Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale
Lead Research Organisation:
National Institute of Agricultural Botany
Department Name: Centre for Research
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Planned Impact
The impact of this proposal relates to the detailed understanding of the population structure of a major wheat pathogen, yellow rust. Project outputs will impact on wheat producers, plant breeders, regulatory and testing authorities, and pathogen surveillance projects. As yellow rust is a global disease, project outcomes will have national and far-reaching international impacts. In the UK, yellow rust control is reliant on a combination of resistance and fungicide use. The latter is under increasing pressure from withdrawal of actives, or tightening regulations on use. The importance of host plant resistance is therefore likely to increase, but it must be at a reasonably high level, and reliable. This project will increase, by several orders of magnitude, the ability of surveillance projects such as the UK Cereal Pathogen Virulence Survey, to detect and characterise damaging yellow rust variants at an early stage. Such information will have immediate impacts for growers, enabling them to change variety choice, or react in season with different fungicide programmes to counter epidemics. A detailed regional understanding of virulence structure will enhance the potential for diversification of varieties, where different resistances could be deployed on a landscape scale to decrease inoculum pressure and preserve the durability of resistance traits. Plant breeders will benefit from earlier and more detailed knowledge of pathogen population structure so that alternative resistance sources can be incorporated into breeding material, and sudden "breakdown" of resistance can be avoided during commercialisation. Testing and regulatory authorities will benefit by having improved information on pathotypes for use in testing programmes. Surveillance projects, such as UKCPVS, would change approaches to use the new technologies devised in the project, becoming more efficient and of greater value to end users. The project outputs will be tested immediately in this survey work at the end of the grant, and could be implemented in routine work within a further three year period. Plant breeders would also benefit in the short term as more comprehensive and in depth undertsanding of yellow rust population structures would be immediately available.
Though targeted at yellow rust in this project, field pathogenomics could be applied to many other plant pathogens which have variable pathotypes interacting with host resistance. Virulence monitoring in cereal rusts is an international effort, with research in the US, China, Australia, Africa and Europe, and the techniques and sampling strategies investigated in the current proposal would be of value wherever cereal rusts occur.
Though targeted at yellow rust in this project, field pathogenomics could be applied to many other plant pathogens which have variable pathotypes interacting with host resistance. Virulence monitoring in cereal rusts is an international effort, with research in the US, China, Australia, Africa and Europe, and the techniques and sampling strategies investigated in the current proposal would be of value wherever cereal rusts occur.
People |
ORCID iD |
Jane Thomas (Principal Investigator) | |
Sarah Holdgate (Co-Investigator) |
Publications
Bueno-Sancho V
(2017)
Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity.
in Genome biology and evolution
Description | Initial data on genotypic and phenotypic descriptors of outbreaks of yellow rust in wheat fields. Intensive sampling of yellow rust in wheat fields has revealed new information on genotypic and pathotypic diversity which will ultimately feed into practical sampling strategies for routine surveillance work. Highly complex populations of yellow rust were recorded in small (<0.3 ha) areas of susceptile wheat cultivars in all years of monitoring. Pathotype testing revealed multiple pathotypes within an area, with some temporal changes occurring as well. Different pathotypes were present on the same leaf in some cases. This has implications both for the timing of sampling and its extent within the United Kingdom Cereal Pathogen Virulence Survey project. samplers, who mat be farmers, agronomists/advisors, breeders and researchers, are encouraged to send at least two samples from an infected field over the season, and to include leaves from different foci of infection. While this generates many more samples than can be tested pathotypically, it provides an essential resource for genotyping. Genotyping has now been included for the first time (2019) in the UKCPVS project and is aimed at identifying genotypic variants which may indicate new pathotypes, and thus be targeted for priority testing. Results will be reported in the AHDB UKCPVS 2020 report. In addition, a "short rotation" DTP student has been investigating gentotyping using the "MinION" Oxford Nanopore platform, to investigate closely related pathotypes, and this may lead to a PhD project in the autumn. Collaboration with JIC (lead partner in Pathogenomics) continues within the UKCPVS, and in an H2020 project "Rustwatch" coordinated by Aarhuis University which builds further on outcomes of the original project. |
Exploitation Route | Eventual use in routine rust survey programmes. The initial steps have already been taken with UKCPVS in 2019, and further research is underway in an H2020 project and the approach may be widely adopted in Europe |
Sectors | Agriculture Food and Drink |
Description | The findings have been used to ecourage improved sampling of yellow rust in the field for routine surveillance by industry stakeholders. Improed sampling leads to more precise information, for use by plant breeders in screening material, and for growers in understanding variety risk from yellow rust, and avoiding economic losses The findings aare used routinely in ongoing surveillance project to monitor the emergece of new yellow rust pathotypes. Genotyping helps to identify potential novel variants which may interact with wheat host rsistance |
First Year Of Impact | 2019 |
Sector | Agriculture, Food and Drink |
Impact Types | Economic |
Title | Pathogemics for yellow rust surveillance |
Description | The genotyping methods developed in the funded project are now being used routinely in a levy board funded yellow rust surveillance project. The tools developed have allowed us to genotype 96 isolates efficiently, and to identify common genetic groups. The method has also identified an genetic variant, which had an unusual pathotype, and this has now been used in field tests evaluating wheat cultivar resistance to yellow rust for the UK industry. There is thus a direct impact of the research on routine surveillance, and the work will continue in 2022. |
Type Of Material | Technology assay or reagent |
Year Produced | 2016 |
Provided To Others? | Yes |
Impact | the potential for eventual rapid screening to detect new pathotypes in a major rust pathogen, with implications for growers, breeders and academia. Further development of the method is under way to generate more precision and potentially to associate genotype with pathotype groupings |
Title | practical application |
Description | The outcomes of field pathogenomics have now been incorporated into a new rust surveillance project in the UK, commencing April 2019. The outcomes have continued to be implemented in the surveillance project (United Kingdom Pathogen Virulence Survey, funded by AHDB) during 2020. Both sampling methodologies and pathogen genotyping aspects have improved the Survey methods, based on the outcome of the funded research |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | More rapid identification of novel and potentially damaging yellow rust races. The genotyping methods for yellow rust are now routinely used in the national virulence surveillance project (UKCPVS), which has direct impact on yellow rust control by growers and agronomists. Genotyping has been used for four years, up to and including 2022, and is fully reported in the Annual Survey report (see AHDB website) |
Description | h2020 Rustwatch (multiple partners in EU) |
Organisation | Aarhus University |
Country | Denmark |
Sector | Academic/University |
PI Contribution | provision of yellow rust isolates for genotyping, testing of wide germplams resources in wheat, integrated control of yellow rust in wheat, provision of pathotype data or Gloal Rust reference Centre databases, grower and researcher workshops |
Collaborator Contribution | A similar set of activities to the above is carried out by all partneers, with some focusing on brown rust and stem rust |
Impact | Outputs re limited as yet, but pathotype data hasbeen provided to the central rust database and to date a single trial in UK has been complted screening a panel of European varieties and landraces, and a single trial on alternative control products. Outputs have been summarised at a number of workshops and agronomist conferences, and at the UKCPVS stakeholder meeting (summary level) |
Start Year | 2018 |