Early diagnosis and management of Phytophthora infection in larch and other forestry trees (PhD Scholarship)

Early diagnosis and management of Phytophthora infection in larch and other forestry trees

Aberystwyth University, IBERS

Project ID: AU30012
Annual Stipend: £14,340
Application Deadline: 20th November 2017

Phytophthora ramorum is a non-native pathogen that can infect a range of commercially important tree species including Japanese larch, Douglas fir, beech and oak. In the UK, Japanese larch has proved to be particularly susceptible to the disease and its spread has led to the death of large areas of larch woodland. There is currently no cure for P.ramorum infection. The removal of infected trees and pre-emptive clear felling remains the most effective means of control. Early diagnosis is therefore an essential tool in the management of the disease.

Biological research at the turn of the century placed heavy emphasis on genome sequencing. However, more recently focus has shifted from a simple description of what genes are present and the identity of their DNA code (genomics) towards a better understanding of how these tens of thousands of genes that make up a species are controlled;a discipline known as epigenetics. Among the many systems of epigenetic control, only one is known to pass between generations; DNA methylation. In this system, gene regulation involves minor chemical changes occurring to the DNA without changing the DNA code. Where and how many of this type of modification takes place (known as DNA methylation marks) affects the ability of the gene to become active. One key property of DNA methylation is that it is easy to methylate a piece of DNA but difficult to remove the methyl group. This means that methylations accumulate during development or ageing, but also accumulate through exposure to biotic or abiotic stresses. This last feature means that we can use the pattering of large numbers of these methylation marks to diagnose various sorts of stress exposure, including exposure to pathogens and pests. Crucially, although the production of eggs and sperm does remove many of these methylation marks, a subset of which are inherited between generations.

The first part of this PhD studentship will use DNA methylation profiling techniques to assemble a set of markers that allow early detection of infection and subsequent progression of the disease. The efficacy of these epigenetic markers as diagnostic tools for the detection of the disease in asymptomatic infected trees will be verified in a time-course study of trees locations where the disease is endemic. Given that the DNA methylation is the only mechanism of epigenetic control of gene expression that can be transmitted between generations, the project will then screen for transmission of epigenetic reprogramming of infected trees into the filial generation. In this section of the work, the epigenetic profiles and resistance to infection of seedlings progenies collected from trees that have been exposed to the disease will be compared to a control set. Thus, the outputs of the project will not only be a new capability to detect infected trees at an early stage of infection (allowing their removal), but potentially also a route by which more tolerant trees may be rapidly generated from sites of infection. Both outcomes offer considerable benefits to NRW and the Welsh Assembly Government.

Knowledge Economy Skills Scholarships (KESS 2) is a pan-Wales higher level skills initiative led by Bangor University on behalf of the HE sector in Wales. It is part funded by the Welsh Government’s European Social Fund (ESF) convergence programme for West Wales and the Valleys.

The successful candidate will need to be resident in the convergence area on registration, and must have the right to work in the region on qualification. The successful applicant should have a minimum of a 1st or good 2:1 in a relevant degree, and be available to take up the studentship by January 2018. The project is part-funded by the European Social Fund (ESF) through the European Union’s Convergence programme administered by the Welsh Government. KESS II PhD scholarships are collaborative awards with external partners. (Applicants need to only apply, they do not need to search for partners).

To apply, please submit the following to the Postgraduate Admissions Office (address below) by 20th November 2017.

  1. A completed Research Programme Application Form, two references. Application and reference forms may be downloaded from http://www.aber.ac.uk/en/postgrad/howtoapply/
  2. A completed KESS II Participant proposal form (put the reference number AU30012 in the top right hand box of the application form) and an up-to-date CV. KESS II application forms are available to download at the link below.


  1. A PhD proposal of up to 1,000 words where you expand on your experience and interests and describe why you are a good candidate for this research studentship. Please refer to the Project Description.

Value of Award: A stipend of £14,340 (rising in accordance with inflation for the remaining two years). Each scholarship has an additional budget for travel, equipment/consumables and training to support your research. KESS II PhD Scholarship holders do not pay fees.

Length: Full-time for 3 years. (Theses must be submitted 6 months after the funded three year study period.)

Training: The achievement of a Postgraduate Skills Development Award (PSDA) is compulsory for each KESS II scholar (The PSDA is based on a 60 credit award, which is an additional award to the PhD).

Eligibility: To be eligible to apply for a KESS II award, you must be resident, upon starting the scholarship, in the Convergence Area of Wales and you must be able to take paid employment in the Convergence area on completion of the scholarship.

The Convergence Area means the following counties of Wales:

Isle of Anglesey
Neath Port Talbot
Rhondda Cynon Taff

For further student eligibility criteria related to the individual projects, please view the details of the individual project above.

Informal enquiries should be made to Prof. Mike Wilkinson at mjw@aber.ac.uk  or 01970 823204

Address for applications:

Postgraduate Admissions Office
Recruitment & Admissions
Student Welcome Centre
Aberystwyth University
SY23 3FB

Quote Reference AU30012

Closing date for applications 20th November 2017