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Understanding the molecular mechanisms of plant disease resistance

Primary Supervisor: Dr Graeme Kettles, School of Biosciences

Secondary supervisor: Prof. Rob Jackson

PhD project title: Understanding the molecular mechanisms of plant disease resistance

University of Registration: University of Birmingham

Project outline:

Plant pathogens pose major challenges both to crop production and to the resilience of natural ecosystems. How we protect plants from their most damaging pathogens is therefore vital to a future of sustainable agriculture and forestry.

The Kettles laboratory combines molecular biology, protein biochemistry and computational approaches to study how fungal and bacterial pathogens cause disease. We are interested in how secreted proteins, termed effectors, allow pathogens to suppress plant immunity and cause disease. Similarly, we investigate how the plant innate immune system functions at the molecular level to recognise effectors and confer resistance.

Two PhD projects are currently available on the following topics;

Project 1. Functional characterisation of immune receptors in oak

Work from model and crop systems has shown that receptor-like proteins (RLPs) and nucleotide-binding domain and leucine-rich repeat (NLR) proteins play essential roles in allowing plants to recognise pathogens. Triggering of these proteins, allows plants to rapidly mount effective immune responses that block pathogen invasion. Many long-lived tree species (including oak) show significant expansion and diversification of these protein families, suggesting an important role in allowing trees to resist many pathogens encountered over a long lifespan1. We have recently screened oak populations to identify individuals that are highly resistant or susceptible to infection with bacteria associated with Acute Oak Decline (AOD) or oak powdery mildew. Our aim is to understand the genetic basis underpinning resistance against these pathogens.

This project will utilise RNAseq data from infected individuals to identify gene expression signatures associated with disease resistance or susceptibility to these two diseases. The student will design follow-on experiments to assess the impact of overexpressing or silencing specific defence genes on pathogen virulence. These experiments will be performed using Agroacterium-mediated transient expression and Virus-Induced Gene Silencing (VIGS) in the model plant Nicotiana benthamiana. These systems will also be adapted for performing experiments in oak leaves and stems. The student will also perform experiments designed to investigate molecular interactions between disease resistance proteins and pathogen effectors. The student will gain experience of such techniques as co-immunoprecipitation, yeast-2-hybrid and proximity labelling.

Project 2. Microbial warfare in the plant microbiome

Plants are colonised by complex communities of microorganisms (microbiomes) that perform functions critical to plant health. Natural microbiomes offer protection from pathogens, whilst disruption of these communities can lead to opportunities for pathogen proliferation. This project will focus on the above-ground (phyllosphere) microbial communities that colonise plants. The objective is to understand how microbes within the phyllosphere interact to ensure their own survival, and how this impacts plant health. This project will focus on the interactions between the oak tree microbiome, the bacteria associated with AOD and the oak powdery mildew fungus.

It has recently been demonstrated that pathogen effectors have roles in microbiome manipulation, in addition to their role in suppressing plant immunity2,3. This project will investigate the importance of this process to both AOD and powdery mildew infection. Specifically, the student will examine how effectors deployed via the bacterial Type 3 and Type 6 secretion systems contribute to microbiome manipulation and suppression of host immunity.

For informal enquiries, please contact Please state on the application form whether you are applying for project 1 or project 2.


  1. Plomion et al. Nat Plants. 2018 Jul;4(7):440-452.
  2. Kettles et al. New Phytol. 2018 Jan;217(1):320-331.
  3. Snelders et al. Nat Plants. 2020 Nov;6(11):1365-1374.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science & Understanding the Rules of Life: Microbiology & Plant Science

Techniques that will be undertaken during the project:

Both projects listed feature wet-lab and computational components. Students will gain extensive experience of techniques related to functional genomics, molecular biology, biochemistry, fungal and bacterial pathogen handling and methods associated with protein expression and purification. In addition, we have in place pathogen bioassays for testing virulence of all pathogens used in the lab. Both projects will involve analysis of genomics and transcriptomics datasets involving using R and programming languages such as Python.

Contact: Dr Graeme Kettles, University of Birmingham