) are widely planted in karst bedrock outcrop areas in southwest China because of their high economic and ecological values. The aims of this study were to investigate the foraging ability of Chinese windmill palm seedlings planted in six different types of karst microhabitat and to identify the main environmental factors that influence root foraging ability. We planted three-year-old Chinese windmill palm seedlings in six typical karst microhabitats (i.e., rocky trough, rocky surface, rocky gully, rocky soil surface, rocky pit, and soil surface microhabitats). One year after transplanting, the seedlings were excavated to determine the morphological parameters values of new roots and the nutrient concentrations of new roots and leaves. The root foraging ability of Chinese windmill palm seedlings, defined as new root length and new root surface area, was significantly greater in the rocky trough, rocky soil surface, and soil surface microhabitats than in the rocky gully, rocky surface, and rocky pit microhabitats (p < 0.05). Redundancy analysis revealed that the main positive factor affecting the rooting ability of Chinese windmill palm seedlings was soil thickness. Chinese windmill palm seedlings improved their root absorption efficiency by increasing their root length and root surface area under soil nutrient deficiency conditions. The organic carbon, total nitrogen, and available potassium in soil positively influenced the concentration of N and K in roots. Total potassium in soil negatively influenced the biomass of new annual leaves and concentrations of N, P and K in new annual roots and leaves. Chinese windmill palm seedlings can be grown in the different karst microhabitats, especially in the rocky trough, rocky soil surface, and soil surface microhabitats, and, therefore, it is suitable for use in the regeneration of karst forests.

Adaptation of Foxtail Millet (Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations

Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C₄ photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.

Modeling of Root Nitrate Responses Suggests Preferential Foraging Arises From the Integration of Demand, Supply and Local Presence Signals

A plants' fitness to a large extent depends on its capacity to adapt to spatio-temporally varying environmental conditions. One such environmental condition to which plants display extensive phenotypic plasticity is soil nitrate levels and patterns. In response to heterogeneous nitrate distribution, plants show a so-called preferential foraging response. Herein root growth is enhanced in high nitrate patches and repressed in low nitrate locations beyond a level that can be explained from local nitrate sensing. Although various molecular players involved in this preferential foraging behavior have been identified, how these together shape root system adaptation has remained unresolved. Here we use a simple modeling approach in which we incrementally incorporate the known molecular pathways to investigate the combination of regulatory mechanisms that underly preferential root nitrate foraging. Our model suggests that instead of involving a growth suppressing supply signal, growth reduction on the low nitrate side may arise from reduced root foraging and increased competition for carbon. Additionally, our work suggests that the long distance CK signaling involved in preferential root foraging may function as a supply signal modulating demand signaling strength. We illustrate how this integration of demand and supply signals prevents excessive preferential foraging under conditions in which demand is not met by sufficient supply and a more generic foraging in search of nitrate should be maintained.

Genetic and physiological analyses of root cracking in radish (Raphanus sativus L.)

A major QTL conferring tolerance to radish (Raphanus sativus) root cracking was mapped for the first time and two calcium regulatory genes were identified that positively associated with the cracking phenomenon. Root cracking is a severe physiological disorder that significantly decreases the yield and commercial value of radish. The genetic and physiological mechanisms underlying this root cracking disorder have not been characterized. In this study, quantitative trait loci (QTLs) putatively associated with radish root cracking were mapped. Ten QTLs were distributed in six linkage groups, among these QTLs, 'RCr1' in LG1 was detected over 3 consecutive years and was considered to be a major QTL for root cracking. The QTL 'RCr1' was responsible for 4.47-18.11% of variance in the root cracking phenotype. We subsequently identified two candidate genes, RsANNAT and RsCDPK. Both genes encode proteins involved in calcium binding, ion transport, and Ca²⁺ signal transduction, which are important for regulating plant development and adaptations to the environment. These genes were co-localized to the major QTL region. Additionally, we analyzed physiological changes (i.e., root firmness, cell wall content, and cell-wall-bound calcium content) in two parental lines during different developmental stages. Moreover, we observed that the RsANNAT and RsCDPK expression levels are positively correlated with Ca²⁺ contents in the roots of the cracking-tolerant '835' cultivar. Thus, these genes may influence root cracking. The data provided herein may support the useful information to understand root cracking behavior in radish and may enable breeders to develop new cultivars exhibiting increased tolerance to root and fruit cracking.

Cadmium stress suppresses lateral root formation by interfering with the root clock

A biological clock activated by oscillating signals, known as root clock, has been linked to lateral root (LR) formation and is essential for regular LR spacing along the primary root. However, it remains unclear how this internal mechanism is influenced by environmental factors known to affect the LR pattern. Here, we report that excessive cadmium (Cd) inhibits LR formation by disrupting the lateral root cap (LRC)-programmed cell death (PCD)-regulated root clock. Cd restricts the frequency of the oscillating signal rather than its amplitude. This could be attributed to the inhibition on meristematic activity by Cd, which resulted in decreased LRC cell number and LRC-PCD frequency. Genetic evidence further showed that LRC cell number is positively correlated with root resistance to Cd. Our study reveals root cap dynamics as a novel mechanism mediating root responses to Cd, providing insight into the signalling pathways of the root clock responding to environmental cues.

Role of cis-zeatin in root responses to phosphate starvation

Phosphate (Pi) is an essential nutrient for all organisms. Roots are underground organs, but the majority of the root biology studies have been done on root systems growing in the presence of light. Root illumination alters the Pi starvation response (PSR) at different intensities. Thus, we have analyzed morphological, transcriptional and physiological responses to Pi starvation in dark-grown roots. We have identified new genes and pathways regulated by Pi starvation that were not described previously. We also show that Pi-starved plants increase the cis-zeatin (cZ) : trans-zeatin (tZ) ratio. Transcriptomic analyses show that tZ preferentially represses cell cycle and PSR genes, whereas cZ induces genes involved in cell and root hair elongation and differentiation. In fact, cZ-treated seedlings show longer root system as well as longer root hairs compared with tZ-treated seedlings, increasing the total absorbing surface. Mutants with low cZ concentrations do not allocate free Pi in roots during Pi starvation. We propose that Pi-starved plants increase the cZ : tZ ratio to maintain basal cytokinin responses and allocate Pi in the root system to sustain its growth. Therefore, cZ acts as a PSR hormone that stimulates root and root hair elongation to enlarge the root absorbing surface and to increase Pi concentrations in roots.

Mitogen-activated protein kinase 6 integrates phosphate and iron responses for indeterminate root growth in Arabidopsis thaliana

A MAPK module, of which MPK6 kinase is an important component, is involved in the coordination of the responses to Pi and Fe in the primary root meristem of Arabidopsis thaliana. Phosphate (Pi) deficiency induces determinate primary root growth in Arabidopsis through cessation of cell division in the meristem, which is linked to an increased iron (Fe) accumulation. Here, we show that Mitogen-Activated Protein Kinase6 (MPK6) has a role in Arabidopsis primary root growth under low Pi stress. MPK6 activity is induced in roots in response to low Pi, and such induction is enhanced by Fe supplementation, suggesting an MPK6 role in coordinating Pi/Fe balance in mediating root growth. The differentiation of the root meristem induced by low Pi levels correlates with altered expression of auxin-inducible genes and auxin transporter levels via MPK6. Our results indicate a critical role of the MPK6 kinase in coordinating meristem cell activity to Pi and Fe availability for proper primary root growth.

Genome-Wide Analysis of Long Intergenic Noncoding RNAs Responding to Low-Nutrient Conditions in Arabidopsis thaliana: Possible Involvement of Trans-Acting siRNA3 in Response to Low Nitrogen

Long intergenic noncoding RNAs (lincRNAs) play critical roles in transcriptional and post-transcriptional regulation of gene expression in a wide variety of organisms. Thousands of lincRNAs have been identified in plant genomes, although their functions remain mostly uncharacterized. Here, we report a genome-wide survey of lincRNAs involved in the response to low-nutrient conditions in Arabidopsis thaliana. We used RNA sequencing data derived from A. thaliana roots exposed to low levels of 12 different nutrients. Using bioinformatics approaches, 60 differentially expressed lincRNAs were identified that were significantly upregulated or downregulated under deficiency of at least one nutrient. To clarify their roles in nutrient response, correlations of expression patterns between lincRNAs and reference genes were examined across the 13 conditions (12 low-nutrient conditions and control). This analysis allowed us to identify lincRNA-RNA pairs with highly positive or negative correlations. In addition, calculating interaction energies of those pairs showed lincRNAs that may act as regulatory interactors; e.g. small interfering RNAs (siRNAs). Among them, trans-acting siRNA3 (TAS3), which is known to promote lateral root development by producing siRNA against Auxin response factor 2, 3, and 4, was revealed as a nitrogen (N)-responsive lincRNA. Furthermore, nitrate transporter 2 was identified as a potential target of TAS3-derived siRNA, suggesting that TAS3 participates in multiple pathways by regulating N transport and root development under low-N conditions. This study provides the first resource for candidate lincRNAs involved in multiple nutrient responses in plants.

Interspecific competition among catch crops modifies vertical root biomass distribution and nitrate scavenging in soils

The potential of a plant species to acquire nutrients depends on its ability to explore the soil by its root system. Co-cultivation of different species is anticipated to lead to vertical root niche differentiation and thus to higher soil nutrient depletion. Using a qPCR-based method we quantified root biomass distribution of four catch crop species in vertical soil profiles in pure vs. mixed stands. Pure stands of mustard and phacelia robustly reached 70 cm soil depth, while oat preferably colonized upper soil layers, and clover developed the shallowest and smallest root system. Analysis of residual nitrate pools in different soil depths and correlation with root biomass showed that, besides rooting depth also root biomass determines soil nitrogen depletion. While occupying the same vertical niches as in pure stands, mustard and phacelia dominated total root biomass of the mix. In contrast, root biomass of clover and oat was severely suppressed in presence of the other species. Below-ground biomass profiling indicated low niche complementarity among the root systems of the examined species. Nonetheless, the mixture mostly overyielded root biomass of the pure stands and thus shows higher potential for efficient soil exploration by roots.

Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures

Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.

Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures

Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.

The interaction of genes controlling root traits is required for the developmental acquisition of deep and thick root traits and improving root architecture in response to low water or nitrogen content in rice (Oryza sativa L.) cultivars

Most of the hot spots about rice research are related to roots; increasing rice yield is mainly associated with improving root traits. Understanding phenotype-gene regulation relationship in different rice cultivars can contribute to the genetic improvement of root system. The expression pattern of root genes in moroberekan (deep and thick roots and high root/shoot ratio "R/S") was compared to that in Giza178 and PM12 (numerous but shallow roots) and IR64 (fewer but deeper roots than the latter ones). In contrast to the other genotypes, moroberekan did not cease developing deep and thick roots even after 60 days from sowing, perhaps because of not only the consistent upregulation but also the interaction of root genes. Xylem sap flow was significantly higher even under drought (low water content) in moroberekan. Auxin signaling-related ARF12 and PIN1 genes could play key roles in improving root traits in response to low water or nitrogen content. Their concurrent upregulation was coincided with developing 1) deeper roots in moroberekan under drought, 2) thicker and deeper roots in PM12 under low nitrogen content (LN) and 3) new roots with thicker and deeper characteristics in the four genotypes after root trimming. The upregulation of PIN1 or ARF12 in Giza178 at LN, PM12 at drought or in IR64 under drought or LN did not greatly change the root traits. Hierarchical analysis showed that ARF12 and PIN1 were distantly related, but overlapped with other genes controlling root traits. Overexpression of ARF12 and PIN1 could improve root traits in rice cultivars.

Calcium-Promoted Interaction between the C2-Domain Protein EHB1 and Metal Transporter IRT1 Inhibits Arabidopsis Iron Acquisition

Iron is a key transition element in the biosphere and is crucial for living organisms, although its cellular excess can be deleterious. Maintaining the balance of optimal iron availability in the model plant Arabidopsis (Arabidopsis thaliana) requires the precise operation of iron import through the principal iron transporter IRON-REGULATED TRANSPORTER1 (IRT1). Targeted inhibition of IRT1 can prevent oxidative stress, thus promoting plant survival. Here, we report the identification of an IRT1 inhibitor, namely the C2 domain-containing peripheral membrane protein ENHANCED BENDING1 (EHB1). EHB1 interacts with the cytoplasmically exposed variable region of IRT1, and we demonstrate that this interaction is greatly promoted by the presence of calcium. We found that EHB1 binds lipids characteristic of the plasma membrane, and the interaction between EHB1 and plant membranes is calcium-dependent. Molecular simulations showed that EHB1 membrane binding is a two-step process that precedes the interaction between EHB1 and IRT1. Genetic and physiological analyses indicated that EHB1 acts as a negative regulator of iron acquisition. The presence of EHB1 prevented the IRT1-mediated complementation of iron-deficient fet3fet4 yeast (Saccharomyces cerevisiae). Our data suggest that EHB1 acts as a direct inhibitor of IRT1-mediated iron import into the cell. These findings represent a major step in understanding plant iron acquisition, a process that underlies the primary production of bioavailable iron for land ecosystems.

Multifunctional food waste fertilizer having the capability of Fusarium-growth inhibition and phosphate solubility: A new horizon of food waste recycle using microorganisms

Organic waste, including food leftovers and trade refuse, has been explored for its use as a nutrient source through a multitude of techniques. Composting; the dominant method, is criticized due to exhaustion of nutrients used for simultaneous microbial growth. Drying of food waste to low moisture levels, besides keeping the nutrition intact, offers the potential of growing desirable phyto-beneficial-cum-functional microbes, which can have additional benefits. Consequently, isolation of fungus from soil was carried out followed by characterization for confrontation against Fusarium, phosphate solubilization and utilization of food waste material. The food waste material was collected from University of Yamanashi Restaurant and dried up to approximately 3.8% moisture using Hitachi Household Garbage Dryer & Processor (ECO-B25). A pot experiment, growing Lactuca sativa (lettuce) and Brassica rapa, in selected fungal isolate-inoculated food waste material was conducted comparing with that of chemical, and organic fertilizer besides uninoculated food waste material. Results showed that one strain UY2015_11 (identified as Aspergillus niger) significantly inhibited the growth of Fusarium besides solubilizing hardly available iron, and calcium-type phosphates. Similarly, in a 13-week incubation experiment, mineralization of nitrate nitrogen from the food waste and fungal strain UY2015_11-inoculated food waste, was 23.9% and 17.0%, respectively. Later pot experiment indicated that the strain UY2015_11-inoculated dried food waste material showed same vegetable growth as chemical and organic fertilizer (rapeseed oil cake). Concluding, Aspergillus niger strain UY2015_11 isolated from soil inhibited the growth of Fusarium and solubilized hardly phosphate. Moreover, the strain UY2015_11 inoculated low moisture-food waste material showed the same vegetable growth as chemical and organic fertilizer (rapeseed oil cake).

Natural variation of BSK3 tunes brassinosteroid signaling to regulate root foraging under low nitrogen

Developmental plasticity of root system architecture is crucial for plant performance in nutrient-poor soils. Roots of plants grown under mild nitrogen (N) deficiency show a foraging response characterized by increased root length but mechanisms underlying this developmental plasticity are still elusive. By employing natural variation in Arabidopsis accessions, we show that the brassinosteroid (BR) signaling kinase BSK3 modulates root elongation under mild N deficiency. In particular, a proline to leucine substitution in the predicted kinase domain of BSK3 enhances BR sensitivity and signaling to increase the extent of root elongation. We further show that low N specifically upregulates transcript levels of the BR co-receptor BAK1 to activate BR signaling and stimulate root elongation. Altogether, our results uncover a role of BR signaling in root elongation under low N. The BSK3 alleles identified here provide targets for improving root growth of crops growing under limited N conditions.

Plant roots elongate under mild nitrogen deficiency as part of a foraging response that facilitates nutrient uptake. Here the authors show that natural variation in this response among Arabidopsis accessions depends on the brassinosteroid (BR) signaling kinase BSK3, which can enhance BR sensitivity and root growth.

Electrical impedance tomography as a tool for phenotyping plant roots

BACKGROUND

Plant roots are complex, three-dimensional structures that play a central role in anchorage, water and nutrient acquisition, storage and interaction with rhizosphere microbes. Studying the development of the plant root system architecture is inherently difficult as soil is not a transparent medium.

RESULTS

This study uses electrical impedance tomography (EIT) to visualise oilseed rape root development in horticultural compost. The development of healthy, control plants and those infected with the gall-forming pathogen, Plasmodiophora brassicae-the causative agent of clubroot disease-were compared. EIT measurements were used to quantify the development of the root system and distinguish between control and infected plants at the onset of gall formation, approximately 20 days after inoculation. Although clear and stark differences between healthy and infected plants were obtained by careful (and hence laborious) packing of the growth medium in layers within the pots; clubroot identification is still possible without a laborious vessel filling protocol.

CONCLUSIONS

These results demonstrate the utility of EIT as a low-cost, non-invasive, non-destructive method for characterising root system architecture and plant-pathogen interactions in opaque growth media. As such it offers advantages over other root characterisation techniques and has the potential to act as a low-cost tool for plant phenotyping.

Independent Regulation of Symbiotic Nodulation by the SUNN Negative and CRA2 Positive Systemic Pathways

Plant systemic signaling pathways allow the integration and coordination of shoot and root organ metabolism and development at the whole-plant level depending on nutrient availability. In legumes, two systemic pathways have been reported in the Medicago truncatula model to regulate root nitrogen-fixing symbiotic nodulation. Both pathways involve leucine-rich repeat receptor-like kinases acting in shoots and proposed to perceive signaling peptides produced in roots depending on soil nutrient availability. In this study, we characterized in the M. truncatula Jemalong A17 genotype a mutant allelic series affecting the Compact Root Architecture2 (CRA2) receptor. These analyses revealed that this pathway acts systemically from shoots to positively regulate nodulation and is required for the activity of carboxyl-terminally encoded peptides (CEPs). In addition, we generated a double mutant to test genetic interactions of the CRA2 systemic pathway with the CLAVATA3/EMBRYO SURROUNDING REGION peptide (CLE)/Super Numeric Nodule (SUNN) receptor systemic pathway negatively regulating nodule number from shoots, which revealed an intermediate nodule number phenotype close to the wild type. Finally, we showed that the nitrate inhibition of nodule numbers was observed in cra2 mutants but not in sunn and cra2 sunn mutants. Overall, these results suggest that CEP/CRA2 and CLE/SUNN systemic pathways act independently from shoots to regulate nodule numbers.

Sustained substrate cycles between hexose phosphates and free sugars in phosphate-deficient potato (Solanum tuberosum) cell cultures

Futile cycling between free sugars and hexose phosphates occurring under phosphate deficiency could be involved in the maintenance of a threshold level of free cellular phosphate to preserve respiratory metabolism. We studied the metabolic response of potato cell cultures growing in Pi sufficient (2.5 mM, +Pi) or deficient (125 µM, -Pi) conditions. Under Pi deficiency, cellular growth was severely affected, however -Pi cells were able to maintain a low but steady level of free Pi. We surveyed the activities of 33 primary metabolic enzymes during the course of a 12 days Pi deficiency period. Our results show that many of these enzymes had higher specific activity in -Pi cells. Among these, we found typical markers of Pi deficiency such as phosphoenolpyruvate phosphatase and phosphoenolpyruvate carboxylase as well as enzymes involved in the biosynthesis of organic acids. Intriguingly, several ATP-consuming enzymes such as hexokinase (HK) and phosphofructokinase also displayed increased activity in -Pi condition. For HK, this was associated with an increase in the steady state of a specific HK polypeptide. Quantification of glycolytic intermediates showed a pronounced decrease in phosphate esters under Pi deficiency. Adenylate levels also decreased in -Pi cells, but the Adenylate Energy Charge was not affected by the treatment. To investigate the significance of HK induction under low Pi, [U-¹⁴C]-glucose tracer studies were conducted. We found in vivo evidence of futile cycling between pools of hexose phosphates and free sugars under Pi deficiency. Our study suggests that the futile cycling between hexose phosphates and free sugars which is active under +Pi conditions is sustained under Pi deficiency. The possibility that this process represents a metabolic adaptation to Pi deficiency is discussed with respect to Pi homeostasis in Pi-deficient conditions.

Molecular and Environmental Regulation of Root Development

In order to optimally establish their root systems, plants are endowed with several mechanisms to use at distinct steps during their development. In this review, we zoom in on the major processes involved in root development and detail important new insights that have been generated in recent studies, mainly using the Arabidopsis root as a model. First, we discuss new insights in primary root development with the characterization of tissue-specific transcription factor complexes and the identification of non-cell-autonomous control mechanisms in the root apical meristem. Next, root branching is discussed by focusing on the earliest steps in the development of a new lateral root and control of its postemergence growth. Finally, we discuss the impact of phosphate, nitrogen, and water availability on root development and summarize current knowledge about the major molecular mechanisms involved.

CLE-CLAVATA1 Signaling Pathway Modulates Lateral Root Development under Sulfur Deficiency

Plant root system architecture changes drastically in response to availability of macronutrients in the soil environment. Despite the importance of root sulfur (S) uptake in plant growth and reproduction, molecular mechanisms underlying root development in response to S availability have not been fully characterized. We report here on the signaling module composed of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) peptide and CLAVATA1 (CLV1) leucine-rich repeat receptor kinase, which regulate lateral root (LR) development in Arabidopsis thaliana upon changes in S availability. The wild-type seedlings exposed to prolonged S deficiency showed a phenotype with low LR density, which was restored upon sulfate supply. In contrast, the clv1 mutant showed a higher daily increase rate of LR density relative to the wild-type under prolonged S deficiency, which was diminished to the wild-type level upon sulfate supply, suggesting that CLV1 directs a signal to inhibit LR development under S-deficient conditions. CLE2 and CLE3 transcript levels decreased under S deficiency and through CLV1-mediated feedback regulations, suggesting the levels of CLE peptide signals are adjusted during the course of LR development. This study demonstrates a fine-tuned mechanism for LR development coordinately regulated by CLE-CLV1 signaling and in response to changes in S availability.

Genetic Dissection of Root System Architectural Traits in Spring Barley

Breeding new crop cultivars with efficient root systems carries great potential to enhance resource use efficiency and plant adaptation to unstable climates. Here, we evaluated the natural variation of root system architectural traits in a diverse spring barley association panel and conducted genome-wide association mapping to identify genomic regions associated with root traits. For six studied traits, root system depth, root spreading angle, seminal root number, total seminal root length, and average seminal root length 1.9- to 4.2-fold variations were recorded. Using a mixed linear model, 55 QTLs were identified cumulatively explaining between 12.1% of the phenotypic variance for seminal root number to 48.1% of the variance for root system depth. Three major QTLs controlling root system depth, root spreading angle and total seminal root length were found on Chr 2H (56.52 cM), Chr 3H (67.92 cM), and Chr 2H (76.20 cM) and explained 12.4%, 18.4%, and 22.2% of the phenotypic variation, respectively. Meta-analysis and allele combination analysis indicated that root system depth and root spreading angle are valuable candidate traits for improving grain yield by pyramiding of favorable alleles.