Impacts of agronomic practices on wheat stem diseases

Background: Wheat stem diseases, e.g. eyespot, rhizoctonia and fusarium stem-rot can cause significant yield-losses. Recent work at Rothamsted on wheat eyespot has found about 35% of ‘eyespot lesions’ were caused by other fungi. To follow up on that, the proposed PhD project would use the UK and Dk one crop health farm sites to collect stem samples in late spring-early summer, which will be sent to Rothamsted, where the student can isolate the pathogens, learn DNA sequencing methods to identify what species were present, develop diagnostic assays to improve environmental monitoring (soil, debris, airborne spores), and analyse data on the geography, varieties and agronomic practices used in the 50 UK and 50 Dk farms for patterns in the distribution and timing of stem diseases. Spore traps will be operated at strategic locations in the UK and DK to enable seasonal timing of airborne spores to be measured for the different pathogens involved. This would be a traditional plant pathology project with training on statistical regression, spore trapping, molecular diagnostic methods and DNA sequencing to equip the student with the necessary skill-set for a future plant pathology career.   

Objectives: 

• Use DNA (amplicon) sequencing to assess incidence of wheat stem diseases caused by Oculimacula, Rhizoctonia, and Fusarium species and other fungi.
• Relate species to symptom phenotype aided by imaging methods.
• Relate the incidence of wheat stem pathogens to differences in location, variety and agronomy (tillage, companion or cover crops, frequency of wheat in rotation, fungicide use, etc). 
• Use existing qPCR diagnostic assays and develop new assays where necessary to detect and quantify inoculum of wheat stem-infecting pathogens in spore trap and other environmental samples.

Novelty and Timeliness: This has been a neglected research area but will build on interesting findings of a current PhD project (practical work due to end in 2025).Background: Wheat stem diseases, e.g. eyespot, rhizoctonia and fusarium stem-rot can cause significant yield-losses. Recent work at Rothamsted on wheat eyespot has found about 35% of ‘eyespot lesions’ were caused by other fungi. To follow up on that, the proposed PhD project would use the UK and Dk one crop health farm sites to collect stem samples in late spring-early summer, which will be sent to Rothamsted, where the student can isolate the pathogens, learn DNA sequencing methods to identify what species were present, develop diagnostic assays to improve environmental monitoring (soil, debris, airborne spores), and analyse data on the geography, varieties and agronomic practices used in the 50 UK and 50 Dk farms for patterns in the distribution and timing of stem diseases. Spore traps will be operated at strategic locations in the UK and DK to enable seasonal timing of airborne spores to be measured for the different pathogens involved. This would be a traditional plant pathology project with training on statistical regression, spore trapping, molecular diagnostic methods and DNA sequencing to equip the student with the necessary skill-set for a future plant pathology career.   

Objectives: 

• Use DNA (amplicon) sequencing to assess incidence of wheat stem diseases caused by Oculimacula, Rhizoctonia, and Fusarium species and other fungi.
• Relate species to symptom phenotype aided by imaging methods.
• Relate the incidence of wheat stem pathogens to differences in location, variety and agronomy (tillage, companion or cover crops, frequency of wheat in rotation, fungicide use, etc). 
• Use existing qPCR diagnostic assays and develop new assays where necessary to detect and quantify inoculum of wheat stem-infecting pathogens in spore trap and other environmental samples.

Novelty and Timeliness: This has been a neglected research area but will build on interesting findings of a current PhD project (practical work due to end in 2025).