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PhD Research Project

Polyploidy-related structural and functional changes in the Arabidopsis genome.


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University of Birmingham
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College of Life Sciences

School of Biosciences
Dr L Leach
Applications accepted all year round
Competition Funded PhD Project (Students Worldwide)

My research interests lie in the dissection of complex trait phenotypes in human, plant and animal populations into their underlying genetic components. This central problem in statistical genetics consists of multiple interrelated parts, from genetic and epigenetic studies to identify genetic variants involved, transcriptomics to explore the genome-wide expression patterns, to the related fields of proteomics and metabolomics. Integrating knowledge from each level of information has the potential to build realistic understanding of the molecular networks underpinning complex trait variation.

Advances in next generation sequencing (NGS) technologies have enabled a high- throughput genome-wide approach to unravelling the genetic components of phenotypic variation at an unprecedented level of resolution. The rapid pace at which new sequencing technologies are emerging is generating a growing disparity between the rate of data generation and its full and biologically meaningful analysis. I am interested in keeping pace with these advances by developing novel methodological and analytical approaches to integrate NGS into theoretical and empirical studies of complex trait genetics.

This PhD project will focus on the structural and functional effects of polyploidy on the genome of the model plant Arabidopsis thaliana. Polyploid organisms possess multiple copies of the genome and display sophisticated patterns of chromosome behaviour in comparison to their diploid counterparts. As such, progress in the genetic study of these species lags far behind the study of diploid species, and yet progress is essential given that many of our agriculturally most important crops are polyploid, including bread wheat, potato, cotton, and oil-seed rape. The aim of the project will be to explore the consequences of polyploidy for meiotic recombination. Meiosis is a crucial process of cell division in all sexually reproducing organisms, in which recombination creates the genetic variation that is the raw material for all plant and animal breeding. The project will use a combination of laboratory and computer-based work to explore the frequency and genome-wide distribution of recombination in A. thaliana at diploid, allotetraploid and autotetraploid levels. This will involve generating large diploid and polyploid plant populations and analysing high-throughput molecular marker datasets (NGS). The application of this work will involve exploring the feasibility of artificially manipulating genome recombination for gene mapping and for generating novel plant varieties in breeding programs of essential food crops. This work will answer some fundamental questions in genome biology and help to address the urgent food security crisis currently facing the growing human population.

Applications are encouraged from graduates with backgrounds in any of the following disciplines: biology, bioinformatics, statistics, mathematics and computer science. The ideal candidate will have a passion for genetics and an aptitude for statistics and large-scale data analysis.

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To find out more about studying for a PhD at the University of Birmingham, including full details of the research undertaken in each school, the funding opportunities for each subject, and guidance on making your application, you can now order your copy of the new Doctoral Research Prospectus, at: www.birmingham.ac.uk/students/drp.aspx
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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 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.


Funding Notes:

All applicants should indicate in their applications how they intend to fund their studies. We have a thriving community of international PhD students and encourage applications at any time from students able to find their own funding or who wish to apply for their own funding (e.g. Commonwealth Scholarship, Islamic Development Bank).

The postgraduate funding database provides further information on funding opportunities available http://www.birmingham.ac.uk/postgraduate/funding/FundingFilter.aspx and further information is also available on the School of Biosciences website http://www.birmingham.ac.uk/schools/biosciences/courses/postgraduate/phd.aspx


References:

1) Jiang, N., Wang, M., Jia, T., Leach, L.J., et al. (2011). A robust statistical method for association-based eQTL analysis. PLoS One 6(8): e231912. doi:10.1371/journal.pone.0023192.
2) Wang M., Jiang N., Jia T., Leach L.J., Cockram J., Thomas B., Ramsay L., Waugh R. and Luo Z.W. (2011). Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars. Theor. Appl. Genet. doi 10.1007/s00122-011-1697-2.
3) Leach, L.J., Wang, L. Kearsey, M.J. and Luo, Z.W. (2010). Multilocus tetrasomic linkage analysis using Hidden Markov chain model. PNAS. 107: 4270 – 4274.
4) Lu, C., Hu, X., Wang, G., Leach, L.J., et al. (2010). Why do essential proteins tend to be clustered in the yeast interactome network? Molecular Biosystems. doi: 10.1039/b921069e.
5) Jiang, N., Leach, L.J., et al. (2008) Methods for evaluating gene expression from Affymetrix microarray datasets. BMC Bioinformatics. 9:284.
6) Leach, L. J., Zhang, Z., Lu, C.Q., Kearsey, M. J. and Luo, Z. W. (2007). The role of cis regulatory motifs and genetical control of expression in the divergence of yeast duplicate genes. Mol. Biol. Evol. 24(11): 2556-2565.
7) Hu, X.H., Wang, M.H., Tan, T., Li, J.R., Leach, L. et al. (2007). Genetic dissection of ethanol tolerance in budding yeast S. cerevisiae. Genetics. 175:1479-1487.
8) Luo, Z.W., Zhang, Z., Leach, L. et al. (2006). Constructing genetic linkage maps under a tetrasomic model. Genetics. 172: 2635-2645.
9) Lu, C., Zhang, Z., Leach, L. et al. (2006). Impacts of yeast metabolic network structure on enzyme evolution. Genome Biology. 8:407.




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