EASTBIO: Functional analysis of RXLR effectors in P. rubi and P.fragariae

The UK berry industry is worth £2.2bn, with 30% (raspberry) and 64% (strawberry) market
penetration. Phytophthoras are a wide group of oomycete pathogens that rapidly destroy their plant hosts in both agricultural and natural ecosystems. In the UK, Phytophthora root rot (PRR) has devastated the raspberry industry with a >80% decline in long term field grown crops with growers unable to continue traditional soil based growing methods. Phytophthora rubi and P. fragariae are PRRs which spread through plant propagation, growth media and water flow in plantations. The RxLR family of effector proteins are a family of proteins that are delivered in host plants during infection to manipulate conditions that promote disease. All the pathogen proteins recognized by host NB-LRR-based resistances have belonged to this rapidly evolving effector family. This highlights the significance of identifying the most essential and highly conserved members of this effector family to better develop durable forms of resistance in crop plants.
We have preliminary results examining the level of conservation of >800 RxLR effectors in the genomes of 20 P. rubi isolates collected from a number of different dates and geographical locations. However, although Phytophthoras have a comparatively large number of effectors encoded in their genomes we can predict that only a fraction of these will be actually essential for virulence and expressed during an interaction with the host. In addition, RxLR transcripts can often be hard to detect in early time points of infection when there is relatively little pathogen present in the host tissues. We propose to, rather than examine gene expression of RxLRs individually by qRT-PCR, adapt our PenSeq technology (Thilliez et al., 2019, Bezanger et al., in preparation). This will allow us to both enrich for low abundance RxLR transcripts from infection timecourse samples and provide global expression analysis of RXLR effectors across a number of our favourite P. rubi isolates of interest. This would allow us to compile a ‘core’ set of highly conserved and expressed effectors which can then be cloned/synthesized into plant expression vectors to then screen for defence suppressing activities in the model plant, N. benthamiana using well established assays such as PAMP-triggered immunity cell death suppression or NB-LRR Cell Death suppression events (Gilroy et al, 2011). Using N. benthamiana as a model has already been successfully utilized to examine effector function from a number of important Phytophthora diseases, including woody species (Guo et al., 2020). The host targets of these effectors could then be examined by Y2H and Co-immunosuppression.

This project would give the chosen student the opportunity to learn from our world-leading team of experts in the field of effector biology. They will learn how to examine pathogen effector function and evolutionary biology with training in both wet lab molecular plant pathology techniques in combination with a large computational element and we would be keen to receive applicants who were interested in developing both skill sets
Application Process:
To apply for an EASTBIO PhD studentship http://www.eastscotbiodtp.ac.uk/, follow the instructions below:
Check FindaPhD https://www.findaphd.com/phds/program/bbsrc-eastbio-doctoral-training-partnership-call-for-applications-for-2021/?p1048 for our available projects and contact potential supervisors before you apply.

After you have discussed the projects of interest to you with the project supervisors, download and complete our Equality, Diversity and Inclusion survey https://edinburgh.onlinesurveys.ac.uk/eastbio-dtp-equality-diversity-inclusion-form-2021 and then fill in the EASTBIO Application Form and submit the application form plus your academic transcripts to [Email Address Removed].

Send the EASTBIO Reference Form to your two academic/professional referees, and ask them to submit these directly to [Email Address Removed] (Link to the form can be found here: http://www.eastscotbiodtp.ac.uk/how-apply-0)

If you are nominated by the supervisor(s) of the EASTBIO PhD project you wish to apply for, they will provide a Supervisor Support Statement.

All EASTBIO (online) interviews will be in the week 8-12 February 2020 with awards made the following week.