Principal Supervisor: Dr Sinéad Drea, Department of Genetics and Genome Biology
Co-supervisor: Dr Eamonn Mallon
PhD project title: Genetic Regulation of Grain Quality in Wheat
University of Registration: University of Leicester
The grain is a single-seeded fruit with a prominent and persistent endosperm component for which many cereals have been domesticated. Globally, the human population is hugely dependent on cereal grains for their calorific requirements. The basis of our work involves linking fundamental development with applied characters of the cereal grain’s structure and composition. Grain quality comprises physical and chemical characters including size/shape (physical) and protein/starch contents in the grain’s endosperm tissues (chemical). Key transcription factors (TFs) have been shown to regulate the development of endosperm tissues and also to regulate the expression of genes in starch and protein metabolism. While “master regulatory genes” dictate the identity and specification of tissues that are targets of domestication - including macro grain characters such as accessibility and size - at some point downstream in the grain’s regulatory network, these master regulators must link to the “local” regulators of specific metabolic and biochemical pathway components such as protein and starch metabolism in the endosperm. To elucidate this regulatory cascade in grain development we aim to adopt a systems approach using transcriptomics to characterise TF expression dynamics at key timepoints but, importantly, we also incorporate other experimental components to complement this approach including phenotypic analyses of candidate TF RNAi /insertion lines that have already been generated and investigating TF protein/promoter interactions using yeast one- and two-hybrid methods.
Brachypodium is a new model system for the economically important temperate crops such as wheat, barley and oats but has the advantages of a short life cycle, small genome and modest stature/growth requirements suitable for lab research. A unique advantage of Brachypodium is that is it a wild grass and so we can also use it to learn much about the process of domestication by comparing it to the related cultivated cereals – we have published a detailed comparison of its grain development to that of wheat and as part of a BBSRC project we generated a transcriptome through its grain development. This PhD proposal builds on this project and uses a comparative approach to identify TFs controlling key points of difference in Brachypodium and wheat grains. The RNAi/insertion lines already available in the lab comprise both species.
The first and second supervisors (Drea and Mallon) are currently collaborating on generating and analysing grain transcriptomics using specialist but complementary approaches: the Drea lab provides expertise in developmental biology and molecular genetics such as staging and harvesting grain material and isolating RNA for Illumina RNA-seq; detailed gene expression analyses and functional analysis of individual genes using mRNA in situ hybridization and RNAi; Dr. Mallon is already using his bioinformatics expertise as part of this existing collaboration to generate transcriptomes and identify differential gene expression patterns at different stages of development and has a strong computational and quantitative approach to his research generally. We include Professor Doonan who runs the national Phenomics Centre in Aberystwyth as a third supervisor for this proposal because he has developed tools and skills in modelling and analysing aspects of grain shape, a key physical determinant of grain quality and a central factor in milling. We feel the project would benefit from his experience and expertise and we have collaborated successfully on various grain-related projects in the past.
The work proposed is suitable for the MIBTP timetable (~2.5 years experimental word) as it is focused on analyses of existing plant lines and transcriptomic data that can be generated efficiently. The main expense will be for sequencing and molecular biology reagents which will be covered by the £4500p.a. (max of £13.5K).
BBSRC Strategic Research Priority: Molecules, cells and systems
Techniques that will be undertaken during the project:
The student will be trained extensively in a range of cutting edge techniques spanning molecular biology, cell biology, biochemistry and bioinformatics. The student will be using microarray (or RNA-seq experiments) to generate a global expression survey of TFs; bioinformatics based analysis of results; verification and detailed expression analyses of selected targets by qRT-PCR and mRNA in situ hybridization; design of gene-silencing constructs for stable transformation; protein-protein interactions will be investigated using yeast two-hybrid techniques.Contact: Dr Sinéad Drea, University of Leicester