Dr Lindsey Compton, Prof Z Luo
Applications accepted all year round
Self-Funded PhD Students Only
About the Project
A highly motivated student is sought to train as a statistical geneticist working on 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.
By developing new experimental and statistical methods for the analysis of complex traits, this PhD project provides the opportunity to answer a broad range of interesting questions in genetics and evolutionary biology, broadly encompassing the following areas. The analysis of complex traits is complicated in many important crop species by the state of autopolyploidy. Many agricultural crops are autotetraploid, including potato, coffee, leek, sugarcane, alfalfa, as well as some economically important aquaculture animals, including Atlantic salmon and trout. In particular, cultivated potatoes (Solanum tuberosum) have become the 3rd most important crop in the world after rice and wheat, and therefore play an important role in addressing world food security. This project provides diverse opportunities to develop novel statistical methods and computational tools to enable the mapping of Quantitative Trait Loci (QTL) in autotetraploids such as potato through linkage analysis or Genome-Wide Association Study (GWAS) approaches. In addition, you may work on comparative genomic and population genetic analyses in diploids versus autotetraploids. This may be combined with experimental field trials to assess important agronomic phenotypes in potato (e.g. stress or disease resistance) and dissect the genetic basis of these traits. The results of this project will inform future autotetraploid crop breeding strategies and hence contribute to world food security.
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. Please visit my personal web page and find out more about the range of work going on in my group (http://www.statisticalgenetics.info).
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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) Chen J, Zhang F, Wang L, Leach L and Luo ZW (2018) Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species. New Phytol. doi.org/10.1111/nph.15284
2) Jiang N, Leach L, et al (2016) A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations. TAG 129:1739-57.
3) Jiang N, Wang L, Chen J, Wang L, Leach L and Luo Z (2014) Conserved and divergent patterns of DNA methylation in higher vertebrates. GBE 6(11): 2998-3014.
4) Leach LJ, Belfield E, Jiang C et al (2014) Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics 15: 276.
5) 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
6) 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.
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