Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants

Abstract

Background Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. Results Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. Conclusion The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.

High frequency root dynamics: sampling and interpretation using replicated robotic minirhizotrons

“…The accelerated clocks used in E1 and E2 also partially demonstrate long-term performance which could capture whole annual cycles if performed at similar rates in the field to those in E3. Minirhizotron studies may also use huge replication—in agricultural settings, this can reach thousands of observatories ( Rajurkar et al , 2022 ). In this case, no matter how affordable at budget an automated system is, entire coverage is unlikely to be possible with robotic systems.…”

Growth kinetics, spatialization and quality of potato tubers monitored in situ by MRI ‐ long‐term effects of water stress

“…The great advantage of these methods is that the same individual plant, either pot‐ or field‐grown, can be studied over time. These techniques range from hydroponics and gel systems, rhizotrons (Mohamed et al, 2017) (including a minirhizotron (Rajurkar et al, 2022)), to the more challenging 3D imaging of roots in pots, including the use of X‐ray computed tomography (Metzner et al, 2015, Pfeifer et al, 2015, Pérez‐Torres et al, 2015, Ferreira et al, 2010) and MRI (van Dusschoten et al, 2016). The monitoring of tuber development in soil, which allows access to spatial and short or long‐term temporal information on tuber quality traits during formation and growth, is less common.…”

A method of cotton root segmentation based on edge devices

“…Problems such as damage to root configuration and loss of small root segments are easy to occur during extraction, which cannot meet the dynamic and accurate identification of root configuration, It has been replaced by in situ root observation (in situ cultivation method and in situ imaging method) (Xiao et al, 2020;Liu et al, 2020b). The root in situ imaging method originated from the micro root canal method (Bates, 1937;Cseresnyeś et al, 2021;Rajurkar et al, 2022) It refers to identifying the root image contacting the glass tube wall by inserting a glass tube into the soil. However, its disadvantages lie in poor resolution (numerical value), slow acquisition speed (time), and low degree of automation.…”