Novel method for the quantification of rosette area from images of Arabidopsis seedlings grown on agar plates.

Abstract

Premise The agar-based culture of Arabidopsis seedlings is widely used for quantifying root traits. Shoot traits are generally overlooked in these studies, probably because the rosettes are often askew. A technique to assess the shoot surface area of seedlings grown inside agar culture dishes would facilitate simultaneous root and shoot phenotyping. Methods We developed an image processing workflow in Python that estimates rosette area of Arabidopsis seedlings on agar culture dishes. We validated this method by comparing its output with other metrics of seedling growth. As part of a larger study on genetic variation in plant responses to nitrogen form and concentration, we measured the rosette areas from more than 2000 plate images. Results The rosette area measured from plate images was strongly correlated with the rosette area measured from directly overhead and moderately correlated with seedling mass. Rosette area in the large image set was significantly influenced by genotype and nitrogen treatment. The broad-sense heritability of leaf area measured using this method was 0.28. Discussion These results indicated that this approach for estimating rosette area produces accurate shoot phenotype data. It can be used with image sets for which other methods of leaf area quantification prove unsuitable.

Plant phenotyping relevance

Arabidopsis幼苗のロゼット面積という植物形質を画像から推定するPython画像処理ワークフローを開発・検証しており、表現型取得手法が研究の中心である。

Code and data availability

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