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

Abstract

A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform's capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P , 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture.

Duplicate and Conquer: Multiple Homologs ofPHOSPHORUS-STARVATION TOLERANCE1Enhance Phosphorus Acquisition and Sorghum Performance on Low-Phosphorus Soils

“…Centroid measures the tendency of a root to grow at different depths (i.e. a larger centroid value is indicative of a more deeply growing root system), whereas bushiness is a measure of the global branching of the root system (Clark et al, 2011). The associations detected for centroid and bushiness for Sb03g031690 suggest that SbPSTOL1 enhances the capacity of the sorghum root system to forage the P that is more available in superficial soil layers.…”

“…In general, the methods described in detail by Clark et al (2011) were used except that the plants were grown as described above hydroponically instead of in gel cylinders. For each plant's root system, 100 2D digital images as the plant was rotated through 360°with 2D images were taken every 3.6°.…”

“…Asterisks are as follows: ****P , 0.001, ***0.001 # P , 0.01, **0.01 # P , 0.05, and *0.05 # P , 0.1. RSA traits were assessed in the SAPst using our RootReader3D platform as described by Clark et al (2011) to image and generate three-dimensional (3D) reconstructions for the entire root systems of the sorghum accessions in the SAPst. Then, the RootReader3D software was used to compute 19 different RSA traits, which were then employed as different phenotypes in the association analysis.…”

Plasticity of the Arabidopsis Root System under Nutrient Deficiencies

“…It is possible to represent the variation for many traits in a relatively small number of data points within the plasticity graph. Plasticity charts can condense the number of data points, particularly in studies involving modern root phenotyping techniques such as those of Ingram et al (2012), Clark et al (2011), or Iyer-Pascuzzi et al (2010 that measured between 16 and 27 root traits in a number of genotypes.…”

“…Thus, it becomes crucial to select the most suitable gelling agent when particular nutrient deficiencies are to be obtained. This is particularly relevant as strategies depending upon the use of gelling media are being developed to overcome the bottleneck that often limits RSA traits from being characterized in high-throughput phenotyping studies (Iyer-Pascuzzi et al, 2010;Clark et al, 2011).…”