PhD: Towards genotype-based monitoring for fungicide resistance management

University of East Anglia has an opening PhD scholarship. To be eligible, candidates must be European students. The deadline for applying is August 02, 2015. 

Evolved resistance to fungicides is a major threat to global food security. Fungicide resistance increases disease losses and imposes higher costs on growers and the fungicide industry. The implementation of validated resistance management strategies for the maximisation of the effective life of existing and new fungicides is of the upmost importance. These strategies involve the use of mixtures and alternation so that selection and rate of resistance evolution is reduced. A key aspect of these strategies is the monitoring of pathogen populations and epidemics so as to measure the prevalence and impact of resistance. To date, monitoring strongly relates to phenotypic data; i.e. field trials are carried out and pathogen isolates are tested for decreased sensitivity.

Whilst there will always be a need for phenotyping, the cost in time and money limits the effectiveness of such methods. Recent advances in gene and genome sequencing methods have brought us to the point where genotypic monitoring might be considered as a first line of investigation. The Saunders group at The Genome Analysis Centre in partnership with the John Innes Centre have recently developed an effective method based on next-generation sequencing techniques to genotype pathogen populations at high resolution. The PhD student will use these existing techniques to develop an effective, rapid genotyping platform specifically focused on monitoring genes targeted by fungicides for mutations that have been shown to induce resistance. Furthermore, the implications of any novel mutations will be investigated using lab-based assays established in the Oliver group at Curtin University, Perth, Western Australia.

This project provides a unique opportunity for the student to undertake multidisciplinary research, embedded within The Genome Analysis Centre that is a hub for innovative bioinformatics to support all computational aspects of the project and within the John Innes Centre that is an international centre of excellence in plant science to support laboratory-based experiments. The student will also work closely with the Oliver group at Curtin University who are renowned experts in the field of fungicide resistance. In addition, as an ICP CASE student they will also work closely with Syngenta a world leader in fungal disease control, at their Stein Laboratory in Switzerland. The student will spend a minimum of 3 months at Syngenta during the course of their PhD.
This 4-year BBSRC funded CASE studentship is available to successful candidates who meet the UK Research Council eligibility criteria including the 3-year UK residency requirements. These requirements are detailed in the BBSRC eligibility guide which can be found below. In most cases UK and EU nationals who have been ordinarily resident in the UK for 3 years prior to the start of the course are eligible for a full-award. Other EU nationals may qualify for a fees only award. Below is the link to the BBSRC PhD studentship eligibility guidelines which all candidates should check to confirm their eligibility for funding. The current stipend for 2015/6 is £ 14,057 per annum.
How to apply?
For full details on eligibility (qualifications and residence criteria) see the BBSRC Guide to Studentship Eligibility:
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