Seedling root system adaptation to water availability during maize domestication and global expansion.

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Setup and characterisation according to NEMA NU 4 of thephenoPET scanner, a PET system dedicated for plant sciences.

Objective.ThephenoPET system is a plant dedicated positron emission tomography (PET) scanner consisting of fully digital photo multipliers with lutetium-yttrium oxyorthosilicate crystals and located inside a custom climate chamber. Here, we present the setup ofphenoPET, its data processing and image reconstruction together with its performance.Approach.The performance characterization follows the national electrical manufacturers association (NEMA) standard for small animal PET systems with a number of adoptions due to the vertical oriented bore of a PET for plant sciences. In addition temperature stability and spatial resolution with a hot rod phantom are addressed.Main results.The spatial resolution for a22Na point source at a radial distance of 5 mm to the center of the field-of-view (FOV) is 1.45 mm, 0.82 mm and 1.88 mm with filtered back projection in radial, tangential and axial direction, respectively. A hot rod phantom with18F gives a spatial resolution of up to 1.6 mm. The peak noise-equivalent count rates are 550 kcps @ 35.08 MBq, 308 kcps @ 33 MBq and 45 kcps @ 40.60 MBq for the mouse, rat and monkey size scatter phantoms, respectively. The scatter fractions for these phantoms are 12.63%, 22.64% and 55.90%. We observe a peak sensitivity of up to 3.6% and a total sensitivity of up toSA,tot= 2.17%. For the NEMA image quality phantom we observe a uniformity of %STD= 4.22% with ordinary Poisson maximum likelihood expectation-maximization with 52 iterations. Here, recovery coefficients of 0.12, 0.64, 0.89, 0.93 and 0.91 for 1 mm, 2 mm, 3 mm, 4 mm and 5 mm rods are obtained and spill-over ratios of 0.08 and 0.14 for the water-filled and air-filled inserts, respectively.Significance.ThephenoPET and its laboratory are now in routine operation for the administration of [11C]CO2and non-invasive measurement of transport and allocation of11C-labelled photoassimilates in plants.

In Vivo Imaging and Quantification of Carbon Tracer Dynamics in Nodulated Root Systems of Pea Plants.

Legumes associate with root colonizing rhizobia that provide fixed nitrogen to its plant host in exchange for recently fixed carbon. There is a lack of understanding of how individual plants modulate carbon allocation to a nodulated root system as a dynamic response to abiotic stimuli. One reason is that most approaches are based on destructive sampling, making quantification of localised carbon allocation dynamics in the root system difficult. We established an experimental workflow for routinely using non-invasive Positron Emission Tomography (PET) to follow the allocation of leaf-supplied 11C tracer towards individual nodules in a three-dimensional (3D) root system of pea (Pisum sativum). Nitrate was used for triggering a reduction of biological nitrogen fixation (BNF), which was expected to rapidly affect carbon allocation dynamics in the root-nodule system. The nitrate treatment led to a decrease in 11C tracer allocation to nodules by 40% to 47% in 5 treated plants while the variation in control plants was less than 11%. The established experimental pipeline enabled for the first time that several plants could consistently be labelled and measured using 11C tracers in a PET approach to quantify C-allocation to individual nodules following a BNF reduction. Our study demonstrates the strength of using 11C tracers in a PET approach for non-invasive quantification of dynamic carbon allocation in several growing plants over several days. A major advantage of the approach is the possibility to investigate carbon dynamics in small regions of interest in a 3D system such as nodules in comparison to whole plant development.

The root system architecture of wheat establishing in soil is associated with varying elongation rates of seminal roots: quantification using 4D magnetic resonance imaging.

Seedling establishment is the first stage of crop productivity, and root phenotypes at seed emergence are critical to a successful start of shoot growth as well as for water and nutrient uptake. In this study, we investigate seedling establishment in winter wheat utilizing a newly developed workflow based on magnetic resonance imaging (MRI). Using the eight parents of the MAGIC (multi-parent advanced generation inter-cross) population we analysed the 4D root architecture of 288 individual seedlings grown in natural soils with plant neighbors over 3 d of development. Time of root and shoot emergence, total length, angle, and depth of the axile roots varied significantly among these genotypes. The temporal data resolved rates of elongation of primary roots and first and second seminal root pairs. Genotypes with slowly elongating primary roots had rapidly elongating first and second seminal root pairs and vice versa, resulting in variation in root system architecture mediated not only by root angle but also by initiation and relative elongation of axile roots. We demonstrated that our novel MRI workflow with a unique planting design and automated measurements allowed medium throughput phenotyping of wheat roots in 4D and could give new insights into regulation of root system architecture.

ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF-containing protein that controls root growth angle in barley and wheat.

The root growth angle defines how roots grow toward the gravity vector and is among the most important determinants of root system architecture. It controls water uptake capacity, nutrient use efficiency, stress resilience, and, as a consequence, yield of crop plants. We demonstrated that the egt2 (enhanced gravitropism 2) mutant of barley exhibits steeper root growth of seminal and lateral roots and an auxin-independent higher responsiveness to gravity compared to wild-type plants. We cloned the EGT2 gene by a combination of bulked-segregant analysis and whole genome sequencing. Subsequent validation experiments by an independent CRISPR/Cas9 mutant allele demonstrated that egt2 encodes a STERILE ALPHA MOTIF domain-containing protein. In situ hybridization experiments illustrated that EGT2 is expressed from the root cap to the elongation zone. We demonstrated the evolutionary conserved role of EGT2 in root growth angle control between barley and wheat by knocking out the EGT2 orthologs in the A and B genomes of tetraploid durum wheat. By combining laser capture microdissection with RNA sequencing, we observed that seven expansin genes were transcriptionally down-regulated in the elongation zone. This is consistent with a role of EGT2 in this region of the root where the effect of gravity sensing is executed by differential cell elongation. Our findings suggest that EGT2 is an evolutionary conserved regulator of root growth angle in barley and wheat that could be a valuable target for root-based crop improvement strategies in cereals.

Spatio-Temporal Variation in Water Uptake in Seminal and Nodal Root Systems of Barley Plants Grown in Soil.

The spatial and temporal dynamics of root water uptake in nodal and seminal roots are poorly understood, especially in relation to root system development and aging. Here we non-destructively quantify 1) root water uptake and 2) root length of nodal and seminal roots of barley in three dimensions during 43 days of growth. We developed a concentric split root system to hydraulically and physically isolate the seminal and nodal root systems. Using magnetic resonance imaging (MRI), roots were visualized, root length was determined, and soil water depletion in both compartments was measured. From 19 days after germination and onwards, the nodal root system had greater water uptake compared to the seminal root system due to both greater root length and greater root conductivity. At 29 days after germination onwards, the average age of the seminal and nodal root systems was similar and no differences were observed in water uptake per root length between seminal and nodal root systems, indicating the importance of embryonic root systems for seedling establishment and nodal root systems in more mature plants. Since nodal roots perform the majority of water uptake at 29 days after germination and onwards, nodal root phenes merit consideration as a selection target to improve water capture in barley and possibly other crops.

Spatially Resolved Root Water Uptake Determination Using a Precise Soil Water Sensor.

To answer long-standing questions about how plants use and regulate water, an affordable, noninvasive way to determine local root water uptake (RWU) is required. Here, we present a sensor, the soil water profiler (SWaP), which can determine local soil water content (θ) with a precision of 6.10-5 cm3 ⋅ cm-3, an accuracy of 0.002 cm3 ⋅ cm-3, a temporal resolution of 24 min, and a one-dimensional spatial resolution of 1 cm. The sensor comprises two copper sheets, integrated into a sleeve and connected to a coil, which form a resonant circuit. A vector network analyzer, inductively coupled to the resonant circuit, measures the resonance frequency, against which θ was calibrated. The sensors were integrated into a positioning system, which measures θ along the depth of cylindrical tubes. When combined with modulating light (4-h period) and resultant modulating plant transpiration, the SWaP enables quantification of the component of RWU distribution that varies proportionally with total plant water uptake, and distinguishes it from soil water redistribution via soil pores and roots. Additionally, as a young, growing maize (Zea mays) plant progressively tapped its soil environment dry, we observed clear changes in plant-driven RWU and soil water redistribution profiles. Our SWaP setup can measure the RWU and redistribution of sandy-soil water content with unprecedented precision. The SWaP is therefore a promising device offering new insights into soil-plant hydrology, with applications for functional root phenotyping in nonsaline, temperature-controlled conditions, at low cost.

Practically Lossless Affine Image Transformation.

In this contribution we introduce an almost lossless affine 2D image transformation method. To this end we extend the theory of the well-known Chirp-z transform to allow for fully affine transformation of general n-dimensional images. In addition we give a practical spatial and spectral zero-padding approach dramatically reducing losses of our transform, where usual transforms introduce blurring artifacts due to sub-optimal interpolation. The proposed method improves the mean squared error by approx. a factor of 1800 compared to the commonly used linear interpolation, and by a factor of 250 to the best competitor. We derive the transform from basic principles with special attention to implementation details and supplement this paper with python code for 2D images. In demonstration experiments we show the superior image quality compared to usual approaches, when using our method. However runtimes are considerably larger than when using toolbox algorithms.

Spatial heterogeneity of flesh-cell osmotic potential in sweet cherry affects partitioning of absorbed water.

A fleshy fruit is commonly assumed to resemble a thin-walled pressure vessel containing a homogenous carbohydrate solution. Using sweet cherry (Prunus avium L.) as a model system, we investigate how local differences in cell water potential affect H2O and D2O (heavy water) partitioning. The partitioning of H2O and D2O was mapped non-destructively using magnetic resonance imaging (MRI). The change in size of mesocarp cells due to water movement was monitored by optical coherence tomography (OCT, non-destructive). Osmotic potential was mapped using micro-osmometry (destructive). Virtual sections through the fruit revealed that the H2O distribution followed a net pattern in the outer mesocarp and a radial pattern in the inner mesocarp. These patterns align with the disposition of the vascular bundles. D2O uptake through the skin paralleled the acropetal gradient in cell osmotic potential gradient (from less negative to more negative). Cells in the vicinity of a vascular bundle were of more negative osmotic potential than cells more distant from a vascular bundle. OCT revealed net H2O uptake was the result of some cells loosing volume and other cells increasing volume. H2O and D2O partitioning following uptake is non-uniform and related to the spatial heterogeneity in the osmotic potential of mesocarp cells.

Localized bursting of mesocarp cells triggers catastrophic fruit cracking.

The so-called rain-cracking of sweet cherry fruit severely threatens commercial production. Simple observation tells us that cuticular microcracking (invisible) always precedes skin macrocracking (visible). The objective here was to investigate how a macrocrack develops. Incubating detached sweet cherry fruit in deionized water induces microcracking. Incubating fruit in D2O and concurrent magnetic resonance imaging demonstrates that water penetration occurs only (principally) through the microcracks, with nondetectable amounts penetrating the intact cuticle. Optical coherence tomography of detached, whole fruit incubated in deionized water, allowed generation of virtual cross-sections through the zone of a developing macrocrack. Outer mesocarp cell volume increased before macrocracks developed but increased at a markedly higher rate thereafter. Little change in mesocarp cell volume occurred in a control zone distant from the crack. As water incubation continued, the cell volume in the crack zone decreased, indicating leaking/bursting of individual mesocarp cells. As incubation continued still longer, the crack propagated between cells both to form a long, deep macrocrack. Outer mesocarp cell turgor did not differ significantly before and after incubation between fruit with or without macrocracks; nor between cells within the crack zone and those in a control zone distant from the macrocrack. The cumulative frequency distribution of the log-transformed turgor pressure of a population of outer mesocarp cells reveals all cell turgor data followed a normal distribution. The results demonstrate that microcracks develop into macrocracks following the volume increase of a few outer mesocarp cells and is soon accompanied by cell bursting.

Non-invasive imaging of plant roots in different soils using magnetic resonance imaging (MRI).

BACKGROUND: Root systems are highly plastic and adapt according to their soil environment. Studying the particular influence of soils on root development necessitates the adaptation and evaluation of imaging methods for multiple substrates. Non-invasive 3D root images in soil can be obtained using magnetic resonance imaging (MRI). Not all substrates, however, are suitable for MRI. Using barley as a model plant we investigated the achievable image quality and the suitability for root phenotyping of six commercially available natural soil substrates of commonly occurring soil textures. The results are compared with two artificially composed substrates previously documented for MRI root imaging. RESULTS: In five out of the eight tested substrates, barley lateral roots with diameters below 300 µm could still be resolved. In two other soils, only the thicker barley seminal roots were detectable. For these two substrates the minimal detectable root diameter was between 400 and 500 µm. Only one soil did not allow imaging of the roots with MRI. In the artificially composed substrates, soil moisture above 70% of the maximal water holding capacity (WHCmax) impeded root imaging. For the natural soil substrates, soil moisture had no effect on MRI root image quality in the investigated range of 50-80% WHCmax. CONCLUSIONS: Almost all tested natural soil substrates allowed for root imaging using MRI. Half of these substrates resulted in root images comparable to our current lab standard substrate, allowing root detection down to a diameter of 300 µm. These soils were used as supplied by the vendor and, in particular, removal of ferromagnetic particles was not necessary. With the characterization of different soils, investigations such as trait stability across substrates are now possible using noninvasive MRI.

Physical rupture of the xylem in developing sweet cherry fruit causes progressive decline in xylem sap inflow rate.

MAIN CONCLUSION: Xylem flow is progressively shut down during maturation beginning with minor veins at the stylar end and progressing to major veins and finally to bundles at the stem end. This study investigates the functionality of the xylem vascular system in developing sweet cherry fruit (Prunus avium L.). The tracers acid fuchsin and gadoteric acid were fed to the pedicel of detached fruit. The tracer distribution was studied using light microscopy and magnetic resonance imaging. The vasculature of the sweet cherry comprises five major bundles. Three of these supply the flesh; two enter the pit to supply the ovules. All vascular bundles branch into major and minor veins that interconnect via numerous anastomoses. The flow in the xylem as indexed by the tracer distribution decreases continuously during development. The decrease is first evident at the stylar (distal) end of the fruit during pit hardening and progresses basipetally towards the pedicel (proximal) end of the fruit at maturity. That growth strains are the cause of the decreased conductance is indicated by: elastic strain relaxation after tissue excision, the presence of ruptured vessels in vivo, the presence of intrafascicular cavities, and the absence of tyloses.

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging.

Precise measurements of root system architecture traits are an important requirement for plant phenotyping. Most of the current methods for analyzing root growth require either artificial growing conditions (e.g. hydroponics), are severely restricted in the fraction of roots detectable (e.g. rhizotrons), or are destructive (e.g. soil coring). On the other hand, modalities such as magnetic resonance imaging (MRI) are noninvasive and allow high-quality three-dimensional imaging of roots in soil. Here, we present a plant root imaging and analysis pipeline using MRI together with an advanced image visualization and analysis software toolbox named NMRooting. Pots up to 117 mm in diameter and 800 mm in height can be measured with the 4.7 T MRI instrument used here. For 1.5 l pots (81 mm diameter, 300 mm high), a fully automated system was developed enabling measurement of up to 18 pots per day. The most important root traits that can be nondestructively monitored over time are root mass, length, diameter, tip number, and growth angles (in two-dimensional polar coordinates) and spatial distribution. Various validation measurements for these traits were performed, showing that roots down to a diameter range between 200 µm and 300 µm can be quantitatively measured. Root fresh weight correlates linearly with root mass determined by MRI. We demonstrate the capabilities of MRI and the dedicated imaging pipeline in experimental series performed on soil-grown maize (Zea mays) and barley (Hordeum vulgare) plants.

phenoVein-A Tool for Leaf Vein Segmentation and Analysis.

Precise measurements of leaf vein traits are an important aspect of plant phenotyping for ecological and genetic research. Here, we present a powerful and user-friendly image analysis tool named phenoVein. It is dedicated to automated segmenting and analyzing of leaf veins in images acquired with different imaging modalities (microscope, macrophotography, etc.), including options for comfortable manual correction. Advanced image filtering emphasizes veins from the background and compensates for local brightness inhomogeneities. The most important traits being calculated are total vein length, vein density, piecewise vein lengths and widths, areole area, and skeleton graph statistics, like the number of branching or ending points. For the determination of vein widths, a model-based vein edge estimation approach has been implemented. Validation was performed for the measurement of vein length, vein width, and vein density of Arabidopsis (Arabidopsis thaliana), proving the reliability of phenoVein. We demonstrate the power of phenoVein on a set of previously described vein structure mutants of Arabidopsis (hemivenata, ondulata3, and asymmetric leaves2-101) compared with wild-type accessions Columbia-0 and Landsberg erecta-0. phenoVein is freely available as open-source software.

Direct comparison of MRI and X-ray CT technologies for 3D imaging of root systems in soil: potential and challenges for root trait quantification.

BACKGROUND: Roots are vital to plants for soil exploration and uptake of water and nutrients. Root performance is critical for growth and yield of plants, in particular when resources are limited. Since roots develop in strong interaction with the soil matrix, tools are required that can visualize and quantify root growth in opaque soil at best in 3D. Two modalities that are suited for such investigations are X-ray Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Due to the different physical principles they are based on, these modalities have their specific potentials and challenges for root phenotyping. We compared the two methods by imaging the same root systems grown in 3 different pot sizes with inner diameters of 34 mm, 56 mm or 81 mm. RESULTS: Both methods successfully visualized roots of two weeks old bean plants in all three pot sizes. Similar root images and almost the same root length were obtained for roots grown in the small pot, while more root details showed up in the CT images compared to MRI. For the medium sized pot, MRI showed more roots and higher root lengths whereas at some spots thin roots were only found by CT and the high water content apparently affected CT more than MRI. For the large pot, MRI detected much more roots including some laterals than CT. CONCLUSIONS: Both techniques performed equally well for pots with small diameters which are best suited to monitor root development of seedlings. To investigate specific root details or finely graduated root diameters of thin roots, CT was advantageous as it provided the higher spatial resolution. For larger pot diameters, MRI delivered higher fractions of the root systems than CT, most likely because of the strong root-to-soil contrast achievable by MRI. Since complementary information can be gathered with CT and MRI, a combination of the two modalities could open a whole range of additional possibilities like analysis of root system traits in different soil structures or under varying soil moisture.

On the numerically predicted spatial BOLD fMRI specificity for spin echo sequences.

This work utilises general numerical magnetic resonance imaging MRI simulations to predict the spatial specificity of the blood oxygenation level-dependent (BOLD) functional MRI (fMRI) signal. A Monte Carlo simulation approach was utilized on a microvascular structure consisting of randomly oriented cylinders representing blood vessels. This framework was employed to numerically investigate the spatial specificity, defined as ratio of pial vessel to microvascular signal, of the spin echo BOLD fMRI signal as a function of field strength, echo time and tissue types [grey matter (GM) and cerebrospinal fluid (CSF), respectively]. Spatial specificity of spin echo BOLD fMRI signal was determined to increase with field strength up to 16 T and with maximal specificity for echo time shorter than tissue T(2). In addition, it was found that, for large pial vessels, the extravascular signal decay could not be described using the oversimplified but nevertheless commonly employed mono-exponential signal decay approximation (MEA). Consequently, a recently proposed model relying on the MEA deviates substantially from our results on the spatial specificity. A refinement of this model is proposed based on an available, more detailed signal description. Finally, the effect of CSF on the spatial specificity was investigated. While a large spatial specificity of the spin echo BOLD fMRI signal is observed if a pial vessel is surrounded by grey matter, this is greatly reduced for a pial vessel situated on a GM/CSF interface, rendering the suppression of pial vessels on the cortex surface unlikely.

High-performance computing MRI simulations.

A new open-source software project is presented, JEMRIS, the Jülich Extensible MRI Simulator, which provides an MRI sequence development and simulation environment for the MRI community. The development was driven by the desire to achieve generality of simulated three-dimensional MRI experiments reflecting modern MRI systems hardware. The accompanying computational burden is overcome by means of parallel computing. Many aspects are covered that have not hitherto been simultaneously investigated in general MRI simulations such as parallel transmit and receive, important off-resonance effects, nonlinear gradients, and arbitrary spatiotemporal parameter variations at different levels. The latter can be used to simulate various types of motion, for instance. The JEMRIS user interface is very simple to use, but nevertheless it presents few limitations. MRI sequences with arbitrary waveforms and complex interdependent modules are modeled in a graphical user interface-based environment requiring no further programming. This manuscript describes the concepts, methods, and performance of the software. Examples of novel simulation results in active fields of MRI research are given.

A comparison of three optimization algorithms for intensity modulated radiation therapy.

In intensity modulated treatment techniques, the modulation of each treatment field is obtained using an optimization algorithm. Multiple optimization algorithms have been proposed in the literature, e.g. steepest descent, conjugate gradient, quasi-Newton methods to name a few. The standard optimization algorithm in our in-house inverse planning tool KonRad is a quasi-Newton algorithm. Although this algorithm yields good results, it also has some drawbacks. Thus we implemented an improved optimization algorithm based on the limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) routine. In this paper the improved optimization algorithm is described. To compare the two algorithms, several treatment plans are optimized using both algorithms. This included photon (IMRT) as well as proton (IMPT) intensity modulated therapy treatment plans. To present the results in a larger context the widely used conjugate gradient algorithm was also included into this comparison. On average, the improved optimization algorithm was six times faster to reach the same objective function value. However, it resulted not only in an acceleration of the optimization. Due to the faster convergence, the improved optimization algorithm usually terminates the optimization process at a lower objective function value. The average of the observed improvement in the objective function value was 37%. This improvement is clearly visible in the corresponding dose-volume-histograms. The benefit of the improved optimization algorithm is particularly pronounced in proton therapy plans. The conjugate gradient algorithm ranked in between the other two algorithms with an average speedup factor of two and an average improvement of the objective function value of 30%.