The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions

Abstract

Single cells offer a simplified model for investigating complex mechanisms such as cell-cell adhesion. Protoplasts, plant cells without cell walls (CWs), have been instrumental in plant research, industrial applications, and breeding. However, due to the absence of a CW, protoplasts are not considered “true” plant cells and making them less relevant for biophysical studies. Current protocols for CW recovery in protoplasts vary widely among laboratories and starting materials, requiring lab-specific optimizations that often depend on expert knowledge and qualitative assessments. To address this, we have developed a user-friendly streamlined workflow, the Q-Warg pipeline, which enables quantitative comparison of various conditions for CW recovery post-protoplasting. This pipeline employs fluorescence imaging and tailored processing to measure parameters such as morphometry, cell viability, and CW staining intensity. Using this approach, we optimized culture conditions to obtain single plant cells (SPCs) with recovered CWs. Additionally, we demonstrated the robustness and versatility of the workflow by quantifying different fluorescent signals in protoplast suspensions. Overall, the Q-Warg pipeline provides a widely available and user-friendly solution for robust and unbiased characterization of protoplasts culture. The quantitative data generated by the pipeline may be useful in the future to decipher the mechanisms regulating protoplast viability and regeneration. Significance statement Several fields of plant biology, ranging from biotechnology to biomechanics, have recently regained a strong interest in using and studying protoplasts and single cells. Here, we developed a widely accessible quantitative workflow to characterize cell culture recovery after protoplasting along with the demonstration of its usefulness and versatility in various cases. We hope this tool can help other research groups to streamline the procedure needed to establish single plant cell approaches in their lab.

Plant phenotyping relevance

植物プロトプラストの形態、 viability、細胞壁染色強度を蛍光画像と専用処理で定量するワークフローを開発し、培養条件の比較・最適化に用いた研究であり、植物状態の取得・抽出法が中心である。

Code and data availability

The paper's data statement declares public Zenodo deposits for raw/processed data (10.5281/zenodo.14971281) and the Q-Warg workflow code (10.5281/zenodo.14973382, github.com/VergerLab/Q-Warg), which are paper-specific and public. However, none of these Zenodo/GitHub URLs appear in the allowed_urls list, so no asset can

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