Image analysis for the automatic phenotyping of Orobanche cumana tubercles on sunflower roots.

Abstract

Abstract Background The parasitic plant Orobanche cumana is one of the most important threats to sunflower crops in Europe. Resistant sunflower varieties have been developed, but new O. cumana races have evolved and have overcome introgressed resistance genes, leading to the recurrent need for new resistance methods. Screening for resistance requires the phenotyping of thousands of sunflower plants to various O. cumana races. Most phenotyping experiments have been performed in fields at the later stage of the interaction, requiring time and space. A rapid phenotyping screening method under controlled conditions would need less space and would allow screening for resistance of many sunflower genotypes. Our study proposes a phenotyping tool for the sunflower/ O. cumana interaction under controlled conditions through image analysis for broomrape tubercle analysis at early stages of the interaction. Results We optimized the phenotyping of sunflower/ O. cumana interactions by using rhizotrons (transparent Plexiglas boxes) in a growth chamber to control culture conditions and Orobanche inoculum. We used a Raspberry Pi computer with a picamera for acquiring images of inoculated sunflower roots 3 weeks post inoculation. We set up a macro using ImageJ free software for the automatic counting of the number of tubercles. This phenotyping tool was named RhizOSun. We evaluated five sunflower genotypes inoculated with two O. cumana races and showed that automatic counting of the number of tubercles using RhizOSun was highly correlated with manual time-consuming counting and could be efficiently used for screening sunflower genotypes at the tubercle stage. Conclusion This method is rapid, accurate and low-cost. It allows rapid imaging of numerous rhizotrons over time, and it enables image tracking of all the data with time kinetics. This paves the way toward automatization of phenotyping in rhizotrons that could be used for other root phenotyping, such as symbiotic nodules on legumes.

Plant phenotyping relevance

根部画像からOrobancheの結節数を自動抽出するRhizOSunを開発・評価しており、植物表現型取得法が研究の中心です。

Code and data availability

The paper's phenotyping analysis code (ImageJ macros for automatic and semiautomatic tubercle counting, Additional files 4 and 5) and the underlying datasets are paper-specific, but no public deposit URL is provided; the authors state data are available upon reasonable request.

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