Complementary Phenotyping of Maize Root Architecture by Root Pulling Force and X-Ray Computed Tomography

Abstract

The root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture, and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root biomass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret root pulling force measurements across a range of experimental contexts, or scaled up as a stand-alone approach in large genetic studies of root system architecture.

Pearl millet response to drought: A review

“…Root architecture and plasticity play an important role in crop growth in drought-prone environments, yet there has been relatively little study on root development due to difficulty in phenotyping this trait. However, the development of models for estimating root length density in pearl millet and other crops such as maize will be important in advancing our knowledge of this vital trait (Das et al, 2015;Faye et al, 2019;Shao et al, 2021).…”

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

“…Although the imaging of samples using photogrammetry is a low-cost process that does not require significant infrastructure, there are several challenges that still remain. Unlike other tomographic techniques, such as X-ray CT (Shao et al, 2021), photogrammetry does not resolve internal structures of the sample as the 2D images are only capturing surface features within line of sight of the 2D-photographs. This means that A B…”

“…dense root crowns or areas of thick matted lateral roots are not resolvable. Thus, we are considering the potential to complement the photogrammetry derived point cloud with Xray CT derived root crown reconstructions (Shao et al, 2021;Zeng et al, 2021). Additionally, photogrammetry at such a large scale can require significant computation power, dedicated software, and can currently take on the order of days to process each sample.…”

4DRoot: Root phenotyping software for temporal 3D scans by X-ray computed tomography

“…Thus, accurate quantification of root traits helps breeders select favorable root characteristics regarding not only carbon farming and crop production but also soil degradation. However, our understanding of RSA has been hindered by its complex three-dimensional branching topology (Morris et al, 2017;Dowd et al, 2021;Shao et al, 2021). Recent improvements in image-based technologies such as X-ray computed tomography (CT) and magnetic resonance imaging (MRI) provide a 3D model of the root.…”