Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems

This paper presents an original spit-and-combine imaging procedure that enables the complete vectorization of complex root systems grown in rhizotrons. The general principle of the method is to (1) separate the root system into a small number of large pieces to reduce root overlap, (2) scan these pieces one by one, (3) analyze separate images with a root tracing software and (4) combine all tracings into a single vectorized root system. This method generates a rich dataset containing morphological, topological and geometrical information of entire root systems grown in rhizotrons. The utility of the method is illustrated with a detailed architectural analysis of a 20-day old maize root system, coupled with a spatial analysis of water uptake patterns.

[1]  F. I. Woodward,et al.  The root system architecture and development of Senecio vulgaris in elevated CO_2 and drought , 1992 .

[2]  Paul R Zurek,et al.  GiA Roots: software for the high throughput analysis of plant root system architecture , 2012, BMC Plant Biology.

[3]  Loïc Pagès,et al.  A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture1[W][OA] , 2011, Plant Physiology.

[4]  Bernd Körfgen,et al.  A grid refinement approach for a three‐dimensional soil‐root water transfer model , 2009 .

[5]  Jan Vanderborght,et al.  A simple three-dimensional macroscopic root water uptake model based on the hydraulic architecture approach , 2012 .

[6]  Harry Ozier-Lafontaine,et al.  The relationships between static and dynamic variables in the description of root growth. Consequences for field interpretation of rooting variability , 2001, Plant and Soil.

[7]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[8]  Vincent C. Tidwell,et al.  X ray and visible light transmission for laboratory measurement of two‐dimensional saturation fields in thin‐slab systems , 1994 .

[9]  W. Otten,et al.  Transparent Soil for Imaging the Rhizosphere , 2012, PloS one.

[10]  J. Lynch.  Root Architecture and Plant Productivity , 1995, Plant physiology.

[11]  Fabrice Martin-Laurent,et al.  Role of a Single Aquaporin Isoform in Root Water Uptake Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008888. , 2003, The Plant Cell Online.

[12]  A. Eshel,et al.  Plant roots : the hidden half , 1991 .

[13]  Mathieu Javaux,et al.  Root water uptake and water flow in the soil-root domain , 2013 .

[14]  Hans Brix,et al.  A rhizotron to study root growth under flooded conditions tested with two wetland Cyperaceae , 2006 .

[15]  Ulrich Schurr,et al.  Combined MRI-PET dissects dynamic changes in plant structures and functions. , 2009, The Plant journal : for cell and molecular biology.

[16]  Claude Doussan,et al.  Water Uptake by Plant Roots: I – Formation and Propagation of a Water Extraction Front in Mature Root Systems as Evidenced by 2D Light Transmission Imaging , 2006, Plant and Soil.

[17]  Graeme L. Hammer,et al.  Can Changes in Canopy and/or Root System Architecture Explain Historical Maize Yield Trends in the U.S. Corn Belt? , 2009 .

[18]  W. R. Gardner,et al.  Dynamic Aspects of Soil-Water Availability to Plants , 1965 .

[19]  Jan Vanderborght,et al.  Use of a Three‐Dimensional Detailed Modeling Approach for Predicting Root Water Uptake , 2008 .

[20]  Hans-Jörg Vogel,et al.  When Roots Lose Contact , 2009 .

[21]  Johannes Auke Postma,et al.  Root Cortical Aerenchyma Enhances the Growth of Maize on Soils with Suboptimal Availability of Nitrogen, Phosphorus, and Potassium1[W][OA] , 2011, Plant Physiology.

[22]  D. Barthélémy,et al.  Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny. , 2007, Annals of botany.

[23]  Loïc Pagès,et al.  DART: a software to analyse root system architecture and development from captured images , 2009, Plant and Soil.

[24]  Timothy S. George,et al.  Strategies and methods for studying the rhizosphere—the plant science toolbox , 2009, Plant and Soil.

[25]  Hans-Jörg Vogel,et al.  Dynamics of soil water content in the rhizosphere , 2010, Plant and Soil.

[26]  Jonathan P Lynch,et al.  The importance of root gravitropism for inter-root competition and phosphorus acquisition efficiency: results from a geometric simulation model , 2004, Plant and Soil.

[27]  M. Crespi,et al.  Plant root growth, architecture and function , 2009, Plant and Soil.

[28]  Mathieu Javaux,et al.  Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils. , 2010, Journal of experimental botany.

[29]  Alastair H. Fitter,et al.  AN ARCHITECTURAL APPROACH TO THE COMPARATIVE ECOLOGY OF PLANT ROOT SYSTEMS , 2008 .

[30]  S. Mooney,et al.  Developing X-ray Computed Tomography to non-invasively image 3-D root systems architecture in soil , 2011, Plant and Soil.