Award details

Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

Reference	BB/M021904/1
Principal Investigator / Supervisor	Dr Jane Thomas
Co-Investigators / Co-Supervisors	Dr Sarah Holdgate
Institution	National Inst of Agricultural Botany
Department	Centre for Research
Funding type	Research
Value (£)	304,798
Status	Completed
Type	Research Grant
Start date	01/07/2015
End date	30/06/2018
Duration	36 months

Abstract

Wheat yellow rust disease, caused by the fungus Puccinia striiformis f. sp tritici (PST), is a devastating disease that affects wheat production worldwide. This gives a deep sense of urgency to breeders and farmers to improve surveillance. To this aim, we developed a novel approach called "field pathogenomics" for pathogen population surveillance based on high-resolution RNA-seq data acquired directly from field samples of PST-infected wheat. Our preliminary study of 39 PST-infected field samples revealed only a single PST genotype within each lesion using the distribution of read counts for biallelic single nucleotide polymorphisms. In addition we also generated genome sequence data from historical PST isolates. None of the 2013 PST field isolates showed genetic similarity to the older UK population indicating that the 2013 population is likely an exotic population that appears to have displaced the previous population. Transcriptome data was also aligned to wheat sequences flanking a set of 18,162 wheat SNPs, and for each sample we could confirm the wheat variety recorded at the point of sample collection as the most likely variety. The proposed research builds on this preliminary study to apply gene-sequencing technology to the surveillance of PST and undertake comprehensive global population genetic analyses of this important plant pathogen. The central hypothesis is that current pathology-based virulence tests only reflect a small proportion of the yellow rust genetic variation at the field level. We hypothesize that "Field pathogenomics" provides the means to gain a better understanding of the yellow rust population dynamics at the genotype level and hasten decision-making from farmers, breeders and agronomists regarding the best wheat varieties and resistances to deploy in the field. This is possible through collaboration with 13 rust pathology laboratories across 6 continents and industrial support from 6 breeding, agronomy and chemical companies and HGCA

Summary

Wheat yellow rust caused by the fungus Puccinia striiformis f. sp tritici is a substantial threat to wheat production worldwide and recently re-emerged as a major constraint on UK agriculture. Its importance to global food security is reflected by the significant contribution of wheat to the calorific and protein intake of human kind (approximately 20%). The devastating impact of this disease gives a deep sense of urgency to breeders, farmers and end users to improve surveillance. To address this, we recently developed a novel approach called "field pathogenomics" for pathogen population surveillance. This method, based on new gene sequencing technology, allows us to acquire data directly from field samples of rust-infected wheat. By implementing this approach we found that the yellow rust population across the UK underwent a major shift in recent years. Genetic analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. The overall aim of this project is to apply gene-sequencing technology to the surveillance of yellow rust and undertake comprehensive global population genetic analyses of this important plant pathogen. Currently, the assessment of genotypic diversity is not included within UK national surveillance activities for wheat rust. Our new approach enables the integration of high-resolution genotypic data into pathogen surveillance activities that is vital to improve our understanding of the genetic sub-structure within a population. The proposed research aims to: (1) Analyze the threat of potential exotic incursions of wheat yellow rust to the UK by mapping the global population structure, (2) exploit the rust genotype data (Obj. 1) to confirm outbreaks on particular wheat varieties and look for associations between pathogen genotypes and host pedigrees, (3) generate information on whether genotypic diversity shifts over time at a locality and whether early appearing rust genotypes are predictive of late season genotypes and (4) develop appropriate open-source tools to ensure all data generated herein is released into the public domain as soon as possible and in a format that is suitable for breeders, pathologists and the wider demographic. This project aims to equip the UK with the latest genomic tools, facilitate more efficient varietal development by breeders, and help reduce the environmental and economic costs associated with fungicide applications, all of which will have a positive impact on the overall competitiveness and sustainability of the UK arable industry. This will be achieved through collaboration with 13 rust pathology laboratories across 6 continents and industrial support from 6 breeding, agronomy and chemical companies and the HGCA.

Impact Summary

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 atthe 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.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Crop Science, Microbiology, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	Industrial Partnership Award (IPA)

Associated awards:

BB/M025497/1 Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

BB/M025519/1 Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

BB/M025519/2 Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

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