Towards genotype-based monitoring for fungicide resistance management
Lead Research Organisation:
University of East Anglia
Department Name: Graduate Office
Abstract
Evolved resistance to fungicides is a major threat to global food security. Fungicide resistance increases disease losses and imposes higher costs on growers and the fungicide industry. The implementation of validated resistance management strategies for the maximisation of the effective life of existing and new fungicides is of the upmost importance. These strategies involve the use of mixtures and alternation so that selection and rate of resistance evolution is reduced.
A key aspect of these strategies is the monitoring of pathogen populations and epidemics so as to measure the prevalence and impact of resistance. To date, monitoring strongly relates to phenotypic data; i.e. field trials are carried out and pathogen isolates are tested for decreased sensitivity. Whilst there will always be a need for phenotyping, the cost in time and money limits the effectiveness of such methods.
Recent advances in gene and genome sequencing methods have brought us to the point where genotypic monitoring might be considered as a first line of investigation. The Saunders group at The Genome Analysis Centre in partnership with the John Innes Centre have recently developed an effective method based on next-generation sequencing techniques to genotype pathogen populations at high resolution. The PhD student will use these existing techniques to develop an effective, rapid genotyping platform specifically focused on monitoring genes targeted by fungicides for mutations that have been shown to induce resistance. Furthermore, the implications of any novel mutations will be investigated using lab-based assays established in the Oliver group at Curtin University, Perth, Western Australia.
This project provides a unique opportunity for the student to undertake multidisciplinary research, embedded within The Genome Analysis Centre that is a hub for innovative bioinformatics to support all computational aspects of the project and within the John Innes Centre that is an international centre of excellence in plant science to support laboratory-based experiments. The student will also work closely with the Oliver group at Curtin University who are renowned experts in the field of fungicide resistance. In addition, as an ICP CASE student they will also work closely with Syngenta a world leader in fungal disease control, at their Stein Laboratory in Switzerland. The student will spend a minimum of 3 months at Syngenta during the course of their PhD.
A key aspect of these strategies is the monitoring of pathogen populations and epidemics so as to measure the prevalence and impact of resistance. To date, monitoring strongly relates to phenotypic data; i.e. field trials are carried out and pathogen isolates are tested for decreased sensitivity. Whilst there will always be a need for phenotyping, the cost in time and money limits the effectiveness of such methods.
Recent advances in gene and genome sequencing methods have brought us to the point where genotypic monitoring might be considered as a first line of investigation. The Saunders group at The Genome Analysis Centre in partnership with the John Innes Centre have recently developed an effective method based on next-generation sequencing techniques to genotype pathogen populations at high resolution. The PhD student will use these existing techniques to develop an effective, rapid genotyping platform specifically focused on monitoring genes targeted by fungicides for mutations that have been shown to induce resistance. Furthermore, the implications of any novel mutations will be investigated using lab-based assays established in the Oliver group at Curtin University, Perth, Western Australia.
This project provides a unique opportunity for the student to undertake multidisciplinary research, embedded within The Genome Analysis Centre that is a hub for innovative bioinformatics to support all computational aspects of the project and within the John Innes Centre that is an international centre of excellence in plant science to support laboratory-based experiments. The student will also work closely with the Oliver group at Curtin University who are renowned experts in the field of fungicide resistance. In addition, as an ICP CASE student they will also work closely with Syngenta a world leader in fungal disease control, at their Stein Laboratory in Switzerland. The student will spend a minimum of 3 months at Syngenta during the course of their PhD.
People |
ORCID iD |
| Diane Saunders (Primary Supervisor) |
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/N503964/1 | 01/01/2016 | 28/02/2017 | |||
| 1719742 | Studentship | BB/N503964/1 | 01/01/2016 | 31/12/2019 |
| Description | Every year our crops come under attack from cereal pathogens, which reduces the yield and the economic viability of growing crops. Without the use of disease control measures, up to 50% of crops could be lost to fungal pathogens alone costing the UK economy £1.3 billion annually. Fungicides are one of the main methods of disease control however fungicides are now under threat from fungal pathogens developing fungicide resistance. This has become more prevalent in recent years as we have moved away from the application of multisite fungicides, due to high levels of off target effects, in favour of single site fungicides which can easily be overcome by a single mutation within the fungicide target site. The single site fungicides include de-methylation inhibitors (DMIs) which target the CYP51 gene. This class has been overcome by a number of mutations which confer low levels of resistance but have an additive effect on the level of fungicide resistance. The most well characterised of these mutations is the Y137F mutation within Zymoseptoria tritici (Septoria leaf blotch). Using data collected from the Field Pathogenomics Study conducted by the Saunders' Lab we have found 6 isolates from New Zealand which contain a Y134F mutation which is homologous to that of Z. tritici. Other fungal pathogens have a homologous mutation but it has never been described before in Yellow Rust (Puccinia striiformis f. sp. tritici). The aim of this project is to determine whether the Y134F mutation does indeed confer fungicide resistance to DMIs. This will be achieved using fungicide spray tests to calculate the EC50 of the New Zealand isolates and compare them to similar experiments in the literature. This project also involves the development of a high-throughput genotyping method that is capable of detecting fungicide resistance mutations. The method is currently set up to monitor several genes that are the targets of different fungicide compounds from multiple economically important fungal pathogens. This can be used, once developed, by industrial companies as part of their monitoring platform to determine the levels of fungicide resistance in the region and enable the processing of a larger number of field samples in a reduced amount of time. This could also be integrated into an early warning system for farmers to advise them which fungicides to apply to best protect their crops. |
| Exploitation Route | Inform farmers how to adapt their current fungicide management strategies to still allow for effective control. |
| Sectors | Agriculture, Food and Drink |
| Description | Genotype-based monitoring for fungicide resistance management |
| Amount | £11,213 (GBP) |
| Organisation | Syngenta International AG |
| Sector | Private |
| Country | Switzerland |
| Start | 02/2020 |
| End | 05/2020 |
| Title | Mobile and Real-Time Plant Disease Diagnostics genotyping platform |
| Description | The MARPLE method allows the identification of Yellow Rust races using an in-field, mobile genotyping platform. The genotyping is performed via sequencing Oxford Nanopore's MinION platform which is a small and portable sequencing device the size of a chocolate bar which can easily be taken into the field, something that would have been impossible using the Illumina platform. The method itself involves DNA extraction, PCR amplification of genotype-specific genes from the Yellow Rust genome and library preparation for the MinION sequencing platform. All steps within the method were optimised so they could be done in labs or in-field where there is little or no access to electricity, with materials that could be easily obtained and that didn't require cold chain infrastructure or consumables which are required to be frozen or refrigerated. |
| Type Of Material | Biological samples |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | A pilot scale project for the MARPLE method has been set up and tested in Ethiopia. A team from my lab, including myself, went to Ethiopia to showcase this method could be implemented to assist farmers within the region. Ethiopia already has a pre-existing early warning system set up to inform farmers if there are any new races of Yellow Rust in the region but samples are currently sent to other countries for analysis which delays the release of the warning. By using the MARPLE method, information about the races of Yellow Rust found in Ethiopia could be communicated to farmers within a matter of weeks rather than months. This will enable the farmers to respond by planting wheat varieties that are resistant to the race or spray fungicides as precautionary measure. As part of this project we also hosted an Ethiopian scientist within our lab for 6 months which enabled us to train them in the MARPLE method. The method is now being used in Ethiopia and the resulting Yellow Rust race information incorporated into the warning system. |
| Description | Field Trial Design and Sampling |
| Organisation | Syngenta International AG |
| Country | Switzerland |
| Sector | Private |
| PI Contribution | I am developing a method which could be used by Syngenta to genotype fungal samples for fungicide resistance mutations in a high throughput manor to replace the currently time consuming phenotype data that is currently collected. |
| Collaborator Contribution | In order to test this method, Syngenta have designed and collected field trial samples which will also be used to answer how the gain of fungicide resistance is effected by different environmental pressures. |
| Impact | I have been trained in how to isolate fungal isolates and undertake fungicide sensitivity assays. This is not multi-disciplinary. |
| Start Year | 2016 |
| Description | AgriTech East Three Horizons 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 | This event brought together people from crop research from multiple institutes, industrial partners and people from the agricultural industry including breeders and farmers to discuss issues currently facing agriculture. I helped run a group at the workshop which looked at what steps we could take through technological advancement as part of the wider community to address these problems. |
| Year(s) Of Engagement Activity | 2016 |
| Description | BGRI workshop conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | BGRI conference - I was an invited Keynote speaker and three further talks were given by my group. This led to many follow-up conversations. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Breeders Day Event, Conference Centre, JIC |
| 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 | This event brought together scientists, plant breeders, agronomists and those in the agricultural sector to discuss issues currently facing agriculture. During the event, scientists from the John Innes Centre gave presentations about the work they are undertaking in collaboration with some of the breeders and how this work would benefit the wider agricultural community. I had a poster during the networking sessions before and after the talks which allowed me to communicate my work and that of the lab group as a whole. |
| Year(s) Of Engagement Activity | 2016 |
| Description | MARPLE genotyping method demonstration and training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | A team from my lab, including myself, went to Ethiopia to train local scientists in a new genotyping method that is capable of determining Yellow Rust races. During the visit I demonstrated the method using samples that the Ethiopian scientists had collected from the field. As part of the demonstration, I was able to teach the method to multiple scientists the method and help them understand how the method could be used within their own research. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://acaciaafrica.org/marple-diagnostics-a-pioneering-step-in-ethiopian-wheat-rust-management/ |
| Description | Poster presentation at 19th International Reinhardsbrunn Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I was awarded a poster presentation at the 19th International Reinhardsbrunn Symposium to showcase some of the work I had performed as part of my PhD. The poster detailed my work to optimise a high-throughput system of monitoring for the presence of fungicide resistance mutations within cereal pathogens which is able to identify fungicide resistance mutations within multiple pathogens simultaneously using one unified method. This information can then be used to inform tailored fungicide management strategies to different areas to reduce the overall application of fungicides and prolong the efficacy of fungicides that are currently in use. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation at International Symposium of Cereal Leaf Blights |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | I was awarded a talk at the International symposium of cereal leaf blights to present the work I had performed as part of my PhD. I gave a presentation which detailed the problems of fungicide resistance within fungal pathogens of cereal crops, the importance of monitoring these pathogens for the presence of fungicide resistance strategies and the method that i had developed as part of my PhD which would enable the identification of such mutations within a high-throughput manner. This information can then be used to inform tailored fungicide management strategies to different areas to reduce the overall application of fungicides and prolong the efficacy of fungicides that are currently in use. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation to visiting students from Belgium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | Agricultural Students from Hogeschool in Belgium visited the John Innes Centre as part of an overseas trip to see the British Agricultural system and visited various places in Norfolk. During their visit to JIC, I gave a presentation on the problems of fungicide resistance, how this resistance can be managed and how my project can help this. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Youth STEMM Award Conference Conference Centre, JIC |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | The Youth STEMM award is aimed at getting children more interested in a career in a scientific field. As part of this event my lab group set up an interactive stand with posters showcasing our work. Activities on the stand included taking mock field samples from wheat plants, first hand experience of yellow rust spores and a story board of microscope images showing yellow rust infection. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Youth STEMM Award Conference, Conference Centre, JIC |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | The Youth STEMM award is aimed at getting children more interested in a career in a scientific field. As part of this event my lab group set up an interactive stand with posters showcasing our work. Activities on the stand included games aimed at teaching the children about selective breeding of crops, fungal pathogens that infect crops, give first-hand experience of yellow and brown rust spores and a story board of microscope images showing yellow rust infection. |
| Year(s) Of Engagement Activity | 2019 |