Identification and characterization of gene networks regulating 3D changes in plant cell shape

The growth of plants occurs through both cell division and expansion. The objective of this PhD project is to uncover gene networks that control changes in plant expansion by using a multidisciplinary approach.

Plant cell expansion is a mechanically-driven process that involves the co-ordination of increases in cellular turgor with the loosening of their rigid surrounding cells walls. While it is known that these processes are responsible for changes in plant cell shape, there is little information as to the direct molecular mechanisms that regulate this process.

Seed germination is an ideal system to understand how changes in plant cell shape can drive a transition in plant growth. Following their development, seeds remain dormant in the soil and the cells within the plant embryo arrest their growth. Dormant seeds receive information from their environment which is used to make a decision to germinate and start growing. The process of seed germination occurs exclusively through cell expansion, and the decision to terminate dormancy involves the induction of cell shape changes within the plant embryo to drive growth.

High confidence genome-wide networks that predict gene interactions within each dormant and germinating seeds have been previously developed (Bassel et al, 2011 PNAS; Bassel et al. 2011, Plant Cell). Using these network models, the function of 14 previously uncharacterized genes controlling the decision of an embryo cell to change shape have been predicted. These genes represent good candidates for further study.

More recent work using high resolution confocal microscopy and novel custom-built image analysis software enables the digital capture of the shape of every cell within the plant embryo in 3D. The changes in cell shape that drive seed germination can be quantified using this computational methodology.

This PhD project will integrate predictions based on the gene networks with associated changes in 3D embryo cell shape. The student will learn how to use networks to identify candidate genes driving cell expansion, and experimentally validate these hypotheses using a combination of molecular biology, plant physiology and computational analysis of 3D images.

Given that seed directly comprise 70% of the world's calorie intake, and are the starting point for the vast majority of world agriculture, outputs of this project will have significant implications in terms of crop establishment and food security in addition to enhacing bioenergy production.

For more details please visit www.GeorgeBasselLab.com
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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 in 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 in January each year.

Please note the only funding available for our PhD is via the Scholarships mentioned. All applicants should indicate in their applications how they intend to fund their studies. Any academically suitable applicant that does not indicate how they intend to fund their studies will be considered for the Darwin and/or the Elite Scholarships if not already indicated. We can only consider applicants who have their own funding or wish to apply for their own funding or are successful in gaining a Scholarship.