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      GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems

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          Abstract

          Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.

          DOI: http://dx.doi.org/10.7554/eLife.07597.001

          eLife digest

          Most plants absorb water and nutrients from the soil via structures called roots. The shape, size, and structure of a plant's root system can change over its lifetime as the plant responds to changes in their local environment. For example, if water is scarce, a plant may develop a very deep root system that is more efficient at capturing water. Understanding how root systems respond to environmental cues may help us to identify the genes and processes involved.

          In this study, Rellán-Álvarez et al. report a new live-imaging platform for analyzing root architecture and its regulation. This platform is called Growth and Luminescence Observatory for Roots (or GLO-Roots for short) and uses ‘luminescent’ markers that allow growing roots to be visualized when plants are grown in thin, soil-filled, transparent pots. GLO-Roots can track the growth of the plant roots as well as the activity of genes that respond to environmental stress. Rellán-Álvarez et al. developed a software tool called GLO-RIA (GLO-Roots Image Analysis) to analyze the resulting images. GLO-RIA performs several different types of image analysis, including one that detects the position, length, and direction of roots, as well as their shape and depth.

          Rellán-Álvarez et al. tested the GLO-Roots techniques in various ways, for example, by analyzing the effects that different conditions have on the growth of the roots of the model plant known as Arabidopsis thaliana. Depriving the plants of a nutrient called phosphorous caused the roots to grow more horizontally than when phosphorus is plentiful, presumably to allow the plants to expand their search for phosphate in the upper layers of the soil, where this nutrient is usually more abundant. On the other hand, a shortage of water caused the roots to grow more vertically to access water stored deeper in the soil. GLO-Roots can also be used to measure the water content of soil at different depths and how this influences the architecture of the root.

          Further experiments on tomato plants and a grass species called Brachypodium distachyon revealed the different architectures of their root systems. Rellán-Álvarez et al. propose that this system could be used to study the roots of other plant species in a variety of environmental conditions. This will provide a more detailed understanding of the ways that different plants adapt in response to changes in their environment.

          DOI: http://dx.doi.org/10.7554/eLife.07597.002

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          Most cited references 47

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          NIH Image to ImageJ: 25 years of image analysis.

          For the past 25 years NIH Image and ImageJ software have been pioneers as open tools for the analysis of scientific images. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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              Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions.

              The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.
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                Author and article information

                Contributors
                Role: Reviewing editor
                Journal
                eLife
                eLife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                2050-084X
                19 August 2015
                2015
                : 4
                Affiliations
                [1 ]deptDepartment of Plant Biology , Carnegie Institution for Science , Stanford, United States
                [2 ]deptPhytoSystems , University of Liège , Liège, Belgium
                [3 ]deptDepartment of Energy , Department of Energy Joint Genome Institute , Walnut Creek, United States
                [4 ]deptDepartment of Biology , Stanford University , Stanford, United States
                [5 ]deptDepartment of Plant Biology , University of California, Davis , Davis, United States
                [6 ]deptDepartment of Genetics, Department of Molecular Biology, Massachusetts General Hospital , Harvard Medical School , Boston, United States
                [7 ]deptWestern Regional Research Center , United States Department of Agriculture , Albany, United States
                Boyce Thompson Institute for Plant Research , United States
                Boyce Thompson Institute for Plant Research , United States
                Author notes
                [* ]For correspondence: jdinneny@ 123456carnegiescience.edu
                [†]

                These authors contributed equally to this work.

                [‡]

                Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico.

                [§]

                Boyce Thompson Institute for Plant Research, United States Department of Agriculture, Ithaca, United States.

                Article
                07597
                10.7554/eLife.07597
                4589753
                26287479
                © 2015, Rellán-Álvarez et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                Product
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: MCB-115795
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000015, U.S. Department of Energy;
                Award ID: DE-SC0008769
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: MCB-0519898
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: IOS-0820854
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: GM48707
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100002661, Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research);
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003141, Consejo Nacional de Ciencia y Tecnología (National Council of Science and Technology, Mexico);
                Award ID: CB-2014-01-238101
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100000015, U.S. Department of Energy;
                Award ID: DE-AI02-07ER64452
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Tools and Resources
                Plant Biology
                Custom metadata
                2.3
                A luminescence-based imaging system is presented that allows soil-based environmental stimuli to be studied in root systems under physiologically relevant conditions.

                Life sciences

                imaging systems, brachypodium distachyon, lycopersicon esculentum, arabidopsis, other

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