3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research

Abstract

SUMMARYRoot architecture plays important roles in plant water and nutrient acquisition. However, accurate modeling of the root system that provides a realistic representation of roots in the soil is limited by a lack of appropriate tools for the non-destructive and precise measurement of the root system architecture in situ. Here we describe a root growth system in which the roots grow in a solid gel matrix that was used to reconstruct 3D root architecture in situ and dynamically simulate its changes under various nutrient conditions with a high degree of precision. A 3D laser scanner combined with a transparent gel-based growth system was used to capture 3D images of roots. The root system skeleton was extracted using a skeleton extraction method based on the Hough transformation, and mesh modeling using Ball-B spline was employed. We successfully used this system to reconstruct rice and soybean root architectures and determine their changes under various phosphorus (P) supply conditions. Our results showed that the 3D root architecture parameters that were dynamically calculated based on the skeletonization and simulation of root systems were significantly correlated with the biomass and P content of rice and soybean based on both the simulation system and previous reports. Therefore, this approach provides a novel technique for the study of crop root growth and its adaptive changes to various environmental conditions.

Root system architecture: insights fromArabidopsisand cereal crops

“…For this reason, several other root growth methods have been trialled, such as growth on moistened germination paper rolls or pouches [131,132], sand rhizotrons [133] and gel-based systems [134 -136], where phenotypic effects can be imaged using flatbed scanners, digital cameras or even lasers [137]. In this issue, Wells et al [138] present novel image acquisition and analysis methods to capture root growth and development.…”

“…From the starting point of programmed 'rules' based on direct phenotypic observations and molecular data, mathematical modelling can prove useful for mapping and integrating root growth and interactions in response to a variety of variables, and has been used to predict root growth patterns under differing conditions, including response to water and nutrient supply [142], various phosphorus concentrations [137], root adaptation to low nitrogen soil under carbon flux modifications [143] and the formation of root cortical aerenchyma in response to soil nutrient status [144], to name just a few. Simulation packages specifically for the study of root architecture have been developed, such as SIMROOT [145].…”

Analyzing Lateral Root Development: How to Move Forward

“…Rice root system architecture can be imaged in gel columns in 3D using optical projection tomography or laser scanning (Fang et al, 2009;Iyer-Pascuzzi et al, 2010). For plants grown in soil, x-ray CT techniques and magnetic resonance imaging (Heeraman et al, 1997;Nagel et al, 2009;Tracy et al, 2010;Lucas et al, 2011;Zhu et al, 2011) have recently increased our capabilities to visualize root system architecture in situ nondestructively.…”

“…These include growth on moistened germination paper rolls or pouches, sand rhizotrons, rhizoboxes, in compost followed by washing, soil columns and gelbased systems where phenotypic effects can be imaged using flatbed scanners, digital cameras, lasers, or even x-ray computed tomography (CT) (Hetz et al, 1996;Whiting et al, 2000;Bengough et al, 2004;Fang et al, 2009;French et al, 2009;Gregory et al, 2009;Hammond et al, 2009;Iyer-Pascuzzi et al, 2010;Trachsel et al, 2010;Tracy et al, 2010Tracy et al, , 2011Chapman et al, 2011;Lobet et al, 2011;Lucas et al, 2011). Magnetic resonance imaging (for noninvasive analysis of root structures) and positron emission tomography (for analysis of carbon transport and accumulation) can be combined to study the dynamics of structure-function relationships of roots in real soils in a noninvasive manner .…”

Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform

“…As a complementary tool to other predictive techniques, gellan gum growth systems with superior optical clarity have been introduced to facilitate noninvasive two-dimensional (2D; Iyer-Pascuzzi et al, 2010) and three-dimensional (3D; Fang et al, 2009) imaging and temporal studies of plant root systems while also allowing reproducible control of the rhizosphere. These recent studies demonstrate the use of gellan gum systems and discuss their enormous potential for high-throughput root phenotyping and novel trait discovery when working with 2D image sets; however, efforts to expand these investigations into the 3D structure remain constrained by low throughput that requires over 1 h to acquire a single root system, small scanning volumes, and limited quantification capabilities.…”