X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture

Rogers, Eric D.; Monaenkova, Daria; Mijar, Medhavinee; Nori, Apoorva; Goldman, Daniel I.; Benfey, Philip N.

doi:10.1104/pp.16.00397

Cited by 98 publications

(69 citation statements)

References 61 publications

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“…This was indicated in a recent study in wheat, for example, which showed that genotypic differences in N uptake observed in soil‐grown plants was not observed when plants were grown in hydroponics or sand (Melino et al ., ). In rice, dramatic differences in root architecture in different growth substrates (gel, beads, sand) have indeed now been documented using 3D X‐ray computed tomography (CT scan; Rogers et al ., ). With this new exciting technology it is also possible to image roots in pots and columns filled with soil, and even with plants grown in competition (e.g.…”

Section: Roots: the Entry Point For Pimentioning

confidence: 97%

Improving phosphorus use efficiency: a complex trait with emerging opportunities

et al. 2017

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SUMMARYPhosphorus (P) is one of the essential nutrients for plants, and is indispensable for plant growth and development. P deficiency severely limits crop yield, and regular fertilizer applications are required to obtain high yields and to prevent soil degradation. To access P from the soil, plants have evolved high-and low-affinity Pi transporters and the ability to induce root architectural changes to forage P. Also, adjustments of numerous cellular processes are triggered by the P starvation response, a tightly regulated process in plants. With the increasing demand for food as a result of a growing population, the demand for P fertilizer is steadily increasing. Given the high costs of fertilizers and in light of the fact that phosphate rock, the source of P fertilizer, is a finite natural resource, there is a need to enhance P fertilizer use efficiency in agricultural systems and to develop plants with enhanced Pi uptake and internal P-use efficiency (PUE). In this review we will provide an overview of continuing relevant research and highlight different approaches towards developing crops with enhanced PUE. In this context, we will summarize our current understanding of root responses to low phosphorus conditions and will emphasize the importance of combining PUE with tolerance of other stresses, such as aluminum toxicity. Of the many genes associated with Pi deficiency, this review will focus on those that hold promise or are already at an advanced stage of testing (OsPSTOL1, AVP1, PHO1 and OsPHT1;6). Finally, an update is provided on the progress made exploring alternative technologies, such as phosphite fertilizer.

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Section: Roots: the Entry Point For Pimentioning

confidence: 97%

Improving phosphorus use efficiency: a complex trait with emerging opportunities

et al. 2017

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“…A range of RSA traits in both 2D and 3D can be extracted depending on researchers' interests and purposes. For example, in one study to investigate the effects of soil on RSA and crop productivities, the extracted RSA traits for cultivars are root depth, width, total length, convex area, diameter, median root number, and crown root number [43]. A more complete review of 3D root system architecture can be found in Morris et al [44].…”

Section: X-ray Ct Imagingmentioning

confidence: 99%

Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots

Valdes

Clarke

2018

Agronomy

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Abstract:Scanning technologies based on X-ray Computed Tomography (CT) have been widely used in many scientific fields including medicine, nanosciences and materials research. Considerable progress in recent years has been made in agronomic and plant science research thanks to X-ray CT technology. X-ray CT image-based phenotyping methods enable high-throughput and non-destructive measuring and inference of root systems, which makes downstream studies of complex mechanisms of plants during growth feasible. An impressive amount of plant CT scanning data has been collected, but how to analyze these data efficiently and accurately remains a challenge. We review statistical and computational approaches that have been or may be effective for the analysis of 3D CT images of plant roots. We describe and comment on different approaches to aspects of the analysis of plant roots based on images, namely, (1) root segmentation, i.e., the isolation of root from non-root matter; (2) root-system reconstruction; and (3) extraction of higher-level phenotypes. As many of these approaches are novel and have yet to be applied to this context, we limit ourselves to brief descriptions of the methodologies. With the rapid development and growing use of X-ray CT scanning technologies to generate large volumes of data relevant to root structure, it is timely to review existing and potential quantitative and computational approaches to the analysis of such data. Summaries of several computational tools are included in the Appendix.

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“…X‐ray micro computed tomography (µCT) has been demonstrated, especially in recent years, to be an effective imaging technique in laboratories for the analysis and examination of root system architectures of soil‐grown plants (Lafond, Han, & Dutilleul, ; Mooney, Pridmore, Helliwell, & Bennett, ). Its non‐invasive nature and ability to acquire three‐dimensional (3D) data have captured the interest of the community, allowing for the observation of root growth over time (Tracy et al., ), and the interaction with and response to their surrounding soil environment at very fine scale (e.g., µm; Schmidt, Bengough, Gregory, Grinev, & Otten, ) as well as at larger scale (e.g., cm; Rogers et al., ). In the following protocol, we outline an integrated workflow pipeline for the 3D in situ analysis of plant root systems grown in soil using X‐ray computed tomography (CT).…”

Section: Introductionmentioning

confidence: 99%

X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil

et al. 2017

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Non‐destructive methods to quantify the root system architecture of a plant grown in soil are essential to aid our understanding of the factors that impact plant root development in natural environments. With environmental change threatening our ability to sustain agricultural productivity for an expanding global population, the application of these methods has never before seen such an increase in demand. X‐ray computed tomography (CT) based phenotyping techniques permit the spatio‐temporal quantification of roots, helping to identify novel adaptive root architectural responses to abiotic and biotic factors. This protocol reports an integrated workflow from column preparation and plant growth to image and quantification of the root system using novel open source software applications, RooTrak and RooTh. © 2017 by John Wiley & Sons, Inc.

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X-Ray Computed Tomography Reveals the Response of Root System Architecture to Soil Texture

Cited by 98 publications

References 61 publications

Improving phosphorus use efficiency: a complex trait with emerging opportunities

Improving phosphorus use efficiency: a complex trait with emerging opportunities

Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots

X‐Ray Computed Tomography of Crop Plant Root Systems Grown in Soil

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