CropQuant: An automated and scalable field phenotyping platform for crop monitoring and trait measurements to facilitate breeding and digital agriculture

Abstract

Automated phenotyping technologies are capable of providing continuous and precise measurements of traits that are key to todays crop research, breeding and agronomic practices. In additional to monitoring developmental changes, high-frequency and high-precision phenotypic analysis can enable both accurate delineation of the genotype-to-phenotype pathway and the identification of genetic variation influencing environmental adaptation and yield potential. Here, we present an automated and scalable field phenotyping platform called CropQuant, designed for easy and cost-effective deployment in different environments. To manage infield experiments and crop-climate data collection, we have also developed a web-based control system called CropMonitor to provide a unified graphical user interface (GUI) to enable realtime interactions between users and their experiments. Furthermore, we established a high-throughput trait analysis pipeline for phenotypic analyses so that lightweight machine-learning modelling can be executed on CropQuant workstations to study the dynamic interactions between genotypes (G), phenotypes (P), and environmental factors (E). We have used these technologies since 2015 and reported results generated in 2015 and 2016 field experiments, including developmental profiles of five wheat genotypes, performance-related traits analyses, and new biological insights emerged from the application of the CropQuant platform.

Plant phenotyping relevance

作物の形質取得を目的とした自動・スケーラブルな圃場フェノタイピング基盤、制御システム、ハイスループット形質解析パイプラインを開発・適用しており、方法論が研究の中心である。

Code and data availability

The authors publicly distribute the CropQuant source code, SD card image, and high-definition field phenotyping movies via a Google Drive folder, with explicit availability statements. The picamera documentation link is a generic third-party library and is excluded.