Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform1[C][W][OA]

By R. Clark, Robert MacCurdy, Janelle K. H. Jung, J. Shaff, Susan McCouch, D. Aneshansley, L. Kochian. Plant Physiology, 2011

430 citations recorded by the source corpus.

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.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/2de59af2cea2690cb02ccaaaa446fda77017b6ea

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Citations in the corpus

GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons. (2012, background): “…visualisation and quantification of entire root system architecture in 2D 19 (Walter et al. 2002; Armengaud et al. 2009; Hargreaves et al. 2009; Nagel et al. 2009) or 20 reconstructions in 3D if images from numerous camera view angles are acquired (Iyer-21 Pascuzzi et al. 2010; Clark et al. 2011).”
Traits and selection strategies to improve root systems and water uptake in water-limited wheat crops. (2012, methodology): “, 2004), and three-dimensional gel-based imaging setups (Iyer-Pascuzzi et al., 2010; Clark et al., 2011).”
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement (2013, background): “…range from surveys of root system architecture (Ibrahim et al. 2012; Landi et al. 2010; Lopes et al. 2011; Steele et al. 2007; Zhu et al. 2011b; Clark et al. 2011) to physiological metrics related to water status (Bartlett et al. 2012a, b; Blum 2009; Gilbert et al. 2011; Ogburn and Edwards…”
GiA Roots: software for the high throughput analysis of plant root system architecture (2012, neutral): “These tools rely on significant user input for processing although they can be used in a batch mode [22,36,37].”
A Review of Imaging Techniques for Plant Phenotyping (2014, background): “In a controlled environment (in a growth chamber or in the greenhouse), visible imaging was primarily adopted for analyzing the shoot biomass [13,15], yield traits [18], panicle traits [44], imbibition and germination rates [46], leaf morphology [49], seedling vigor [23,32], coleoptile length and bi”