Subterranean space exploration: the development of root system architecture

Above and belowground phenotypic response to exogenous auxin across Arabidopsis thaliana mutants and natural accessions varies from seedling to reproductive maturity

Background

Plant hormones influence phenology, development, and function of above and belowground plant structures. In seedlings, auxin influences the initiation and development of lateral roots and root systems. How auxin-related genes influence root initiation at early life stages has been investigated from numerous perspectives. There is a gap in our understanding of how these genes influence root size through the life cycle and in mature plants. Across development, the influence of a particular gene on plant phenotypes is partly regulated by the addition of a poly-A tail to mRNA transcripts via alternative polyadenylation (APA). Auxin related genes have documented variation in APA, with auxin itself contributing to APA site switches. Studies of the influence of exogenous auxin on natural plant accessions and mutants of auxin pathway gene families exhibiting variation in APA are required for a more complete understanding of genotype by development by hormone interactions in whole plant and fitness traits.

Methods

We studied Arabidopsis thaliana homozygous mutant lines with inserts in auxin-related genes previously identified to exhibit variation in number of APA sites. Our growth chamber experiment included wildtype Col-0 controls, mutant lines, and natural accession phytometers. We applied exogenous auxin through the life cycle. We quantified belowground and aboveground phenotypes in 14 day old, 21 day old seedlings and plants at reproductive maturity. We contrasted root, rosette and flowering phenotypes across wildtype, auxin mutant, and natural accession lines, APA groups, hormone treatments, and life stages using general linear models.

Results

The root systems and rosettes of mutant lines in auxin related genes varied in response to auxin applications across life stages and varied between genotypes within life stages. In seedlings, exposure to auxin decreased size, but increased lateral root density, whereas at reproductive maturity, plants displayed greater aboveground mass and total root length. These differences may in part be due to a shift which delayed the reproductive stage when plants were treated with auxin. Root traits of auxin related mutants depended on the number of APA sites of mutant genes and the plant's developmental stage. Mutants with inserts in genes with many APA sites exhibited lower early seedling belowground biomass than those with few APA sites but only when exposed to exogenous auxin. As we observed different responses to exogenous auxin across the life cycle, we advocate for further studies of belowground traits and hormones at reproductive maturity. Studying phenotypic variation of genotypes across life stages and hormone environments will uncover additional shared patterns across traits, assisting efforts to potentially reach breeding targets and enhance our understanding of variation of genotypes in natural systems.

Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth

Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.

Effect of Deep Placement Fertilization on the Distribution of Biomass, Nutrients, and Root System Development in Potato Plants

The study was carried out in designed pots-rhizoboxes. Root systems were evaluated using computer scanning to determine total length, root area, and root diameter. The study showed a favorable effect of deep placement of fertilizers on total yield, increasing biomass yield by 7-17% relative to surface fertilization. The largest biomass increase under the influence of deep fertilization was obtained in the case of tuber yield, in which a yield increase of 18-34% was obtained. Higher yields of potato tubers were obtained under depth fertilization compared to surface application of fertilizers. Under the influence of deep fertilization at a depth of 20 cm, the uptake of nitrogen and phosphorus by potato biomass increased by 20-21%. Increased depth of fertilization increased the proportion of nitrogen accumulated in the tubers, while in the case of phosphorus, no effect of depth on P distribution was shown. An analysis of root system parameters showed a positive effect on increases in length and total root area under deep fertilization of potato plants. Based on the study, it was found that the distribution of dry matter, nutrients, and potato root development parameters were most optimal when fertilizer granules were applied at a depth of 20 cm.

OsRLR4 binds to the OsAUX1 promoter to negatively regulate primary root development in rice

Root architecture is one of the most important agronomic traits that determines rice crop yield. The primary root (PR) absorbs mineral nutrients and provides mechanical support; however, the molecular mechanisms of PR elongation remain unclear in rice. Here, the two loss-of-function T-DNA insertion mutants of root length regulator 4 (OsRLR4), osrlr4-1 and osrlr4-2 with longer PR, and three OsRLR4 overexpression lines, OE-OsRLR4-1/-2/-3 with shorter PR compared to the wild type/Hwayoung (WT/HY), were identified. OsRLR4 is one of five members of the PRAF subfamily of the regulator chromosome condensation 1 (RCC1) family. Phylogenetic analysis of OsRLR4 from wild and cultivated rice indicated that it is under selective sweeps, suggesting its potential role in domestication. OsRLR4 controls PR development by regulating auxin accumulation in the PR tip and thus the root apical meristem activity. A series of biochemical and genetic analyses demonstrated that OsRLR4 functions directly upstream of the auxin transporter OsAUX1. Moreover, OsRLR4 interacts with the TRITHORAX-like protein OsTrx1 to promote H3K4me3 deposition at the OsAUX1 promoter, thus altering its transcription level. This work provides insight into the cooperation of auxin and epigenetic modifications in regulating root architecture and provides a genetic resource for plant architecture breeding.

Vacuolar fructose transporter SWEET17 is critical for root development and drought tolerance

Root growth and architecture are markedly influenced by both developmental and environmental cues. Sugars integrate different stimuli and are essential building blocks and signaling molecules for modulating the root system. Members from the SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET) family facilitate the transport of different sugars over cellular membranes and steer both inter and intracellular distribution of sugars. SWEET17 represents a fructose-specific sugar porter localized to the vacuolar membrane, the tonoplast. Here, we analyzed how SWEET17-dependent fructose released from vacuoles affects root growth during drought stress in Arabidopsis (Arabidopsis thaliana). We found that the SWEET17 gene was predominantly expressed in the root vasculature and in meristematic cells of the root tip. SWEET17 expression appeared markedly induced during lateral root (LR) outgrowth and under drought. Moreover, fructose repressed primary root growth but induced density and length of first order LRs. Consistently, sweet17 knock-out mutants exhibited reduced LR growth and a diminished expression of LR-development-related transcription factors during drought stress, resulting in impaired drought tolerance of sweet17 mutants. We discuss how SWEET17 activity integrates drought-induced cellular responses into fructose signaling necessary for modulation of the root system and maximal drought tolerance.

Root Traits and Biomechanical Properties of Three Tropical Pioneer Tree Species for Forest Restoration in Landslide Areas

Frequent earthquakes, monsoon torrential rains and typhoons cause severe landslides and soil erosion in Taiwan. Hibiscus taiwanensis, Macaranga tanarius, and Mallotus paniculatus are major pioneer tree species appearing on landslide-scarred areas. Thus, these species can be used to restore the self-sustaining native vegetation on forest landslides, to control erosion, and to stabilize slope. However, their growth performance, root traits and biomechanical properties have not been well characterized. In this study, root system and root traits were investigated using the excavation method, and biomechanical tests were performed to determine the uprooting resistance, root tensile strength and Young’s modulus of 1-year-old Hibiscus taiwanensis, Macaranga tanarius, and Mallotus paniculatus seedlings. The results reveal that relative to H. taiwanensis, M. tanarius and M. paniculatus seedlings had significantly larger root collar diameter, longer taproot length, higher root biomass, higher root density, higher root length density, heavier root mass, larger external root surface area, higher root tissue density, larger root volume, longer total root length, and a higher root tip number. Additionally, the height of M. paniculatus seedlings was significantly higher than those of H. taiwanensis and M. tanarius. Furthermore, the uprooting resistance and root tensile strength of M. paniculatus seedlings was significantly higher than those of H. taiwanensis and M. tanarius. Young’s modulus of M. paniculatus and M. tanarius seedlings was also significantly higher than that of H. taiwanensis. These growth characteristics and biomechanical properties demonstrate M. paniculatus and M. tanarius are superior than H. taiwanensis, considering growth performance, root anchorage capability, tensile strength and Young’s modulus. Taken as a whole, the rank order for species selection of these pioneer species for reforestation comes as: M. paniculatus M. tanarius H. taiwanensis. These results, along with knowledge on vegetation dynamics following landslides, allow us to better evaluate the effect of selective removal management of pioneer species on the resilience and sustainability of landslides.

High-efficient utilization and uptake of N contribute to higher NUE of 'Qinguan' apple under drought and N-deficient conditions compared with 'Honeycrisp'

Drought and nitrogen (N) deficiency are common factors that limit apple production in the Loess Plateau region of China. Different apple cultivars respond to drought and low N differently; however, the mechanism that underlies the difference in nitrogen-use efficiency (NUE) under drought conditions is not well understood. In this study, by comparing the physiological responses of two apple (Malus domestica Borkh.) cultivars with contrasting NUE, 'Qinguan' (higher NUE) and 'Honeycrisp' (lower NUE), under low N and drought conditions, we discovered that, 'Qinguan' had larger stomatal apertures, higher chlorophyll fluorescence levels, more active N metabolism and antioxidant enzymes, higher abscisic acid and auxin concentrations, larger root size and more efficient N uptake mediated by higher expression of MdNRT2.4 in rootstock than that of 'Honeycrisp'. Additionally, we experimentally confirmed that MdNRT2.4 enhanced low N and osmotic stress tolerance in Arabidopsis when being overexpressed. Taken together, our findings shed light on the mechanism that underlies the difference in NUE of apple under drought and N-deficient conditionss and provide MdNRT2.4 as a candidate gene for future genetic engineering.

Coupling Seq-BSA and RNA-Seq Analyses Reveal the Molecular Pathway and Genes Associated with Heading Type in Chinese Cabbage

In Chinese cabbage, heading type is a key agricultural trait of significant economic importance. Using a natural microspore-derived doubled haploid plant, we generated self-crossed progeny with overlapping or outward curling head morphotypes. Sequencing-based bulked segregant analysis (Seq-BSA) revealed a candidate region of 0.52 Mb (A06: 1,824,886~2,347,097 bp) containing genes enriched for plant hormone signal transduction. RNA Sequencing (RNA-Seq) analysis supported the hormone pathway enrichment leading to the identification of two key candidate genes, BrGH3.12 and BrABF1. The regulated homologous genes and the relationship between genes in this pathway were also revealed. Expression of BrGH3.12 varied significantly in the apical portion of the leaf, consistent with the morphological differences between overlapping and outward curling leaves. Transcript levels of BrABF1 in the top, middle and basal segments of the leaf were significantly different between the two types. The two morphotypes contained different concentrations of IAA in the apical portion of their leaves while levels of ABA differed significantly between plant types in the top, middle, and basal leaf segments. Results from Seq-BSA, RNA-Seq and metabolite analyses all support a role for IAA and ABA in heading type formation. These findings increase our understanding of the molecular basis for pattern formation of the leafy head in Chinese cabbage and will contribute to future work developing more desirable leafy head patterns.

Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root

Hormonal interactions are crucial for plant development. In Arabidopsis, cytokinins inhibit root growth through effects on cell proliferation and cell elongation. Here, we define key mechanistic elements in a regulatory network by which cytokinin inhibits root cell elongation in concert with the hormones auxin and ethylene. The auxin importer AUX1 functions as a positive regulator of cytokinin responses in the root; mutation of AUX1 specifically affects the ability of cytokinin to inhibit cell elongation but not cell proliferation. AUX1 is required for cytokinin-dependent changes of auxin activity in the lateral root cap associated with the control of cell elongation. Cytokinin regulates root cell elongation through ethylene-dependent and -independent mechanisms, both hormonal signals converging on AUX1 as a regulatory hub. An autoregulatory circuit is identified involving the control of ARR10 and AUX1 expression by cytokinin and auxin, this circuit potentially functioning as an oscillator to integrate the effects of these two hormones. Taken together, our results uncover several regulatory circuits controlling interactions of cytokinin with auxin and ethylene, and support a model in which cytokinin regulates shootward auxin transport to control cell elongation and root growth.

Inoculation insensitive promoters for cell type enriched gene expression in legume roots and nodules

BACKGROUND

Establishment and maintenance of mutualistic plant-microbial interactions in the rhizosphere and within plant roots involve several root cell types. The processes of host-microbe recognition and infection require complex signal exchange and activation of downstream responses. These molecular events coordinate host responses across root cell layers during microbe invasion, ultimately triggering changes of root cell fates. The progression of legume root interactions with rhizobial bacteria has been addressed in numerous studies. However, tools to globally resolve the succession of molecular events in the host root at the cell type level have been lacking. To this end, we aimed to identify promoters exhibiting cell type enriched expression in roots of the model legume Lotus japonicus, as no comprehensive set of such promoters usable in legume roots is available to date.

RESULTS

Here, we use promoter:GUS fusions to characterize promoters stemming from Arabidopsis, tomato (Lycopersicon esculentum) or L. japonicus with respect to their expression in major cell types of the L. japonicus root differentiation zone, which shows molecular and morphological responses to symbiotic bacteria and fungi. Out of 24 tested promoters, 11 showed cell type enriched activity in L. japonicus roots. Covered cell types or cell type combinations are epidermis (1), epidermis and cortex (2), cortex (1), endodermis and pericycle (2), pericycle and phloem (4), or xylem (1). Activity of these promoters in the respective cell types was stable during early stages of infection of transgenic roots with the rhizobial symbiont of L. japonicus, Mesorhizobium loti. For a subset of five promoters, expression stability was further demonstrated in whole plant transgenics as well as in active nodules.

CONCLUSIONS

11 promoters from Arabidopsis (10) or tomato (1) with enriched activity in major L. japonicus root and nodule cell types have been identified. Root expression patterns are independent of infection with rhizobial bacteria, providing a stable read-out in the root section responsive to symbiotic bacteria. Promoters are available as cloning vectors. We expect these tools to help provide a new dimension to our understanding of signaling circuits and transcript dynamics in symbiotic interactions of legumes with microbial symbionts.

Cation transporters/channels in plants: Tools for nutrient biofortification

Cation transporters/channels are key players in a wide range of physiological functions in plants, including cell signaling, osmoregulation, plant nutrition and metal tolerance. The recent identification of genes encoding some of these transport systems has allowed new studies toward further understanding of their integrated roles in plant. This review summarizes recent discoveries regarding the function and regulation of the multiple systems involved in cation transport in plant cells. The role of membrane transport in the uptake, distribution and accumulation of cations in plant tissues, cell types and subcellular compartments is described. We also discuss how the knowledge of inter- and intra-species variation in cation uptake, transport and accumulation as well as the molecular mechanisms responsible for these processes can be used to increase nutrient phytoavailability and nutrients accumulation in the edible tissues of plants. The main trends for future research in the field of biofortification are proposed.

Impact of heavy metal stresses on the growth and auxin homeostasis of Arabidopsis seedlings

The phytohormone auxin is an essential mediator in many aspects of plant development. Its dynamic and differential distribution within the plant is regulated by a variety of environmental cues including heavy metal stimuli. In the present study, we first evaluated the toxic effects of seven heavy metals including Pb(2+), Cd(2+), Hg(2+), Ni(2+). Zn(2+), Co(2+) and Cu(2+) in their excess on the model plant, Arabidopsis thaliana. Various morphological defects including loss in fresh weight and leaf area, decrease of the primary root length and stimulation of the lateral root density occurred to a different extent among seven heavy metals. Next, using an indicative DR5:GUS reporter line of Arabidopsis, the auxin accumulation and distribution within plant seedlings were found to be dramatically and differentially affected by these heavy metals. We further analyzed the transcriptional changes of 27 selected auxin homeostasis-related genes by qRT-PCR technique and found that upon various heavy metals, the expressions of the candidate genes were distinctly altered in shoots and roots. Our data indicated that when confronted with excessive heavy metals, plants could dynamically and differentially regulate the transcription of auxin-related genes to adjust the location and effective accumulation of auxin within the plant for better adaptation and survival under the adverse environment.

Hypocotyl adventitious root organogenesis differs from lateral root development

Wound-induced adventitious root (AR) formation is a requirement for plant survival upon root damage inflicted by pathogen attack, but also during the regeneration of plant stem cuttings for clonal propagation of elite plant varieties. Yet, adventitious rooting also takes place without wounding. This happens for example in etiolated Arabidopsis thaliana hypocotyls, in which AR initiate upon de-etiolation or in tomato seedlings, in which AR initiate upon flooding or high water availability. In the hypocotyl AR originate from a cell layer reminiscent to the pericycle in the primary root (PR) and the initiated AR share histological and developmental characteristics with lateral roots (LRs). In contrast to the PR however, the hypocotyl is a determinate structure with an established final number of cells. This points to differences between the induction of hypocotyl AR and LR on the PR, as the latter grows indeterminately. The induction of AR on the hypocotyl takes place in environmental conditions that differ from those that control LR formation. Hence, AR formation depends on differentially regulated gene products. Similarly to AR induction in stem cuttings, the capacity to induce hypocotyl AR is genotype-dependent and the plant growth regulator auxin is a key regulator controlling the rooting response. The hormones cytokinins, ethylene, jasmonic acid, and strigolactones in general reduce the root-inducing capacity. The involvement of this many regulators indicates that a tight control and fine-tuning of the initiation and emergence of AR exists. Recently, several genetic factors, specific to hypocotyl adventitious rooting in A. thaliana, have been uncovered. These factors reveal a dedicated signaling network that drives AR formation in the Arabidopsis hypocotyl. Here we provide an overview of the environmental and genetic factors controlling hypocotyl-born AR and we summarize how AR formation and the regulating factors of this organogenesis are distinct from LR induction.

Nitric oxide is required for determining root architecture and lignin composition in sunflower. Supporting evidence from microarray analyses

Nitric oxide (NO) is a signal molecule involved in several physiological processes in plants, including root development. Despite the importance of NO as a root growth regulator, the knowledge about the genes and metabolic pathways modulated by NO in this process is still limited. A constraint to unravel these pathways has been the use of exogenous applications of NO donors that may produce toxic effects. We have analyzed the role of NO in root architecture through the depletion of endogenous NO using the scavenger cPTIO. Sunflower seedlings growing in liquid medium supplemented with cPTIO showed unaltered primary root length while the number of lateral roots was deeply reduced; indicating that endogenous NO participates in determining root branching in sunflower. The transcriptional changes induced by NO depletion have been analyzed using a large-scale approach. A microarray analysis showed 330 genes regulated in the roots (p≤0.001) upon endogenous NO depletion. A general cPTIO-induced up-regulation of genes involved in the lignin biosynthetic pathway was observed. Even if no detectable changes in total lignin content could be detected, cell walls analyses revealed that the ratio G/S lignin increased in roots treated with cPTIO. This means that endogenous NO may control lignin composition in planta. Our results suggest that a fine tuning regulation of NO levels could be used by plants to regulate root architecture and lignin composition. The functional implications of these findings are discussed.

Regulation of root morphogenesis in arbuscular mycorrhizae: what role do fungal exudates, phosphate, sugars and hormones play in lateral root formation?

BACKGROUND

Arbuscular mycorrhizae (AMs) form a widespread root-fungus symbiosis that improves plant phosphate (Pi) acquisition and modifies the physiology and development of host plants. Increased branching is recognized as a general feature of AM roots, and has been interpreted as a means of increasing suitable sites for colonization. Fungal exudates, which are involved in the dialogue between AM fungi and their host during the pre-colonization phase, play a well-documented role in lateral root (LR) formation. In addition, the increased Pi content of AM plants, in relation to Pi-starved controls, as well as changes in the delivery of carbohydrates to the roots and modulation of phytohormone concentration, transport and sensitivity, are probably involved in increasing root system branching.

SCOPE

This review discusses the possible causes of increased branching in AM plants. The differential root responses to Pi, sugars and hormones of potential AM host species are also highlighted and discussed in comparison with those of the non-host Arabidopsis thaliana.

CONCLUSIONS

Fungal exudates are probably the main compounds regulating AM root morphogenesis during the first colonization steps, while a complex network of interactions governs root development in established AMs. Colonization and high Pi act synergistically to increase root branching, and sugar transport towards the arbusculated cells may contribute to LR formation. In addition, AM colonization and high Pi generally increase auxin and cytokinin and decrease ethylene and strigolactone levels. With the exception of cytokinins, which seem to regulate mainly the root:shoot biomass ratio, these hormones play a leading role in governing root morphogenesis, with strigolactones and ethylene blocking LR formation in the non-colonized, Pi-starved plants, and auxin inducing them in colonized plants, or in plants grown under high Pi conditions.

Light modulates the root tip excision induced lateral root formation in tomato

During plant growth and development, root tip performs multifarious functions integrating diverse external and internal stimuli to regulate root elongation and architecture. It is believed that a signal originating from root tip inhibits lateral root formation (LRF). The excision of root tip induced LRF in tomato seedlings associated with accumulation of auxin in pericycle founder cells. The excision of cotyledons slightly reduced LRF, whereas severing shoot from root completely abolished LRF. Exogenous ethylene application did not alter LRF. The response was modulated by light with higher LRF in seedlings exposed to light. Our results indicate that light plays a role in LRF in seedlings by likely modulating shoot derived auxin.

To branch or not to branch: the role of pre-patterning in lateral root formation

The establishment of a pre-pattern or competence to form new organs is a key feature of the postembryonic plasticity of plant development, and the elaboration of such pre-patterns leads to remarkable heterogeneity in plant form. In root systems, many of the differences in architecture can be directly attributed to the outgrowth of lateral roots. In recent years, efforts have focused on understanding how the pattern of lateral roots is established. Here, we review recent findings that point to a periodic mechanism for establishing this pattern, as well as roles for plant hormones, particularly auxin, in the earliest steps leading up to lateral root primordium development. In addition, we compare the development of lateral root primordia with in vitro plant regeneration and discuss possible common molecular mechanisms.

Correlation between hormonal homeostasis and morphogenic responses in Arabidopsis thaliana seedlings growing in a Cd/Cu/Zn multi-pollution context

To date, almost no information is available in roots and shoots of the model plant Arabidopsis thaliana about the hierarchic relationship between metal accumulation, phytohormone levels, and glutathione/phytochelatin content, and how this relation affects root development. For this purpose, specific concentrations of cadmium, copper and zinc, alone or in triple combination, were supplied for 12 days to in vitro growing seedlings. The accumulation of these metals was measured in roots and shoots, and a significant competition in metal uptake was observed. Microscopic analyses revealed that root morphology was affected by metal exposure, and that the levels of trans-zeatin riboside, dihydrozeatin riboside, indole-3-acetic acid and the auxin/cytokinin ratio varied accordingly. By contrast, under metal treatments, minor modifications in gibberellic acid and abscisic acid levels occurred. Real-time polymerase chain reaction analysis of some genes involved in auxin and cytokinin synthesis (e.g. AtNIT in roots and AtIPT in shoots) showed on average a metal up-regulated transcription. The production of thiol-peptides was induced by all the metals, alone or in combination, and the expression of the genes involved in thiol-peptide synthesis (AtGSH1, AtGSH2, AtPCS1 and AtPCS2) was not stimulated by the metals, suggesting a full post-transcriptional control. Results show that the Cd/Cu/Zn-induced changes in root morphology are caused by a hormonal unbalance, mainly governed by the auxin/cytokinin ratio.

Root apex transition zone as oscillatory zone

Root apex of higher plants shows very high sensitivity to environmental stimuli. The root cap acts as the most prominent plant sensory organ; sensing diverse physical parameters such as gravity, light, humidity, oxygen, and critical inorganic nutrients. However, the motoric responses to these stimuli are accomplished in the elongation region. This spatial discrepancy was solved when we have discovered and characterized the transition zone which is interpolated between the apical meristem and the subapical elongation zone. Cells of this zone are very active in the cytoskeletal rearrangements, endocytosis and endocytic vesicle recycling, as well as in electric activities. Here we discuss the oscillatory nature of the transition zone which, together with several other features of this zone, suggest that it acts as some kind of command center. In accordance with the early proposal of Charles and Francis Darwin, cells of this root zone receive sensory information from the root cap and instruct the motoric responses of cells in the elongation zone.

Longitudinal zonation pattern in plant roots: conflicts and solutions

Despite the relative simplicity of Arabidopsis root organization, there is no general agreement regarding the terminology used to describe the longitudinal zonation pattern (LZP) of this model system. In this opinion article, we examine inconsistencies in the terminology and provide a conceptual framework for the LZP that may be applied to all angiosperms. We propose that the root apical meristem (RAM) consists of the cell-proliferation domain where cells maintain a high probability to divide and the transition domain with a low probability of cell division; in both domains cells grow at the same, relatively low, rate. Owing to stochastic termination of cell proliferation in the RAM, the border between the domains is 'fuzzy'. Molecular markers analyzed together with quantitative growth and cell analyses could help to identify developmental zones along the root and lead to a better understanding of the LZP in angiosperms.

Auxin metabolism and homeostasis during plant development

Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.

Tissue-specific expression of SMALL AUXIN UP RNA41 differentially regulates cell expansion and root meristem patterning in Arabidopsis

Among the three primary auxin-induced gene families, Auxin/Indole-3-Acetic Acid (Aux/IAA), Gretchen Hagen3 (GH3) and SMALL AUXIN UP RNA (SAUR), the function of SAUR genes remains unclear. Arabidopsis SAUR genes have been phylogenetically classified into three clades. Recent work has suggested that SAUR19 (clade II) and SAUR63 (clade I) promote cell expansion through the modulation of auxin transport. Herein, we present our work on SAUR41, a clade III SAUR gene with a distinctive expression pattern in root meristems. SAUR41 was normally expressed in the quiescent center and cortex/endodermis initials; upon auxin stimulation, the expression was provoked in the endodermal layer. During lateral root development, SAUR41 was expressed in prospective stem cell niches of lateral root primordia and in expanding endodermal cells surrounding the primordia. SAUR41-EGFP (enhanced green fluorescent protein) fusion proteins localized to the cytoplasm. Overexpression of SAUR41 from the Cauliflower mosaic virus 35S promoter led to pleiotropic auxin-related phenotypes, including long hypocotyls, increased vegetative biomass and lateral root development, expanded petals and twisted inflorescence stems. Ectopic SAUR41 proteins were able to promote auxin transport in hypocotyls. Tissue-specific expression of SAUR41 from the PIN1, WOX5, PLT2 and ACR4 promoters induced the formation of new auxin accumulation/signaling peaks above the quiescent centers, whereas tissue-specific expression of SAUR41 from the PIN2 and PLT2 promoters enhanced root gravitropic growth. Cells in the root stem cell niches of these transgenic seedlings were differentially enlarged. The distinctive expression pattern of the SAUR41 gene and the explicit function of SAUR41 proteins implied that further investigations on the loss-of-function phenotypes of this gene in root development and environmental responses are of great interest.

Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis

Plants are necessarily highly competitive and have finely tuned mechanisms to adjust growth and development in accordance with opportunities and limitations in their environment. Sugars from photosynthesis form an integral part of this growth control process, acting as both an energy source and as signaling molecules in areas targeted for growth. The plant hormone auxin similarly functions as a signaling molecule and a driver of growth and developmental processes. Here, we show that not only do the two act in concert but that auxin metabolism is itself regulated by the availability of free sugars. The regulation of the biosynthesis and degradation of the main auxin, indole-3-acetic acid (IAA), by sugars requires changes in the expression of multiple genes and metabolites linked to several IAA biosynthetic pathways. The induction also involves members of the recently described central regulator PHYTOCHROME-INTERACTING FACTOR transcription factor family. Linking these three known regulators of growth provides a model for the dynamic coordination of responses to a changing environment.

Roots, water, and nutrient acquisition: let's get physical

Improved root water and nutrient acquisition can increase fertiliser use efficiency and is important for securing food production. Root nutrient acquisition includes proliferation, transporter function, exudation, symbioses, and the delivery of dissolved nutrients from the bulk soil to the root surface via mass flow and diffusion. The widespread adoption of simplified experimental systems has restricted consideration of the influence of soil symbiotic organisms and physical properties on root acquisition. The soil physical properties can directly influence root growth and explain some of the disparities obtained from different experimental systems. Turning this to an advantage, comparing results obtained with the same model plant Arabidopsis (Arabidopsis thaliana) in different systems, we can tease apart the specific effects of soil physical properties.

Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana

Circadian clocks synchronized with the environment allow plants to anticipate recurring daily changes and give a fitness advantage. Here, we mapped the dynamic growth phenotype of leaves and roots in two lines of Arabidopsis thaliana with a disrupted circadian clock: the CCA1 over-expressing line (CCA1ox) and the prr9 prr7 prr5 (prr975) mutant. We demonstrate leaf growth defects due to a disrupted circadian clock over a 24 h time scale. Both lines showed enhanced leaf growth compared with the wild-type during the diurnal period, suggesting increased partitioning of photosynthates for leaf growth. Nocturnal leaf growth was reduced and growth inhibition occurred by dawn, which may be explained by ineffective starch degradation in the leaves of the mutants. However, this growth inhibition was not caused by starch exhaustion. Overall, these results are consistent with the notion that the defective clock affects carbon and energy allocation, thereby reducing growth capacity during the night. Furthermore, rosette morphology and size as well as root architecture were strikingly altered by the defective clock control. Separate analysis of the primary root and lateral roots revealed strong suppression of lateral root formation in both CCA1ox and prr975, accompanied by unusual changes in lateral root growth direction under light-dark cycles and increased lateral extension of the root system. We conclude that growth of the whole plant is severely affected by improper clock regulation in A. thaliana, resulting not only in altered timing and capacity for growth but also aberrant development of shoot and root architecture.