3D cellular morphodynamics of plant growth

Multicellular organs grow through a combination of cell division and expansion. Understanding how these events are genetically co-ordinated between different cell types within large organs remains largely unknown primarily due to technical limitations.

We have developed a computational method to analyse the growth of whole plant organs and gene expression in 3D at cellular resolution. The combination of high-resolution confocal microscopy with the image analysis software MorphoGraphX (www.morphographx.org) enables the 3D shape of every cell and gene expression within each cell to be quantified. This technology provides the possibility of looking at the relationship between gene expression and the development of all cells within a complete multicellular organ in 3D.

This project will use this technology to investigate the relationship between gene expression and 3D organ development over time. This approach will both elucidate how cells come together to form organs and as well how signals move through cellular networks to guide their growth.

Using seed germination and seedling establishment as a model system, the relationship between gene expression, hormone signalling and cell shape changes will be established within the 3D context of this (Bassel et al. 2012, Bassel et al. 2014). These data will be analysed using computational and statistical tools (Roeder et al. 2011).

In the final phases of the project, these data will be used to generate a 4D growing model of an Arabidopsis embryo and seedling.

Seed germination and seedling establishment are critical starting points for agriculture, and a vulnerable stage of the plant life cycle. Understanding how signals move through seedlings to drive the grow other these organs will establish a framework to understand and improve the means by which crops are established in the field. This will lay a foundation which can be built upon to modulate and enhance these processes which are critical for food security.


Key experimental skills involved:
Molecular biology, confocal microscopy, plant growth analysis and transformation, computer analyses including quantitative 3D image analysis and computational analysis of large-scale datasets.

Please find additional funding text below. For further funding details, please see the ‘Funding’ section.

The School of Biosciences offers a number of UK Research Council (e.g. BBSRC, NERC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for research council studentships is 31 January each year.

Each year we also have a number of fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this scheme is also 31 January each year.