Plant phenotyping: From whole plant to subcellular resolution


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Plant phenotyping: from whole plant to subcellular resolution. Plant phenotyping is assessing the complex plant traits, including growth, development, stress tolerance, root, and shoot architecture, based on the quantitative measurement of individual parameters. Each plant organ consists of units called cells, and cells, in turn, have organelles like the nucleus, mitochondria, etc. Functional plant phenotyping must include the whole organ's phenotype as a sum of the phenotype of each cell's phenotype, including functional activity and dissection of the cell's contribution to organ development. So far automatic methods of whole plant phenotyping have been developed. However, a shortfall of precise plant phenotyping methods at subcellular resolution limits our ability to dissect the genotype-environment interactions that are critical for understanding plant adaptation to different types of stresses and for linking genes with their function, expression, and localization. Here, we describe an effective, high-resolution phenotyping platform that allows the detection of tissues, cell files, and cell shapes, as well as quantified gene expressions, chromatin organization, cell cycle kinetics, cell polarity, and protein-protein interactions at subcellular resolution. The platform does not require endogenous markers and is plant-species independent. The platform has been tested for the analysis of diverse organs in several plant species, including grasses. Application of the platform requires minimal time and experience from researchers and can be completed in 3–4 working days (including complete data extraction for each cell). The method requires a highresolution microscope and state-of-the-art computer. We present the results of platform applications in diverse developmental contexts. The platform is free and open source, with a user-friendly graphical interface.


1. Pasternak T., Paponov I., Falk T. 2021. Deep-resolution plant phenotyping platform description.

2. Pasternak, T. P., Kircher, S., Palme, K. 2021. Estimation of cell cycle kinetics in higher plant root meristem with cellular fate and positional resolution. bioRxiv, 2021-02. doi:

Speaker Information

Short Bio:

Dr. Taras Pasternak has been working in plant biology since 1983. His first project was connected with plant cell genetic transformation (1983-1986), where he chose microinjection as a tool. Then, he participated in projects related to plant phenotyping, stress response, hormonal signaling. These projectes were performed in several countries: Kyiv (Ukraine); Szeged (Hungary); Antwerpen (Belgium); Freiburg (Germany). His main interest is to find links between whole plant phenotypes and changes in gene expression and chromatin status of cells.  All his findings were published in 62 papers. According to Google they have 4033 citations.


Anyone who is interested and wants to apply deep phenotyping can directly contact Taras Pasternak. He is currently searching for a job and will be happy to help set procedures. If you have a task/ position to fill, contact him here!