Intrinsic and environmental response pathways that regulate root system architecture

Root system development is an important agronomic trait. The right architecture in a given environment allows plants to survive periods of water of nutrient deficit, and compete effectively for resources. Root systems also provide an optimal system for studying developmental plasticity, a characteristic feature of plant growth. This review proposes a framework for describing the pathways regulating the development of complex structures such as root systems: intrinsic pathways determine the characteristic architecture of the root system in a given plant species, and define the limits for plasticity in that species. Response pathways co-ordinate environmental cues with development by modulating intrinsic pathways. The current literature describing the regulation of root system development is summarized here within this framework. Regulatory pathways are also organized based on their specific developmental effect in the root system. All the pathways affect lateral root formation, but some specifically target initiation of the lateral root, while others target the development and activation of the lateral root primordium, or the elongation of the lateral root. Finally, we discuss emerging approaches for understanding the regulation of root system architecture.     

Ongoing modifications to root system architecture of Pinus ponderosa growing on a sloped site revealed by tree-ring analysis

Our knowledge of the root system architecture of trees is still incomplete, especially concerning how biomass partitioning is regulated to achieve an optimal, but often unequal, distribution of resources. In addition, our comprehension of root system architecture development as a result of the adaptation process is limited because most studies lack a temporal approach. To add to our understanding, we excavated 32-year-old Pinus ponderosa trees from a steep, forested site in northern Idaho USA. The root systems were discretized by a low magnetic field digitizer and along with AMAPmod software we examined their root traits (i.e. order category, topology, growth direction length, and volume) in four quadrants: downslope, upslope, windward, and leeward. On one tree, we analyzed tree rings to compare the ages of lateral roots relative to their parental root, and to assess the occurrence of compression wood. We found that, from their onset, first-order lateral roots have similar patterns of ring eccentricity suggesting an innate ability to respond to different mechanical forces; more root system was allocated downslope and to the windward quadrant. In addition, we noted that shallow roots, which all presented compression wood, appear to be the most important component of anchorage. Finally, we observed that lateral roots can change growth direction in response to mechanical forces, as well as produce new lateral roots at any development stage and wherever along their axis. These findings suggest that trees adjust their root spatial deployment in response to environmental conditions, these roots form compression wood to dissipate mechanical forces, and new lateral roots can arise anywhere and at any time on the existing system in apparent response to mechanical forces.     

长柄水青冈幼苗根系构型及动态变化

长柄水青冈（Fagus longipetiolata）是我国亚热带山地林的重要组成树种,本研究在温室中用河砂培养长柄水青冈幼苗,采用直接测量法研究了长柄水青冈的根系构型。结果表明,生长50 d的长柄水青冈幼苗的根系呈倒圆锥形,根宽小于根深;基根平均生长角度较小,基根的向地性小;一级侧根与主根的夹角从根系上部至下部逐渐变小;二级侧根首先发生于根系的中下部,然后其发生范围向根系上、下部扩展。虽然长柄水青冈幼苗根系构型存在较大的个体差异性,但一级侧根与主根的夹角则具有较好的稳定性。研究揭示了实验条件下长柄水青冈幼苗的根系构型及其在幼苗建成过程中的生长变化规律,为长柄水青冈的进一步研究提供科学依据。     

An auxin transport-based model of root branching in Arabidopsis thaliana

Root architecture is a crucial part of plant adaptation to soil heterogeneity and is mainly controlled by root branching. The process of root system development can be divided into two successive steps: lateral root initiation and lateral root development/emergence which are controlled by different fluxes of the plant hormone auxin. While shoot architecture appears to be highly regular, following rules such as the phyllotactical spiral, root architecture appears more chaotic. We used stochastic modeling to extract hidden rules regulating root branching in Arabidopsis thaliana. These rules were used to build an integrative mechanistic model of root ramification based on auxin. This model was experimentally tested using plants with modified rhythm of lateral root initiation or mutants perturbed in auxin transport. Our analysis revealed that lateral root initiation and lateral root development/emergence are interacting with each other to create a global balance between the respective ratio of initiation and emergence. A mechanistic model based on auxin fluxes successfully predicted this property and the phenotype alteration of auxin transport mutants or plants with modified rhythms of lateral root initiation. This suggests that root branching is controlled by mechanisms of lateral inhibition due to a competition between initiation and development/emergence for auxin.     

Statistical modeling of nitrogen-dependent modulation of root system architecture in Arabidopsis thaliana

Plant root development is strongly affected by nutrient availability. Despite the importance of structure and function of roots in nutrient acquisition,statistical modeling approaches to evaluate dynamic and temporal modulations of root system architecture in response to nutrient availability have remained as widely open and exploratory areas in root biology. In this study,we developed a statistical modeling approach to investigate modulations of root system architecture in response to nitrogen availability. Mathematical models were designed for quantitative assessment of root growth and root branching phenotypes and their dynamic relationships based on hierarchical con figuration of primary and lateral roots formulating the fishbone-shaped root system architecture in Arabidopsis thaliana. Time-series datasets reporting dynamic changes in root developmental traits on different nitrate or ammonium concentrations were generated for statistical analyses. Regression analyses unraveled key parameters associated with:(i) inhibition of primary root growth under nitrogen limitation or on ammonium;(ii) rapid progression of lateral root emergence in response to ammonium; and(iii) inhibition of lateral root elongation in the presence of excess nitrate or ammonium. This study provides a statistical framework for interpreting dynamic modulation of root system architecture,supported by metaanalysis of datasets displaying morphological responses of roots to diverse nitrogen supplies.     

The role of nutrient availability in regulating root architecture

The ability of plants to respond appropriately to nutrient availability is of fundamental importance for their adaptation to the environment. Nutrients such as nitrate, phosphate, sulfate and iron act as signals that can be perceived. These signals trigger molecular mechanisms that modify cell division and cell differentiation processes within the root and have a profound impact on root system architecture. Important developmental processes, such as root-hair formation, primary root growth and lateral root formation, are particularly sensitive to changes in the internal and external concentration of nutrients. The responses of root architecture to nutrients can be modified by plant growth regulators, such as auxins, cytokinins and ethylene, suggesting that the nutritional control of root development may be mediated by changes in hormone synthesis, transport or sensitivity. Recent information points to the existence of nutrient-specific signal transduction pathways that interpret the external and internal concentrations of nutrients to modify root development. Progress in this field has led to the cloning of regulatory genes that play pivotal roles in nutrient-induced changes to root development.     

Osmotic regulation of root system architecture

Although root system architecture is known to be highly plastic and strongly affected by environmental conditions, we have little understanding of the underlying mechanisms controlling root system development. Here we demonstrate that the formation of a lateral root from a lateral root primordium is repressed as water availability is reduced. This osmotic-responsive regulatory mechanism requires abscisic acid (ABA) and a newly identified gene, LRD2. Mutant analysis also revealed interactions of ABA and LRD2 with auxin signaling. Surprisingly, further examination revealed that both ABA and LRD2 control root system architecture even in the absence of osmotic stress. This suggests that the same molecules that mediate responses to environmental cues can also be regulators of intrinsic developmental programs in the root system.     

Phosphate availability regulates root system architecture in Arabidopsis

Plant root systems are highly plastic in their development and can adapt their architecture in response to the prevailing environmental conditions. One important parameter is the availability of phosphate, which is highly immobile in soil such that the arrangement of roots within the soil will profoundly affect the ability of the plant to acquire this essential nutrient. Consistent with this, the availability of phosphate was found to have a marked effect on the root system architecture of Arabidopsis. Low phosphate availability favored lateral root growth over primary root growth, through increased lateral root density and length, and reduced primary root growth mediated by reduced cell elongation. The ability of the root system to respond to phosphate availability was found to be independent of sucrose supply and auxin signaling. In contrast, shoot phosphate status was found to influence the root system architecture response to phosphate availability.     

A role for the root cap in root branching revealed by the non-auxin probe naxillin

The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture.     

Arabidopsis Lateral Root Development 3 is essential for early phloem development and function, and hence for normal root system development

We have identified a gene, Lateral Root Development 3 (LRD3), that is important for maintaining a balance between primary and lateral root growth. The lrd3 mutant has decreased primary root growth and increased lateral root growth. We determined that the LRD3 gene encodes a LIM-domain protein of unknown function. LRD3 is expressed only in the phloem companion cells, which suggested a role in phloem function. Indeed, while phloem loading and export from the shoot appear to be normal, delivery of phloem to the primary root tip is limited severely in young seedlings. Abnormalities in phloem morphology in these seedlings indicate that LRD3 is essential for correct early phloem development. There is a subsequent spontaneous recovery of normal phloem morphology, which is correlated tightly with increased phloem delivery and growth of the primary root. The LRD3 gene is one of very few genes described to affect phloem development, and the only one that is specific to early phloem development. Continuous growth on auxin also leads to recovery of phloem development and function in lrd3, which demonstrates that auxin plays a key role in early phloem development. The root system architecture and the pattern of phloem allocation in the lrd3 root system suggested that there may be regulated mechanisms for selectively supporting certain lateral roots when the primary root is compromised. Therefore, this study provides new insights into phloem-mediated resource allocation and its effects on plant root system architecture.     

Effect of water stress on root meristems in woody and herbaceous plants during the first stage of development

We investigated the effect of water stress on the root system architecture of pine saplings and pea seedlings during the first stage of development. Attention was focused on meristematic tissue situated at the root tip because of the leading role played by the tissue in the planning of root system architecture. The data showed that both species are extremely sensitive and that plants arrest their growth immediately during water stress treatment. When stress treatment was not intense, both species recovered growth but presented modifications in the root system architecture. In pine saplings, the modification in root system architecture was the consequence of fine root meristems not recovering from water stress. The saplings survived by producing new lateral meristems from the cortical tannin zone above the fine root tip. In the case of pea seedlings, the meristematic tissues in the primary root arrested proliferation during water stress although they recovered when the event occurred during the first hours of germination. The response was different when water stress was enforced on older seedlings. In this case, root meristems never completely recovered their proliferation despite the increase in proline content observed in the cells. The modification of root system architecture in pea seedlings depended on the arrest of primary root elongation and the formation of new root laterals. As regards the primary roots, water stress treatment induced along the axis the formation of irregular ‘swellings’ in the cortical zone above the meristematic zone. Anatomical investigations suggested that such swellings may have derived from the changes in elongation direction of derivatives. The formation of new laterals was observed in hydroponic cultures when water stress treatment was enforced slowly and prolonged for a long time. The production of new lateral meristems may have been a similar response of woody and herbaceous plants to water stress conditions. It is not known whether these new meristems present characteristics of resistance to water stress. This revised version was published online in June 2006 with corrections to the Cover Date.     

Distribution of Lateral Root Primordia in Root Tips of Musa

The distribution of lateral root primordia in the root tipsof four Musa landraces (Grande Naine, Pisang Berlin, Ngok Egomeand Yangambi Km5) grown in the field has been investigated toevaluate the range of genetic variation of lateral root initiation.In banana (Musa sp.), lateral roots are initiated in the roottip, 0.6–4 mm behind the root/cap junction and arise inseveral protoxylem-based longitudinal rows or ‘ranks’.Significant differences were observed among landraces for theposition of the most distal primordium, however the longitudinalspacing between successive primordia along the ranks was similarfor all landraces. All ranks were involved in lateral root initiation.The number of ranks also showed significant variations amonglandraces and was proportional to the stelar diameter. Hencethe density of lateral roots (roots cm^-1) was affected by stelardiameter variations. Finally, root elongation in the root tipwas landrace-specific and not necessarily exponential, unlikesuggested in previous studies. It is concluded that lateralroot initiation in Musa is not involved in the genetic variationsof root architecture in the field. A dissection of root architectureinto components which may account for these variations is proposedin relation to the improvement of root system architecture.Copyright 1999 Annals of Botany Company Lateral root initiation, root architecture, Musa, banana.     

Phosphate availability alters architecture and causes changes in hormone sensitivity in the Arabidopsis root system

The postembryonic developmental program of the plant root system is plastic and allows changes in root architecture to adapt to environmental conditions such as water and nutrient availability. Among essential nutrients, phosphorus (P) often limits plant productivity because of its low mobility in soil. Therefore, the architecture of the root system may determine the capacity of the plant to acquire this nutrient. We studied the effect of P availability on the development of the root system in Arabidopsis. We found that at P-limiting conditions (<50 microM), the Arabidopsis root system undergoes major architectural changes in terms of lateral root number, lateral root density, and primary root length. Treatment with auxins and auxin antagonists indicate that these changes are related to an increase in auxin sensitivity in the roots of P-deprived Arabidopsis seedlings. It was also found that the axr1-3, axr2-1, and axr4-1 Arabidopsis mutants have normal responses to low P availability conditions, whereas the iaa28-1 mutant shows resistance to the stimulatory effects of low P on root hair and lateral root formation. Analysis of ethylene signaling mutants and treatments with 1-aminocyclopropane-1-carboxylic acid showed that ethylene does not promote lateral root formation under P deprivation. These results suggest that in Arabidopsis, auxin sensitivity may play a fundamental role in the modifications of root architecture by P availability.     

External Nitrogen and Carbon Source-Mediated Response on Modulation of Root System Architecture and Nitrate Uptake in Wheat Seedlings

Nitrogen uptake efficiency is an important component trait that could be targeted for improving nitrogen use efficiency of crop plants. To understand the responses of different nitrate transport systems and the influence of root system architecture on nitrate uptake under limited nitrate conditions in wheat (Triticum aestivum L.) at the seedling stage, we studied nitrate uptake, root system architecture, and expression of different nitrate transporter genes in induced and non-induced wheat seedlings. Further, effects of inclusion of sucrose and two amino acids (glutamine and asparagine) in induction medium on these parameters were also studied. We observed that the induced wheat root system took up more nitrate as compared to non-induced root system in a dose-dependent manner. Gene expression of both high- and low-affinity nitrate transporter gene showed differential expression in the induced root tissues, as compared to non-induced tissues, depending on the concentration of nitrate present in induction medium. External nutrient media containing sucrose, glutamine, and asparagine reduce nitrate concentration in both root and shoot tissues and also influence the gene expression of these transporters. Our observations indicate that upon induction with milder external nitrate concentrations, the root architecture is modulated by changing overall lateral root size and 1st order lateral root numbers along with activation of nitrate transporters which acquire and transport nitrate in roots and shoots, respectively, depending on the carbon and nitrogen source available to seedlings.

     

The effect of root exudates on root architecture in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Root architecture is of key importance for plant nutrition and performance. It is known that root architecture is determined by genetics and environmental conditions. The aim of the present study was to evaluate if root exudation within a given plant has a role in the development of root architecture. We conducted a series of experiments using Arabidopsis thaliana Ler and Col grown with and without activated charcoal (AC). The addition of AC lowered the concentration of secondary metabolites in the growth media by more than 90%. Our results consistently showed that the addition of AC significantly decreased the number of lateral roots (38% in Ler and 27% in Col), but this decrease was compensated by an increase in the root length per unit of lateral root (83% in Ler and 96% in Col). This compensation resulted in a non-significant effect of AC on the total length of lateral roots. The effects of AC on root architecture were partially or totally reverted by the differential supplementation of root exudates from other plants of the same ecotype. Our results indicate a direct role of secondary metabolites present in the root exudates in the development of root architecture.     

Quantitative trait loci controlling root growth and architecture in Arabidopsis thaliana confirmed by heterogeneous inbred family

Arabidopsis thaliana provides a scientifically attractive and simple model for studying root growth and architecture and, subsequently, for discovering new genes involved in the control of these characters in plants. We have used the natural variation available in Arabidopsis accessions and mapped quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN) and density (LRD) and for total length of the lateral root system (LRL) in the Bay-0 × Shahdara population. Total phenotypic variation was very large, and despite the importance of the environmental component we were able to map 13 QTLs and one epistatic interaction between QTLs. Our results highlight the biological relevance and genetic control of lateral root density in this material. We were also able to show that variation in the extent of the lateral root system depends mainly on the growth of the existing lateral roots rather than in a change in LRN. Factors controlling lateral root growth seemed to have no major effect on primary root growth. Moreover, Shahdara QTL alleles always increased the length of the lateral roots, which may be taken as an adaptation to its very dry natural environment in Tadjikistan. A QTL for PRL was confirmed using a type of near-isogenic line called a heterogeneous inbred family (HIF), and this QTL is a candidate for further fine-mapping and cloning.     

Localized iron supply triggers lateral root elongation in Arabidopsis by altering the AUX1-mediated auxin distribution

Root system architecture depends on nutrient availability, which shapes primary and lateral root development in a nutrient-specific manner. To better understand how nutrient signals are integrated into root developmental programs, we investigated the morphological response of Arabidopsis thaliana roots to iron (Fe). Relative to a homogeneous supply, localized Fe supply in horizontally separated agar plates doubled lateral root length without having a differential effect on lateral root number. In the Fe uptake-defective mutant iron-regulated transporter1 (irt1), lateral root development was severely repressed, but a requirement for IRT1 could be circumvented by Fe application to shoots, indicating that symplastic Fe triggered the local elongation of lateral roots. The Fe-stimulated emergence of lateral root primordia and root cell elongation depended on the rootward auxin stream and was accompanied by a higher activity of the auxin reporter DR5-β-glucuronidase in lateral root apices. A crucial role of the auxin transporter AUXIN RESISTANT1 (AUX1) in Fe-triggered lateral root elongation was indicated by Fe-responsive AUX1 promoter activities in lateral root apices and by the failure of the aux1-T mutant to elongate lateral roots into Fe-enriched agar patches. We conclude that a local symplastic Fe gradient in lateral roots upregulates AUX1 to accumulate auxin in lateral root apices as a prerequisite for lateral root elongation.     

N-acyl-L-homoserine lactones: a class of bacterial quorum-sensing signals alter post-embryonic root development in Arabidopsis thaliana

N-acyl-homoserine lactones (AHLs) belong to a class of bacterial quorum-sensing signals important for bacterial cell-to-cell communication. We evaluated Arabidopsis thaliana growth responses to a variety of AHLs ranging from 4 to 14 carbons in length, focusing on alterations in post-embryonic root development as a way to determine the biological activity of these signals. The compounds affected primary root growth, lateral root formation and root hair development, and in particular, N-decanoyl-HL (C10-HL) was found to be the most active AHL in altering root system architecture. Developmental changes elicited by C10-HL were related to altered expression of cell division and differentiation marker lines pPRZ1:uidA, CycB1:uidA and pAtEXP7:uidA in Arabidopsis roots. Although the effects of C10-HL were similar to those produced by auxins in modulating root system architecture, the primary and lateral root response to this compound was found to be independent of auxin signalling. Furthermore, we show that mutant and overexpressor lines for an Arabidopsis fatty acid amide hydrolase gene (AtFAAH) sustained altered growth response to C10-HL. All together, our results suggest that AHLs alter root development in Arabidopsis and that plants posses the enzymatic machinery to metabolize these compounds.