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Concept: Weyl group


Root systems are complex structures key to plant health. The three-dimensional distribution of the root system, known as the root architecture, is important for optimal uptake of water and nutrients, as well as anchorage in the soil. Despite the importance of root systems, little is known about the genes that control root architecture, in part because of the difficulty of non-destructively viewing root systems. The Benfey lab has developed a gel-based imaging method to non-invasively examine root system architecture over time. Root systems of a variety of plant species can be quickly imaged daily or weekly. The platform is relatively inexpensive, high-throughput, and is ideally suited for researchers aiming to understand the genetic control of root architecture. Here we describe the application of this method to rice and maize root systems.

Concepts: Scientific method, Species, Plant, Soil, Root, Weyl group, Dynkin diagram


The number of image analysis tools supporting the extraction of architectural features of root systems has increased over the last years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tool is able to extract in an efficient way growing array of static and dynamic features for different types of images and species. . We describe the Root System Markup Language (RSML) that has been designed to overcome two major challenges: (i) to enable portability of root architecture data between different software tools in an easy and interoperable manner allowing seamless collaborative work, and (ii) to provide a standard format upon which to base central repositories which will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store 2D or 3D image metadata, plant and root properties and geometries, continuous functions along individual root paths and a suite of annotations at the image, plant or root scales, at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An xml-schema describes the features and constraints of RSML and open-source packages have been developed in several languages (R, Excel, Java, Python, C#) to enable researchers to integrate RSML files into popular research workflow.

Concepts: Mathematics, Computer program, Annotation, Root, Software architecture, XML, Markup language, Weyl group


Increasing maize nitrogen acquisition efficiency is a major goal for the 21st century. Nitrate uptake kinetics (NUK) are defined byImaxandKm, which denote the maximum uptake rate and the affinity of transporters, respectively. Because NUK have been studied predominantly at the molecular and whole-root system levels, little is known about the functional importance of NUK variation within root systems. A novel method was created to measure NUK of root segments that demonstrated variation in NUK among root classes (seminal, lateral, crown, and brace).Imaxvaried among root class, plant age, and nitrate deprivation combinations, but was most affected by plant age, which increasedImax, and nitrate deprivation time, which decreasedImaxKmwas greatest for crown roots. The functional-structural simulationSimRootwas used for sensitivity analysis of plant growth to root segmentImaxandKm, as well as to test interactions ofImaxwith root system architectural phenes. Simulated plant growth was more sensitive toImaxthanKm, and reached an asymptote near the maximumImaxobserved in the empirical studies. Increasing theImaxof lateral roots had the largest effect on shoot growth. Additive effects ofImaxand architectural phenes on nitrate uptake were observed. Empirically, only lateral root tips aged 20 d operated at the maximumImax, and simulations demonstrated that increasing all seminal and lateral classes to this maximum rate could increase plant growth by as much as 26%. Therefore, optimizingImaxfor all maize root classes merits attention as a promising breeding goal.

Concepts: Scientific method, Empiricism, Empirical, Root, Maize, 21st century, Weyl group, Dynkin diagram


The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydropatterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 and PIN-FORMED 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.

Concepts: Plant, Water, Tree, Vascular plant, Root, Weyl group, Dynkin diagram


The potential exists to breed for root system architectures that optimize resource acquisition. However, this requires the ability to screen root system development quantitatively, with high resolution, in as natural an environment as possible, with high throughput. This paper describes the construction of a low-cost, high-resolution root phenotyping platform, requiring no sophisticated equipment and adaptable to most laboratory and glasshouse environments, and its application to quantify environmental and temporal variation in root traits between genotypes of Brassica rapa L. Plants were supplied with a complete nutrient solution through the wick of a germination paper. Images of root systems were acquired without manual intervention, over extended periods, using multiple scanners controlled by customized software. Mixed-effects models were used to describe the sources of variation in root traits contributing to root system architecture estimated from digital images. It was calculated that between one and 43 replicates would be required to detect a significant difference (95% CI 50% difference between traits). Broad-sense heritability was highest for shoot biomass traits (>0.60), intermediate (0.25-0.60) for the length and diameter of primary roots and lateral root branching density on the primary root, and lower (<0.25) for other root traits. Models demonstrate that root traits show temporal variations of various types. The phenotyping platform described here can be used to quantify environmental and temporal variation in traits contributing to root system architecture in B. rapa and can be extended to screen the large populations required for breeding for efficient resource acquisition.

Concepts: Evolution, Computer graphics, Root, Image resolution, Digital image, Brassica rapa, Weyl group, Dynkin diagram


X-ray computed tomography (CT) has become a powerful tool for root phenotyping. Compared to rather classical, destructive methods, CT encompasses various advantages. In pot experiments the growth and development of the same individual root can be followed over time and in addition the unaltered configuration of the 3D root system architecture (RSA) interacting with a real field soil matrix can be studied. Yet, the throughput, which is essential for a more widespread application of CT for basic research or breeding programs, suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. Using available methods, root segmentation is done to a large extent manually, as it requires a lot of interactive parameter optimization and interpretation and therefore needs a lot of time.

Concepts: Medical imaging, Radiography, Tomographic reconstruction, Root, Weyl group, Dynkin diagram, Network performance


In water-limited ecosystems, spatial and temporal partitioning of water sources is an important mechanism that facilitates plant survival and lessens the competition intensity of co-existing plants. Insights into species-specific root functional plasticity and differences in the water sources of co-existing plants under changing water conditions can aid in accurate prediction of the response of desert ecosystems to future climate change. We used stable isotopes of soil water, groundwater and xylem water to determine the seasonal and inter- and intraspecific differences variations in the water sources of six C3and C4shrubs in the Gurbantonggut desert. We also measured the stem water potentials to determine the water stress levels of each species under varying water conditions. The studied shrubs exhibited similar seasonal water uptake patterns, i.e., all shrubs extracted shallow soil water recharged by snowmelt water during early spring and reverted to deeper water sources during dry summer periods, indicating that all of the studied shrubs have dimorphic root systems that enable them to obtain water sources that differ in space and time. Species in the C4shrub community exhibited differences in seasonal water absorption and water status due to differences in topography and rooting depth, demonstrating divergent adaptations to water availability and water stress. Haloxylon ammodendron and T. ramosissima in the C3/C4mixed community were similar in terms of seasonal water extraction but differed with respect to water potential, which indicated that plant water status is controlled by both root functioning and shoot eco-physiological traits. The two Tamarix species in the C3shrub community were similar in terms of water uptake and water status, which suggests functional convergence of the root system and physiological performance under same soil water conditions. In different communities, Haloxylon ammodendron differed in terms of summer water extraction, which suggests that this species exhibits plasticity with respect to rooting depth under different soil water conditions. Shrubs in the Gurbantonggut desert displayed varying adaptations across species and communities through divergent root functioning and shoot eco-physiological traits.

Concepts: Plant, Water, Climate, Root, Water resources, Weyl group, Dynkin diagram


The ability of plants to take up water from the soil depends on both the root architecture and the distribution and evolution of the hydraulic conductivities among root types and along the root length. The mature maize (Zea mays L.) root system is composed of primary, seminal, and crown roots together with their respective laterals. Our understanding of root water uptake of maize is largely based on measurements of primary and seminal roots. Crown roots might have a different ability to extract water from the soil, but their hydraulic function remains unknown. The aim of this study was to measure the location of water uptake in mature maize and investigate differences between seminal, crown, and lateral roots. Neutron radiography and injections of deuterated water were used to visualize the root architecture and water transport in 5-week-old maize root systems. Water was mainly taken up by crown roots. Seminal roots and their laterals, which were the main location of water uptake in younger plants, made a minor contribution to water uptake. In contrast to younger seminal roots, crown roots were also able to take up water from their most distal segments. The greater uptake of crown roots compared with seminal roots is explained by their higher axial conductivity in the proximal parts and by the fact that they are connected to the shoot above the seminal roots, which favors the propagation of xylem tension along the crown roots. The deeper water uptake of crown roots is explained by their shorter and fewer laterals, which decreases the dissipation of water potential along the roots.

Concepts: Measurement, Root, Maize, Rapping, Weyl group, Dynkin diagram, Incubus


Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years.

Concepts: Plant, Soil, Vascular plant, Root, Weyl group, Dynkin diagram


Roots interact with soil properties and irrigation water quality leading to changes in root growth, structure and function. We studied these interactions in an orchard and in lysimeters with clay and sandy loam soils. Minirhizotron imaging and manual sampling showed that root growth was three times lower in the clay relative to sandy loam soil. Treated wastewater (TWW) led to a large reduction in root growth with clay (45-55%) but not with sandy loam soil (<20%). Treated wastewater increased salt uptake, membrane leakage and proline content, and decreased root viability, carbohydrate content and osmotic potentials in the fine roots, especially in clay. These results provide evidence that TWW challenges and damages the root system. The phenology and physiology of root orders were studied in lysimeters. Soil type influenced diameter, specific root area, tissue density and cortex area similarly in all root orders, while TWW influenced these only in clay soil. Respiration rates were similar in both soils, and root hydraulic conductivity was severely reduced in clay soil. Treated wastewater increased respiration rate and reduced hydraulic conductivity of all root orders in clay but only of the lower root orders in sandy loam soil. Loss of hydraulic conductivity increased with root order in clay and clay irrigated with TWW. Respiration and hydraulic properties of all root orders were significantly affected by sodium-amended TWW in sandy loam soil. These changes in root order morphology, anatomy, physiology and hydraulic properties indicate rapid and major modifications of root systems in response to differences in soil type and water quality.

Concepts: Biology, Water, Root, Irrigation, Weyl group, Dynkin diagram