Wheat is a major UK food crop with an annual value of approximately £1.2 bn. In order to meet increasing worldwide demand for wheat a step change in breeding methods is required. As part of our BBSRC wheat genomics grant, funded at the start of 2009, we aim to sequence the genic regions of four UK breeding lines Avalon, Cadenza, Rialto and Savannah, identifying single nucleotide polymorphisms (SNPs) between these varieties. Although, with recent technology advances, this number may increase to 30. In this PhD project we propose to take a first step in interpreting the biological relevance of some of the varietal SNPs identified. The project will have two components, one bioinformatics and one lab based RNAseq component. The bioinformatics component will aim to develop a pipe-line for scoring the significance of non-synonymous SNPs based on sequence conservation across monocot species. Similar genome wide approaches have already been used in other species (Burke
2007). Here, we will specifically focus on key pathways associated with yield, fitness and stress. Secondly, an RNAseq experiment will investigate differential gene expression between the four varieties. This will provide data on whether a SNP containing variant is expressed, a key factor in an allohexaploid genome such as wheat. It will also allow us to identify potential pathways to target for identification of useful SNPs. We will use loci alignment methods to identify true isofunctional orthologs of genes with promising SNPs and use gene proximity data along with pathway mapping for gene functional characterization. The output of this project would be a set of valuable candidate SNPs, the exploitation of which we would ensure, via ongoing collaboration with the UK wheat breeding community and NIAB.
The project will provide training in the areas of:
Next generation sequencing:
The student will be trained in next-generation DNA sequencing, in particular in the bioinformatics analysis associated with handling the massive amounts of data that the 454 and SOLiD sequencing systems generate (
Training will be provided in basic script writing to develop pipelines for dealing with large data sets, they will also attend specific modules from the Bioinformatics MSc run at Liverpool.
Transferring knowledge between model and crop species:
The project will involve identifying wheat homologs of Arabidopsis/rice genes in key pathways. Thus, giving training in how to transfer knowledge and understanding between models and crops. The project will provide training in plant genomics and crop genetics. The student will also attend UK crop science workshops and networking meetings. For more information please contact Dr Anthony Hall or visit the centre website ( http://www.liv.ac.uk/cgr/index.htm
References: Burke, D.F., Worth, C.L., Priego, E.M., Cheng, T., Smink, L.J., Todd, J.A. and Blundell, T.L.
(2007) Genome bioinformatic analysis of nonsynonymous SNPs.
Schuster S.C. (2008).
Next-generation sequencing transforms today's biology.
, 16 - 18 Applications are invited from students who either hold or expect to obtain, a First or Upper Second class Honours degree in a relevant subject. Application by email, indicating the project(s) of interest (and supervisors) in priority order, giving the reasons for this, together with a c.v. including the names and contact details of two academic referees, should be sent as soon as possible to: Mrs. Linda J. Marsh, Research Support Office, School of Biological Sciences, The Life Sciences Building, Crown Street, Liverpool L69 7ZB (email:
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, Fax: 0151 795 5122). Review of applications begins from mid February 2010. Please indicate where you first saw the project(s) advertised.