Development and Deployment of a Portable Field Phenotyping Platform

Abstract

Accurate and efficient phenotyping has become the biggest hurdle for evaluating large populations in plant breeding and genetics. Contrary to genotyping, high‐throughput approaches to field‐based phenotyping have not been realized and fully implemented. To address this bottleneck, a novel, low‐cost, flexible phenotyping platform, named Phenocart, was developed and tested on a field trial consisting of 10 historical and current elite wheat (Triticum aestivium L.) breeding lines at the International Maize and Wheat Improvement Center (CIMMYT). The lines were cultivated during the 2013 and 2014 growing cycle in Ciudad Obregon, Mexico, and evaluated multiple times throughout the growing season. The phenotyping platform was developed by integrating several sensors: a GreenSeeker for spectral reflectance, an infrared thermometer (IRT), and a global navigation satellite system (GNSS) receiver into one functional unit. The Phenocart enabled simultaneous collection of normalized difference vegetation index (NDVI) and canopy temperature (CT) with precise assignment of all measurements to plot location by georeferenced data points. Across the set of varieties, the Phenocart temperature measurements were highly correlated to a handheld IRT. In addition, CT and NDVI were both significantly correlated to yield throughout the growing season. The Phenocart is a flexible, low‐cost, and easily deployable platform to increase the amount of phenotypic data that crop breeders obtain as well as provide high‐resolution phenotypic data for genetic discovery.

A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops

“…However, our comparative GWAS demonstrated that, at least for plant height and stem diameter estimations at the end of the season, the genomic regions controlling these traits were coincident with those identified previously in studies that utilized the commercially used narrow row spacing. Our approach is an important technological breakthrough in high-throughput phenotyping because (1) Phenobot is auto-steered while other reported ground-based high-throughput phenotyping platforms must be operated by a driver (Montes et al, 2011;Comar et al, 2012;Barker et al, 2016); (2) our sensors (RGB stereo cameras) are inexpensive and readily available to researchers, although to date not frequently used in high-throughput phenotyping projects (Comar et al, 2012;Busemeyer et al, 2013;Crain et al, 2016); (3) stereo cameras were particularly selected to enable 3D plant reconstructions; (4) our lateral camera view facilitates the characterization of yield component traits such as stem diameter that cannot be estimated by aerial or top-view cameras; (5) our advances in feature extraction and algorithm development could be leveraged in other image-based phenotyping systems that employ alternative mobile platforms; and finally, (6) our platform that runs parallel to crop rows can be deployed to tall dense canopy crops such as sorghum, where high-clearance platforms (Andrade-Sanchez et al, 2014;Barker et al, 2016) could not be used.…”

“…A modified sprayer holding three types of sensors (infrared thermometers, sonar proximity sensor, and multispectral crop canopy sensor) was deployed in cotton fields to acquire plant height, normalized difference vegetation index (NDVI), and canopy temperature in differently irrigated conditions (Andrade-Sanchez et al, 2014) and to map QTLs for those traits (Pauli et al, 2016). A similar high-clearance vehicle with similar sensors was developed with a novel modular design, and its functionality was verified in wheat and soybean fields (Barker et al, 2016). A novel enclosed structure for controlled wind and lighting conditions was created to collect hyperspectral images of wheat genotypes to characterize and differentiate them using vegetation coverage and NDVI (Svensgaard et al, 2014).…”

“…In another study, RGB cameras were mounted on a horizontal beam carried by a tractor and used to estimate the fraction of green area per unit ground area as a growth descriptor of wheat plots (Comar et al, 2012). A color camera also was included on the Phenocart, a low-cost portable platform mounted on a cart, to evaluate its potential to estimate green pixels per wheat plot (Crain et al, 2016). While this study showed promising results, it was only partially tested over 1 year and 10 varieties.…”

QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities

“…The ground-based and unmanned aerial HTFP platforms that were developed for real-world phenotyping of above-ground traits include the following: (i) phenomobiles; (ii) pheno-fields; (iii) breedvision; (iv) phenocart; (v) pheno-towers; (vi) blimps; and (vii) infrared imagery (IR radiation sensor mounted on a light aircraft) [92][93][94][95]. However, the cost of HTFP platforms is rather high (cost $100,000 [96]), although recently, cheaper platforms such as "Phenocart" (cost $12,000) have also become available [97]. These platforms will be increasingly used in future for the phenotyping of traits that are relevant to drought tolerance [57].…”

Assessing Wheat Traits by Spectral Reflectance: Do We Really Need to Focus on Predicted Trait-Values or Directly Identify the Elite Genotypes Group?

“…One strategy for improving and expediting the selection of these elite genotypes is the acquisition of high-dimensional phenotypic data (high-throughput phenotyping) (Bowman et al, 2015; Camargo and Lobos, 2016; Crain et al, 2016). …”