Harnessing the power of epidemiological modelling in the fight against a cereal killer

Lead Research Organisation: University of East Anglia
Department Name: Graduate Office

Abstract

Wheat yellow rust disease, caused by the fungus Puccinia striiformis f. sp tritici (PST), is a substantial threat to wheat production worldwide and has recently re-emerged as a major constraint on UK agriculture. We recently developed a novel approach called "field pathogenomics" for pathogen population surveillance. This method uses high-resolution genotypic data to improve our understanding of the genetic sub-structure within a population, which provides essential information on the evolutionary forces that drive pathogen evolution within an agroecosystem. However, for wheat yellow rust our understanding of the patterns of transmission and dispersal remain limited. Building effective agro-ecological models that address this lack of knowledge could contribute to a proactive early warning system for wheat yellow rust in the UK.

A mathematical model of the spatio-temporal population dynamics of yellow rust would have a number of applications, including optimizing surveillance, targeting chemical sprays and designing regional diversification schemes. Predictive models are already used by the UK Government to inform policy surrounding tree diseases. However, models are less well developed for crop pathogens. Obtaining detailed information on PST genetics through our field pathogenomics study provides an opportunity to link epidemiological modelling and genomic data, improving the predictive power of models.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011216/1 01/10/2015 30/09/2023
1771866 Studentship BB/M011216/1 01/10/2016 30/09/2020 Vanessa Bueno Sancho
 
Description I designed a set of genetic markers that can be used to genotype field-collected yellow rust (a disease that affects wheat) isolates and determine which race they belong to. Using this, we were able to genotype and study the yellow rust population in the UK in 2016 and 2017.
Exploitation Route People can use this set of markers to identify yellow rust genetic races in the future.
Sectors Agriculture, Food and Drink

 
Description Pathogenomics Workshop at the BGRI Conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact At the beginning of The Borlaug Global Rust Initiative conference in Morocco (April 2018), we organised a Pathogenomics Workshop in which we taught other researchers how to analyse sequencing data to gather phylogenetic information. We were able to teach people from different backgrounds (from PhD students to PIs) skills from Linux command line to data quality analysis, aligning tools, SNP calling and Phylogenetic analysis. Also, the people who attended the workshop were from all over the world and especially from areas in which they don't have access to this type of training.
Year(s) Of Engagement Activity 2018
 
Description Python course for summer students 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Every summer, the John Innes Centre organises a summer school for a selected group of students. These students come to our institute to carry out a research project and they are also taught, by PhD students on side, several courses. One of the courses was a Python programming course.Three other students and me were in charge of organising this python course and taught it to the students.
This helped me improve my communication skills and also learned how to teach a programming language to an audience that had never coded before.
Year(s) Of Engagement Activity 2016,2017
 
Description Thought for Food Competition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact We entered the Thought for Food competition by designing an idea to help feed the growing population. We were selected to go to the conference (in Amsterdam) to give a short talk about how our business idea could help the communities. Our project consisted in a portable device to analyse soil components to then determine whether the soil quality was good enough to do urban gardening. Besides, we were aiming to create a community of urban gardeners in cities to promote this practice and reduce transport contamination.
Year(s) Of Engagement Activity 2017
 
Description Three-horiszons, Agritech East Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact People that were in the Agricultural business came to the institute to have a discussion panel about how research can help us improve agriculture. We also discussed the limitations in current agriculture and the lack of communication in many cases between industrial partners and researchers, which is why this type of events are so beneficial
Year(s) Of Engagement Activity 2016
 
Description Youth STEMM Mid-Term conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Pupils from different schools around Norwich area came to the John Innes Centre to learn about the science that we do here. We had several stands in which we showed them the research that we do in a very interactive way. We had the opportunity to explain the importance of the work we carry out and the students enjoyed getting involve in the activities and learning all about our research. They asked many questions and at the end they had a good understanding of our work
Year(s) Of Engagement Activity 2017