Next generation shovelomics: set up a tent and REST

Abstract

Aims Root system architecture traits (RSAT) are crucial for crop productivity, especially under drought and low soil fertility. The Bshovelomics^method of field excavation of mature root crowns followed by manual phenotyping enables a relatively high throughput as needed for breeding and quantitative genetics. We aimed to develop a new sampling protocol in combination with digital imaging and new software. Methods Sampled rootstocks were split lengthwise, photographed under controlled illumination in an imaging tent and analysed using Root Estimator for Shovelomics Traits (REST). A set of 33 diverse maize hybrids, grown at 46 and 192 kg N ha −1 , was used to evaluate the method and software.Results Splitting of the crowns enhanced soil removal and enabled access to occluded traits: REST-derived median gap size correlated negatively (r=−0.62) with lateral root density based on counting. The manually measured root angle correlated with the image-derived root angle (r=0.89) and the horizontal extension of the root system (r=0.91). The heritabilities of RSAT ranged from 0.45 to 0.81, comparable to heritabilities of plant height and leaf biomass. Conclusion The combination of the novel crown splitting method, combined with imaging under controlled illumination followed by automatic analysis with REST, allowed for higher throughput while maintaining precision. The REST Software is available as supplement.

Quantitative 3D Analysis of Plant Roots Growing in Soil Using Magnetic Resonance Imaging

“…Shallow rooting has been proposed to increase phosphorus uptake efficiency, while deep rooting have been proposed as beneficial for nitrate and water uptake (Wasson et al, 2012;Lynch, 2013;Trachsel et al, 2013). However, accurate determination of angles is often possible only in 2D systems or, after excavation, for relatively stiff roots (Trachsel et al, 2010;Colombi et al, 2015). Our NMRooting approach calculated branching angles of every root of a single plant in 3D (for details, see "Materials and Methods").…”

Biochar amendment increases maize root surface areas and branching: a shovelomics study in Zambia

“…were recently further optimized with regards to the sampling strategy and software solution 112 (Colombi et al, 2015) where instead of sampling the whole root system, only half of the root 113 system is sampled. This method enhanced on the one hand the transportation and cleaning 114 process and enabled on the other hand a better insight into the root system without excessive 115 overlapping of the roots on the image.…”

Genetic Diversity under Soil Compaction in Wheat: Root Number as a Promising Trait for Early Plant Vigor

“…In common bean instead, a high number of basal roots in the top soil improved phosphorus uptake and plant vigor in low phosphorus soils (Miguel et al, 2013). A major advantage of root system architectural traits and root numbers in particular is that they can be assessed in large diversity panels under field conditions at high throughput rates (Trachsel et al, 2011; Colombi et al, 2015; Burridge et al, 2016). The quantification of root dry weight or length instead is much more laborious and not feasible under field conditions.…”

“…The quantification of root dry weight or length instead is much more laborious and not feasible under field conditions. The heritability of root numbers was reported to be relatively high in a wide range of crop species (Wilcox and Farmer, 1968; Bucksch et al, 2014; Colombi et al, 2015; Li et al, 2015; Richard et al, 2015; Burridge et al, 2016). Besides increasing awareness about the importance of roots for crop production, it has been suggested that holistic phenotyping approaches are needed to understand plant responses to abiotic stress.…”