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.
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.
Organisations
People |
ORCID iD |
| Diane Saunders (Primary Supervisor) | |
| Vanessa Bueno Sancho (Student) |
Publications
Bueno-Sancho V
(2021)
Aeciospore ejection in the rust pathogen Puccinia graminis is driven by moisture ingress.
in Communications biology
Bueno-Sancho V
(2019)
K-PIE: using K-means algorithm for Percentage Infection symptoms Estimation
in Zenodo
Bueno-Sancho V
(2017)
Field Pathogenomics: An Advanced Tool for Wheat Rust Surveillance.
in Methods in molecular biology (Clifton, N.J.)
Bueno-Sancho V
(2017)
Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity
in Genome Biology and Evolution
Islam M
(2016)
Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae
in BMC Biology
Lewis CM
(2018)
Potential for re-emergence of wheat stem rust in the United Kingdom.
in Communications biology
Radhakrishnan GV
(2019)
MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens.
in BMC biology
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011216/1 | 01/10/2015 | 31/03/2024 | |||
| 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. I have also made progress in understand the mechanism of release of a rust fungi that has never previously been described before. Finally, I have developed a model to inform about the risk of planting barberries near wheat fields, with a website for the public to use. This would be helpful for ecologist working on the barberry moth that would like to plant bushes without posing a risk to UK agriculture |
| Exploitation Route | People can use this set of markers to identify yellow rust genetic races in the future. The butterfly conservation group could use my model to decide best places for barberry planting in the UK. |
| Sectors | Agriculture, Food and Drink |
| Description | European Researchers' Night at Peterborough Museum |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | On the 27th of September, I participated at the European Researchers' Night at Peterborough Museum. Peterborough Museum organised a night to showcase how collaborative work of scientists around the world is helping us to understand the interconnected nature of our planet and to conserve the web of natural connections that we depend on to survive. This was very related to my research, since I am working on a project that cares about helping agriculture while maintaining species diversity and taking into account conservational programmes. We had a stand with photos, samples and information about the research and had to explain my project to a general audience. I had to organise the stand, get all the material and display it in a way that would engage non scientists. I also had to overcome the difficulty of explaining a very specific project to an audience who don't necessarily know biology. Thus, I learned how to engage people in my research and how to explain it in simple terms. Besides, I got to talk to other researchers and learned about other projects taking place around the UK. |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Talk at the Early Career Researchers Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I went to the ECR Conference taking place in Barcelona (November, 2019) and gave a talk about my project. I created an awareness of my project and the importance of it. I also got to improve my communication skills and talked about my research which also allowed me to have interesting discussions with other scientists. Their questions helped me see what people were more interested in and also identify the weaknesses of my research that I could afterwards improve. |
| Year(s) Of Engagement Activity | 2019 |
| 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 |