All Publications

  • Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nature communications Waidmann, S., Ruiz Rosquete, M., Scholler, M., Sarkel, E., Lindner, H., LaRue, T., Petrik, I., Dunser, K., Martopawiro, S., Sasidharan, R., Novak, O., Wabnik, K., Dinneny, J. R., Kleine-Vehn, J. 2019; 10 (1): 3540


    Directional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and reveal that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach proposes that two phytohormonal cues at opposite organ flanks counterbalance each other's negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.

    View details for DOI 10.1038/s41467-019-11483-4

    View details for PubMedID 31387989

  • GRANAR, a computational tool to better understand the functional importance of monocotyledon root anatomy. Plant physiology Heymans, A., Couvreur, V., LaRue, T., Paez-Garcia, A., Lobet, G. 2019


    Root hydraulic conductivity is a limiting factor along the water pathways between the soil and the leaf, and root radial conductivity is itself defined by cell-scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex time-consuming experimental procedures. We present an open-source computational tool, the Generator of Root ANAtomy in R (GRANAR that can be used to rapidly generate digital versions of contrasted monocotyledon root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties. We used GRANAR to re-analyse large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA (Model of Explicit Cross-section Hydraulic Architecture). Our simulations highlight the large importance of the width of the stele and the cortex. GRANAR is a computational tool that generates root anatomical networks from experimental data. It enables the quantification of the effect of individual anatomical features on the root radial conductivity.

    View details for DOI 10.1104/pp.19.00617

    View details for PubMedID 31744934

  • Understanding and engineering plant form. Seminars in cell & developmental biology Brophy, J. A., LaRue, T., Dinneny, J. R. 2017


    A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.

    View details for PubMedID 28864344

  • GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems ELIFE Rellan-Alvarez, R., Lobet, G., Lindner, H., Pradier, P., Sebastian, J., Yee, M., Geng, Y., Trontin, C., LaRue, T., Schrager-Lavelle, A., Haney, C. H., Nieu, R., Maloof, J., Vogel, J. P., Dinneny, J. R. 2015; 4


    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.

    View details for DOI 10.7554/eLife.07597

    View details for Web of Science ID 000373814300001

    View details for PubMedID 26287479

    View details for PubMedCentralID PMC4589753