Understanding wheat take-all infection spread, chemical resistance and biocontrol

Vacancy details:

Supervisor: Prof Neil Hall / Dr Mark McMullan
Contact email: neil.hall@earlham.ac.uk
Co-supervisor: Prof Anne Osbourn (JIC)
Reference: HALL_E24JIF
Start date: 01 October 2024
Application deadline: 30 May 2024
Funding 4-year PhD funded by the John Innes Foundation.

Take-all is the most important root disease of wheat worldwide and is caused by the fungus Gaeumannomyces tritici. G. tritici belongs to an important group of grass-infecting pathogens including rice and wheat blast fungi (Magnaporthales, Ascomycota), but take-all of wheat is an understudied disease. 

Little is known about how far the fungus spreads and the intraspecific diversity within fields, landscapes and among continents. 

Surveillance or diagnostics for G. tritici in the field are almost non-existent. Understanding G. tritici virulence partitioning within and between populations, its spread, virulence mechanism, and its polymorphic resistance to silthiofam fungicide will also be essential to developing improved crop protection regimes.

In this PhD project, you will develop skills (GWAS and population genomics) to analyse genetic diversity in a pangenomics era. You will initially address fundamental questions on the diversity and spread of the fungus across landscapes and continents, as well as through time. This understanding will frame questions on the evolution of fungicide resistance. Finally, you will use expression analysis to test predictions from your previous work on the virulence mechanisms employed by this pathogen, as well as a closely related biocontrol agent.

This PhD studentship will benefit from Delivering Sustainable Wheat investment in re-sequencing of hundreds of G. tritici isolates sampled in the UK and globally over the last seventy years. It will also make use of a UK pangenome resource for G. tritici which has been developed by the Earlham Institute in collaboration Rothamsted Research as part of the Designing Future Wheat programme.

For further information and to apply, please visit our website: http://www.earlham.ac.uk/application-guidance

The project will be jointly supervised by Dr Mark McMullan and Prof Neil Hall at the Earlham Institute, Prof Anne Osbourn at the John Innes Centre, and conducted in close collaboration with Dr Kim Hammond-Kosack at Rothamsted Research.

Entry requirements

At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Master's degree. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).


This project is awarded with a 4-year fully funded John Innes Foundation PhD studentship. Tuition fees are covered, and a stipend will be provided for each year of the studentship (2024/5 rate will be £19,237.00). Research training support funding is available.

The John Innes Foundation Studentship is open to UK and international candidates with relevant undergraduate degrees for entry in October 2024 and offers the opportunity to undertake a fully-funded 4-year PhD research project.

Candidates will be contacted if they are selected for interview.

John Innes Foundation is committed to equality, diversity and inclusion. Students are selected without regard to age, disability, gender identity, marriage or civil partnership, pregnancy or maternity, ethnicity, religion or belief, sex or sexual orientation or social background. We value curiosity, independence of thought, plus an aptitude for research that combines laboratory work and bioinformatics.

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Neil Hall Group

The Microbial Genomics group are developing genomic methods for understanding microbial organisms.