The ‘PhenoBox’, a flexible, automated, open‐source plant phenotyping solution

Abstract

Summary There is a need for flexible and affordable plant phenotyping solutions for basic research and plant breeding. We demonstrate our open source plant imaging and processing solution (‘PhenoBox’/‘PhenoPipe’) and provide construction plans, source code and documentation to rebuild the system. Use of the PhenoBox is exemplified by studying infection of the model grass Brachypodium distachyon by the head smut fungus Ustilago bromivora , comparing phenotypic responses of maize to infection with a solopathogenic Ustilago maydis (corn smut) strain and effector deletion strains, and studying salt stress response in Nicotiana benthamiana . In U. bromivora ‐infected grass, phenotypic differences between infected and uninfected plants were detectable weeks before qualitative head smut symptoms. Based on this, we could predict the infection outcome for individual plants with high accuracy. Using a PhenoPipe module for calculation of multi‐dimensional distances from phenotyping data, we observe a time after infection‐dependent impact of U. maydis effector deletion strains on phenotypic response in maize. The PhenoBox/PhenoPipe system is able to detect established salt stress responses in N. benthamiana . We have developed an affordable, automated, open source imaging and data processing solution that can be adapted to various phenotyping applications in plant biology and beyond.

Plant phenotyping relevance

植物画像取得・処理システム自体の開発、オープンソース化、再構築可能な設計とコード提供が中心であり、植物表現型の測定・解析に直接対応するため。

Code and data availability

The paper explicitly states that the complete PhenoBox/PhenoPipe source code, documentation, and analysis modules (including the R code for classification and multidimensional distance calculation) are publicly available in the authors' GitHub repository under the GNU General Public Licence v.2. This is a paper-phenot​