'Macrobot' - an automated segmentation-based system for powdery mildew disease quantification

Abstract

Plant diseases, as one of the perpetual problems in agriculture, is increasingly difficult to manage due to intensifying of the field production, global trafficking, reduction of genetic variability of crops, climatic changes-driven expansion of pests, redraw and loss of effectiveness of pesticides and rapid breakdown of the disease resistance in the field. The substantial progress in genomics of both plants and pathogens, achieved in the last decades has the potential to counteract this negative trend, however, only when the genomic data is supported by relevant phenotypic data that allows linking the genomic information to specific traits. In this respect, phenotyping is and will remain an essential element of any comprehensive functional genomics study. We have developed a set of methods and equipment and combined them into a “Macrophenomics pipeline”. The pipeline has been optimized for the quantification of powdery mildew infection symptoms on wheat and barley but it can be adapted to other diseases and host plants. The Macrophenomics pipeline scores the visible disease symptoms, typically 5-7 days after inoculation (dai) in a highly automated manner. The system can precisely and reproducibly quantify the percentage of the infected leaf area with a throughput of the image acquisition module of up to 10 000 individual samples per day, making it appropriate for phenotyping of large germplasms collections and crossing populations.

Plant phenotyping relevance

うどんこ病の葉面感染面積を自動画像 segmentation で定量する方法・装置・パイプラインの開発と精度再現性評価が中心であり、植物病害表現型の取得手法に該当する。

Code and data availability

The paper describes the Macrobot phenotyping pipeline and states that the analysis source code is available (Lueck 2019), but no public repository URL or identifier is provided in the supplied blocks, and no public phenotype dataset, images, or trained model deposit is mentioned. The only URL present is the preprint's,

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