The Arabidopsis embryo as a quantifiable model for studying pattern formation

Abstract

Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.

Keywords: cell specification; computational cell biology; gene expression; pattern formation; plant development; plant embryogenesis.

Fig. 1.

Quantification of cell morphology during pattern formation. Data extracted from 3D reconstructed Arabidopsis embryogenesis (a) transferred into computational modelling environment using MorphoGraphX or PlanSeg (b) to accurately assess morphologies of individual cells (c), determine positioning of division planes (d) and trace fluorescently tagged subcellular structures (e). The data can be used in simulation modelling, allowing to trace interactions between shapes and cellular responses.

Fig. 2.

Gaining insight into biochemical and mechanical responses during pattern formation in plants. (a) Study of cell identity establishment through generation of cell type-specific gene expression profiles. Following disintegration of embryos to single cells using lysis solution, cells are sorted according to the presence of fate-specific markers. The collected cells are further used in either droplet-based or plate-based single-cell RNA Seq assays that allow to interrogate cells for changes in transcriptome (b) Exploring cell-to-cell signaling during cell specification and pattern formation. A cell (pink) divides producing daughters with different fates (lilac and yellow). The molecular basis of fate specification is inferred using high-throughput approaches, such as Chip-seq and Dap-seq. (c) Visualisation of mechanical patterns in plants using mechano-probes. Cellular turgor pressure (gray shapes) causes tensile stress (red arrows) in the cell wall. The resulting tensile stress can be visualised and quantified using rotor dyes that change their fluorescence lifetime depending on the mechanical properties of the cell wall.