DART: a software to analyse root system architecture and development from captured images

Image analysis is used in numerous studies of root system architecture (RSA). To date, fully automatic procedures have not been good enough to completely replace alternative manual methods. DART (Data Analysis of Root Tracings) is freeware based on human vision to identify roots, particularly across time-series. Each root is described by a series of ordered links encapsulating specific information and is connected to other roots. The population of links constitutes the RSA. DART creates a comprehensive dataset ready for individual or global analyses and this can display root growth sequences along time. We exemplify here individual tomato root growth response to shortfall in solar radiation and we analyse the global distribution of the inter-root branching distances. DART helps in studying RSA and in producing structured and flexible datasets of individual root growth parameters. It is written in JAVA and relies on manual procedures to minimize the risks of errors and biases in datasets.     

Responses of root architecture development to low phosphorus availability: a review

Background

Phosphorus (P) is an essential element for plant growth and development but it is often a limiting nutrient in soils. Hence, P acquisition from soil by plant roots is a subject of considerable interest in agriculture, ecology and plant root biology. Root architecture, with its shape and structured development, can be considered as an evolutionary response to scarcity of resources.

Scope

This review discusses the significance of root architecture development in response to low P availability and its beneficial effects on alleviation of P stress. It also focuses on recent progress in unravelling cellular, physiological and molecular mechanisms in root developmental adaptation to P starvation. The progress in a more detailed understanding of these mechanisms might be used for developing strategies that build upon the observed explorative behaviour of plant roots.

Conclusions

The role of root architecture in alleviation of P stress is well documented. However, this paper describes how plants adjust their root architecture to low-P conditions through inhibition of primary root growth, promotion of lateral root growth, enhancement of root hair development and cluster root formation, which all promote P acquisition by plants. The mechanisms for activating alterations in root architecture in response to P deprivation depend on changes in the localized P concentration, and transport of or sensitivity to growth regulators such as sugars, auxins, ethylene, cytokinins, nitric oxide (NO), reactive oxygen species (ROS) and abscisic acid (ABA). In the process, many genes are activated, which in turn trigger changes in molecular, physiological and cellular processes. As a result, root architecture is modified, allowing plants to adapt effectively to the low-P environment. This review provides a framework for understanding how P deficiency alters root architecture, with a focus on integrated physiological and molecular signalling.     

Modelling and simulation of the architecture and development of the oil-palm (Elaeis guineensis Jacq.) root system

A stochastic model of oil-palm (Elaeis guineensis Jacq.) root system architecture and development has been developed. This model enabled us to create 3-D numerical models of complete root systems by simulation. The application of a postprocessor software, called RACINES, to these 3-D numerical models, provided an estimation of some parameters of plant root systems. The objective of this paper is to present oil-palm root characteristics as possible outputs of the application of this RACINES software. The outputs described in this article cover (i) spatial distribution of roots under plantation conditions, (ii) the estimation and distribution of total root biomass, per root type or per soil horizon and (iii) the location and quantification of absorbent surfaces. The computing techniques used were based on voxellization of space and creation of 3-D virtual sceneries exactly reproducing observed planting designs. By comparing the results of observations and simulations for spatial distribution (by trench wall density maps) and root biomasses (by real and virtual sampling) we were able to carry out additional numerical validations of the model.     

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.     

脱落酸被土壤“掩盖”了的功能:调节根系构型形态建成

植物根系发育是一个重要的农艺性状。由于根系具有结构和生长模式简单、信号感受灵敏等,有可能成为研究植物发育可塑性的良好材料。通过分析脱落酸在主根、侧根和根毛的发生和生长中及根构型形成中的可能信号转导过程中的作用,提出未来研究应关注的科学问题。对ABA调控根系发育分子机制的探讨不仅有利于阐明如何调控根发育可塑性这一复杂和困难的生物学问题,而且对农业生产也极为重要。     

Modelling and simulation of the architecture and development of the oil-palm (t Elaeis guineensis Jacq.) root system

The objective of this work was to model the architecture and growth dynamics of the oil-palm root system. The morphological and functional unit of the root system, called root architectural unit and its development sequence enabled us to establish the basis of a mathematical formalization of the root system architecture. The topology of the branched structures and the processes of growth, branching and mortality were described and modelled by stochastic processes (graph model, automata, laws of probability). The models obtained were then combined with geometrical parameters in an overall mathematical model: the reference axis. Simulation of this model provided 3-D numerical models. Validations of the overall model based on comparing the 3-D numerical models with observed root systems, appeared satisfactory.     

Ground-penetrating radar-based automatic reconstruction of three-dimensional coarse root system architecture

Background and aims

The diverse functions of roots set requirements on specific root system architecture (RSA). Investigation on RSA holds potentials for studying the adaptation of plants to environmental stresses and to interspecific competitions. Ground-penetrating radar (GPR) has provided a non-invasive method for studying in situ RSA. However, previous GPR method relied on manually connecting root points detected between radargrams to restore each root branch, resulting in limited accuracy and efficiency of reconstructing RSA. The objective of this study is to improve the effectiveness of 3D RSA reconstruction using GPR root detection data.

Methods

A total of 213 coarse root sections (with diameter >0.5 cm) were extracted from a distribution map of a reference shrub (Arctostaphylos pungens) root system to simulate the coarse roots identified by GPR. An automatic method was established to trace each root point to its optimum growing source point. Connections between discrete root points recovered the topology of the reference RSA. A spline curve smoothing method was applied to restore the 3D morphology of the reference RSA. The proposed protocol was then tested to rebuild the 3D RSA of a shrub (Caragana microphylla) growing in the sandy soils after in situ GPR survey. The accuracy of RSA reconstruction was quantitatively evaluated by a relationship matrix method and qualitatively assessed by direct comparisons between the reconstructed and the actual RSAs after in situ excavation.

Results

For both simulated and field collected GPR detection datasets, the reconstructed RSAs strongly corresponded to the real topology of the actual root systems. When adapting the best strategy, 186 of the 213 (87.32 %) root points on the reference root system of A. pungens were interlinked with correct topology, and the relationship matrix method detected an overall similarity of 82.75 % between the reconstructed and the actual RSAs.

Conclusion

The proposed automatic RSA reconstruction method greatly enhances the interpretation of GPR detection data regarding coarse roots, making in situ non-invasive and long-term mapping and monitoring of RSA possible.     

A novel image-analysis toolbox enabling quantitative analysis of root system architecture

We present in this paper a novel, semiautomated image-analysis software to streamline the quantitative analysis of root growth and architecture of complex root systems. The software combines a vectorial representation of root objects with a powerful tracing algorithm that accommodates a wide range of image sources and quality. The root system is treated as a collection of roots (possibly connected) that are individually represented as parsimonious sets of connected segments. Pixel coordinates and gray level are therefore turned into intuitive biological attributes such as segment diameter and orientation as well as distance to any other segment or topological position. As a consequence, user interaction and data analysis directly operate on biological entities (roots) and are not hampered by the spatially discrete, pixel-based nature of the original image. The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements. The use of the software is illustrated with a time-lapse analysis of cluster root formation in lupin (Lupinus albus) and an architectural analysis of the maize (Zea mays) root system. The software, SmartRoot, is an operating system-independent freeware based on ImageJ and relies on cross-platform standards for communication with data-analysis software.     

Influence of wind loading on root system development and architecture in oak (Quercus robur L.) seedlings.

The effect of wind loading on seedlings of English oak (Quercus robur L.) was investigated. Instead of using a traditional wind tunnel, an innovative ventilation system was designed. This device was set up in the field and composed of a rotating arm supporting an electrical fan, which emitted an air current similar to that of wind loading. Oaks were sown from seed in a circle around the device. A block of control plants was situated nearby, and was not subjected to artificial wind loading. After 7 months, 16 plants from each treatment were excavated, and root architecture and morphological characteristics measured using a 3D digitiser. The resulting geometrical and topological data were then analysed using AMAPmod software. Results showed that total lateral root number and length in wind stressed plants were over two times greater than that in control trees. However, total lateral root volume did not differ significantly between treatments. In comparing lateral root characters between the two populations, it was found that mean root length, diameter and volume were similar between the two treatments. In trees subjected to wind loading, an accentuated asymmetry of root distribution and mean root length was found between the windward and leeward sides of the root system, with windward roots being significantly more numerous and longer than leeward roots. However, no differences were found when the two sectors perpendicular to the wind direction were compared. Mean tap root length was significantly higher in control samples compared to wind stressed plants, whilst mean diameter was greater in the latter. Wind loading appears to result in increased growth of lateral roots at the expense of the tap root. Development of the lateral root system may therefore ensure better anchorage of young trees subjected to wind loading under certain conditions.     

Natural genetic variation of root system architecture from Arabidopsis to Brachypodium: towards adaptive value

Root system architecture is a trait that displays considerable plasticity because of its sensitivity to environmental stimuli. Nevertheless, to a significant degree it is genetically constrained as suggested by surveys of its natural genetic variation. A few regulators of root system architecture have been isolated as quantitative trait loci through the natural variation approach in the dicotyledon model, Arabidopsis. This provides proof of principle that allelic variation for root system architecture traits exists, is genetically tractable, and might be exploited for crop breeding. Beyond Arabidopsis, Brachypodium could serve as both a credible and experimentally accessible model for root system architecture variation in monocotyledons, as suggested by first glimpses of the different root morphologies of Brachypodium accessions. Whether a direct knowledge transfer gained from molecular model system studies will work in practice remains unclear however, because of a lack of comprehensive understanding of root system physiology in the native context. For instance, apart from a few notable exceptions, the adaptive value of genetic variation in root system modulators is unknown. Future studies should thus aim at comprehensive characterization of the role of genetic players in root system architecture variation by taking into account the native environmental conditions, in particular soil characteristics.     

Branching out in new directions: the control of root architecture by lateral root formation

Plant roots are required for the acquisition of water and nutrients, for responses to abiotic and biotic signals in the soil, and to anchor the plant in the ground. Controlling plant root architecture is a fundamental part of plant development and evolution, enabling a plant to respond to changing environmental conditions and allowing plants to survive in different ecological niches. Variations in the size, shape and surface area of plant root systems are brought about largely by variations in root branching. Much is known about how root branching is controlled both by intracellular signalling pathays and by environmental signals. Here, we will review this knowledge, with particular emphasis on recent advances in the field that open new and exciting areas of research.     

Measuring root system traits of wheat in 2D images to parameterize 3D root architecture models

Plant and Soil - The main difficulty in the use of 3D root architecture models is correct parameterization. We evaluated distributions of the root traits inter-branch distance, branching angle and...     

Die for living better: Plants modify root system architecture through inducing PCD in root meristem under severe water stress

Plant root development is highly plastic in order to cope with various environmental stresses; many questions on the mechanisms underlying developmental plasticity of root system remain unanswered. Recently, we showed that autophagic PCD occurs in the region of root apical meristem in response to severe water deficit. We provided evidence that reactive oxygen species (ROS) accumulation may trigger the cell death process of the meristematic cells in the stressed root tips. Analysis of BAX inhibitor-1 (AtBI1) expression and the phenotypic response of atbi1-1 mutant under the severe water stress revealed that AtBI1 and the endoplasmic reticulum (ER) stress response pathway modulate water stress-induced PCD. As a result, the thick and short lateral roots with increased tolerance to the stress are induced. We propose that under severe drought condition, plants activate PCD program in the root apical root meristem, so that apical root dominance is removed. In this way, they can remodel their root system architecture to adapt the stress environment.Key words: Arabidopsis, adaptation, PCD, root system architecture, water stressPlant shoot apical dominance is well known. The axillary buds are inhibited by the growing shoot apical meristem, and they would not grow until the shoot apical meristems are decapitated.¹ The same phenomenon has been found in the roots of dicot plants. Primary roots exhibit apical dominance over lateral roots and are able to penetrate deeply into the soil. Lateral root primordia were rapidly activated when primary root tips of lettuce (Lactuca sativa) were removed.² It is apparent that apical meristem activity in shoots and roots determines lateral organs and the shapes of above ground and root system architecture under normal conditions. Many plants have active meristematic activity in their shoot and root tips through their whole life resulting in indeterminate development of their shoots and primary roots, whereas others generate branches at certain developmental stages when the meristematic activity and apical dominance become low.It has long been known that plants modify their root morphology, orientation and increase root biomass to maximize water and nutrient absorption.^3,4 However, how the root morphology and architecture are changed in response to water shortage and what the underlying mechanisms are largely unknown. Previously, it has been reported that plants, due to their sessile nature, have developed a very important adaptive mechanism, namely hydrotropism to avoid the damage caused by water shortage. Plant roots can sense the moisture gradient and grow toward to water or moisture when they are grown at conditions with non-uniform water distribution.⁵ Recently, we found another key mechanism through which plants can remove root apical dominance and remodel their root system architecture, thus to minimize the damage caused by a uniform severe water shortage condition.⁶Firstly, we found that growth rates of the Arabidopsis plants germinated on normal conditions were reduced when the concentrations of PEG in the growth media was increased, and primary roots of the stressed plants completely ceased growth when the PEG concentrations reached 40% (w/v) in the agar medium, a severe water stress. The results showed that growth cessation of the stressed plants was caused by PCD of the cells in the region of root apical meristems, and the cells underwent autophagic cell death upon the most severe water deficit. Secondly, we demonstrated that AtBI-1, a marker gene which plays a critical role in protecting the cells from ER stress-induced PCD in plants, mediates water stress-induced PCD of the root meristem. Further observation of ROS accumulation in the root tips upon to the severe water stress suggests that the high level of the ROS may disrupt the ER homeostasis and ROS may act as a signal to trigger the PCD. Importantly, we found that the occurrence of PCD of the meristematic cells of the stressed plants promoted the development of lateral roots. These short and tublized lateral roots grew slowly under severe water stress, but they could immediately become normal lateral roots and resume their elongation and after rehydration. Plant growth is subsequently restored to complete their entire life cycle. However, the lateral roots induced by decapitating primary root tips under normal conditions did not continue elongation like the stress induced lateral roots, and they cannot restore their growth after rehydration.Based on these results, we propose that plants can sense the severity of water stress, initiate autophagic PCD of meristematic cells in Arabidopsis root tips through ER stress signaling pathway and stimulate lateral root development (Fig. 1). Death of meristematic cells results in the loss of mitotic cell division activity in meristem and eventual root meristem function. The outcome of PCD caused-loss of root meristem activity is same as the surgical removal of apical root tips. In both cases, lateral root primordia are activated and lateral root emergence is promoted. However, the main difference between water stress induced-loss of root meristem function and surgical decapitation of root tips is that the former induces lateral roots with enhanced stress tolerance plays key roles in post-stress recovery, whereas the latter promotes development of lateral roots do not alter stress response. This implicates that stress-induced loss of meristem function and subsequent occurrence of specified lateral roots are adaptive mechanisms for plants to cope with the severe water stress. In other words, plants induce cell death of root meristem for living better.Open in a separate windowFigure 1A simplified model depicting the role of PCD in root meristem in plastic development of root system architecture in response to water stress.It is known that auxin distribution and maxima play key roles in lateral root initiation and emergence.^7–10 Alteration in auxin polar transport has been proposed as the main reason of decapitation induced lateral root development.¹¹ It is conceivable that auxin is also involved in stress induced-lateral root formation and development, but it is clear that interplay between stress signaling cascades and developmental signalings occurs after perception of the stress signals by plant cells resulting in root system development remodeling. These findings provide novel insights into mechanisms of plants to adapt to the uniform severe water stress at organ, cellular and molecular levels. However, the research of plastic development of root system in response to water stress is still in its infancy. Combinatorial strategies for the investigation of stress induced-PCD of root meristematic cells and subsequent lateral root development will help to uncover the molecular mechanisms underlying this positive response of plants in response to severe water stress. In particular, further study of auxin redistribution under water stress and interaction between auxin and stress hormone signalings in remodeling root system architecture will further our understanding of how developmental plasticity of plant root system is regulated. The results will facilitate the improvement of drought tolerance in crops.     

Crop root behavior coordinates phosphorus status and neighbors: from field studies to three-dimensional in situ reconstruction of root system architecture

Root is a primary organ to respond to environmental stimuli and percept signals from neighboring plants. In this study, root responses in maize (Zea mays)/soybean (Glycine max) intercropping systems recognized soil phosphorus (P) status and neighboring plants in the field. Compared to self culture, the maize variety GZ1 intercropping with soybean HX3 grew much better on low P, but not in another maize variety, NE1. This genotypic response decreased with increasing distance between plants, suggesting that root interactions were important. We further conducted a detailed and quantitative study of root behavior in situ using a gel system to reconstruct the three-dimensional root architecture. The results showed that plant roots could integrate information on P status and root behavior of neighboring plants. When intercropped with its kin, maize or soybean roots grew close to each other. However, when maize GZ1 was grown with soybean HX3, the roots on each plant tended to avoid each other and became shallower on stratified P supply, but not found with maize NE1. Furthermore, root behavior in gel was highly correlated to shoot biomass and P content for field-grown plants grown in close proximity. This study provides new insights into the dynamics and complexity of root behavior and kin recognition among crop species in response to nutrient status and neighboring plants. These findings also indicate that root behavior not only depends on neighbor recognition but also on a coordinated response to soil P status, which could be the underlying cause for the different growth responses in the field.     

Effects of dichromate on growth and root system architecture of Arabidopsis thaliana seedlings

The hexavalent form of chromium [Cr(VI)] is toxic for most organisms; however, very little information is available regarding the effects of this metal on plant morphogenesis. In this work, we investigated the effects of Cr(VI) on the growth and development of Arabidopsis thaliana, a species widely used as a model for studying the diverse physiological and cellular processes in plants. Elongation of root hairs and biomass production were stimulated by relatively low concentrations (100 μM) of Cr(VI) as potassium dichromate. Concentrations of Cr(VI) greater than 200 μM were toxic to plants as revealed both by arrested growth of roots and shoots and the development of chlorosis in leaves. At 200 μM the primary root growth was totally inhibited but the plants continued their growth manifesting different alterations in root development. These alterations correlated with changes in mitotic activity and in cellular expansion. The analyses of A. thaliana transgenic plants that express the auxin-inducible marker DR5:uidA, and the response of the auxin-resistant mutants axr2 and aux1–7 to dichromate suggest that auxins do not participate as mediators in the cellular and physiological responses to this metal. The primary root growth inhibition by 200 μM dichromate was alleviated by more than 70% by increasing the sulfate, phosphate or nitrate concentration in the media, which suggests a relation of dichromate with these mineral nutrients.