Genomic Approaches for Strain Improvement of Hyphal-Parasitic Fungi at University of Greenwich

Fungal pathogens are responsible for up to 16% of global crop losses, acting both pre-harvest and post-harvest as well as through mycotoxin contamination. There is a growing need for alternatives to chemical control, with emergence of pathogens that are resistant to fungicides, compounding the loss of many plant protection products due risks to human and environmental health. However, a range of beneficial fungi have been demonstrated as effective biocontrol agents for protection against insect pests and against disease-causing fungi.

Biocontrols offer an excellent environmentally favourable solution for crop protection. However, they remain less effective than chemical control alternatives. Using advanced genomics we have the opportunity to study and implement new breeding strategies for strain improvement, thus offering a greater biocontrol efficacy and persistence in the environment.

There is evidence for cryptic sexuality, parasexuality and genetic exchange within a number of biocontrol fungi. Where sexuality can be identified, this opens new opportunities for crossing experiments to (A) understand the genetic control of important traits (e.g. persistence/infection), and (B) to harness the natural genetic diversity of biocontrol populations through biocontrol breeding programmes.

At the core of this project, the student will perform bioinformatic analyses of fungal genomes to identify signatures of genetic exchange and sexuality within natural populations of biocontrol fungi (e.g. Clonostachys spp., Trichoderma spp.) and wider fungi as control species. This will be supported by lab-based study of biocontrol interactions to identify key genes in biocontrol activity, such as hyphal parasitism. Where sexuality or genetic exchange can be observed or manipulated, this will unlock new tools for breeding better biocontrols.

 Objective 1: Generate reference genome assemblies for the biocontrol agent Clonostachys rosea