Molecular networks underpinning root development in Arabidopsis and crops.

Control of plant root architecture is critical to ensure plant survival in the face of changing environmental conditions. We have recently shown that an Arabidopsis transcription factor, AtMYB93, which is localised to just a few specific cells in the endodermis of the root, regulates root branching, or lateral root development (Gibbs et al 2014 New Phytologist). AtMYB93 expression is induced by the plant hormones auxin and abscisic acid, and is also under environmental control. AtMYB93 negatively regulates root branching, making it the first auxin-induced negative regulator of lateral root development and suggesting that it is part of a negative feedback loop that ensures that a new root is only made when absolutely required.

Our bioinformatic analysis suggests that AtMYB93 is intimately involved with regulating suberin biosynthesis. Suberin is localized in specific areas of the endodermis, a cell layer recently implicated in lateral root development, and AtMYB93 shows similar endodermal localization.

The overarching aims of this proposal are (i) to understand how AtMYB93 performs its function at a molecular level, (ii) to determine how changing suberin biosynthesis can affect LR development and (iii) to determine whether MYB93 homologues in crops are good targets for manipulation of root development for crop improvement.

To achieve these aims, the project has the following objectives:
(i) identification and confirmation of AtMYB93 transcriptional targets using Chromatin Immunoprecipitation (ChIP) methods.
(ii) determination of the localisation of endogenous AtMYB93 protein
(iii) manipulation of suberin biosynthesis in Arabidopsis and determination of the effects on root architecture
(iv) characterisation of MYB93 homologues in crop plants including barley/rice/Brassica.

Key experimental skills involved:
The project uses a mixture of well-established and newly-emerging experimental techniques, combined in a novel way. Initially, the project will involve both ChIP and next-generation sequencing. Standard molecular biology approaches will be used to quantify small-scale or targeted gene expression, while relatively new bioinformatic approaches will be required to analyse RNA-seq data (the JEHC at the University of Birmingham will train the student in these techniques).
To test gene function, Arabidopsis offers unique advantages due to (i) the availability of mutants for nearly every gene in the genome, including previously identified suberin biosynthesis mutants, and (ii) well established techniques for gene manipulation (e.g. tagging a protein with a fluorescent protein and elucidating its endogenous localisation). These techniques are already established in the Coates and Gibbs labs.
Molecular, functional genomic and bioinformatic approaches will be combined with a move into crop plant systems including barley, rice and Brassica. This represents a novel fusion of techniques to answer an important biological question. Towards the end of the project, we would expect that some genetic manipulation of crop plants would take place, using expertise and transformation techniques developed in Birmingham (Brassica, Barley) and elsewhere (Rice), and emergent methods for disrupting gene- or protein function such as siRNAs, TALENs, TILLING and Zinc-finger nucleases.

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.