Understanding the rules of life

Category: Standard Studentships

Understanding the interplay of plant genetics and microbiome for improved disease resistance

Project No. 2450


Primary Supervisor

Dr Matevz Papp-Rupar – NIAB East Malling


Dr Tomislav Cernava – University of Southampton

Dr Mark Chapman – University of Southampton


Control of pests and disease in food production have so far relied on high pesticide inputs resulting in significant negative environmental impact.

Use of biocontrol microorganisms to replace chemical pesticides is more sustainable but its efficacy can vary significantly depending on the plant host and environment and is thus often unreliable. Breeding has so far been focused mainly on improving yield, quality and introgression of resistance genes which pest and pathogens overcome through rapid evolution. This project will explore a new paradigm in pest and pathogen control, namely, breeding of crops to be able to assemble better phyllosphere microbiomes which could provide disease resistance and other beneficial traits.

This project will focus on apple canker (Neonectria ditissima), a major pathogen of apple worldwide. It is causing tree mortality, reducing yields and is extremely difficult to control with currently available methods. In our previous work we identified and isolated specific apple endophytes from bacterial genus Sphingomonas of which the abundance was associated with several quantitative trait loci (QTL) in the apple genome. The same endophytes also positively correlate with healthy tree canopy size on canker-inoculated trees and they were significantly more abundant in resistant apple scions in a separate experiment.

The aim of this project is to validate the QTLs associated with Sphingomonas abundance in apple, to pinpoint genetic and potentially metabolic mechanisms of apple – Sphingomonas interactions and also study the wider significance of Sphingomonas in plant disease control. The main approaches will include transcriptomics and microbiome analysis, microbial survival and disease control efficacy in plants, literature meta-analysis and others. The project will contribute to fundamental understanding of plant-microbiome interactions and has the potential to provide novel breeding markers for establishing and maintaining a functional microbiome.

Experience in plant-microbe interactions, genetics, bioinformatics or the use of high-performance computing is desired but not essential.