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

Lead Research Organisation: Earlham Institute
Department Name: Research Faculty

Abstract

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.

Technical Summary

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

Planned Impact

PI Saunders will lead the impact plan that will be an agenda item at monthly project meetings with Co-I's. All Co-I's have excellent track records in communicating the outcomes of their research to a broad audience and sharing tools, resources and code in a free and open manner. The PI and Co-I's also are regularly invited to speak about their research at national/international meetings and at various other venues.

Beneficiaries include:

Those involved in wheat yellow rust surveillance such as the UK cereal pathogen virulence survey (funded by Fera and the HGCA). They will benefit from development of high-resolution genotyping methods that will be incorporated into the UKCPVS. During the project, information will also be relayed to the UKCPVS as soon as relevant and reported in the NIAB-TAG's quarterly journal (Landmark) to reach the > 3000 NIAB-TAG members including agronomists, breeders and farmers.

Researchers working with wheat yellow rust disease. All data will be made freely available where practical, at the earliest opportunity. The data will initially be hosted via a modified version of the TGAC http://opendata.tgac.ac.uk website to ensure rapid release under a creative commons license. Once submitted for publication all data will be deposited in public repositories and linked to via the project-specific website.

Farmers, breeders, agronomists and wheat variety testing authorities will benefit from the rapid means of confirming whether previously resistant wheat varieties have been broken by virulent races of the pathogen. Our research will also confirm outbreaks on particular wheat varieties and look for associations between pathogen genotypes and host pedigrees. Participation of four major UK wheat breeders (KWS, Limagrain, Syngenta, RAGT) as partners reflects the urgency of the problem. Understanding the underlying variation and how this affects resistance breeding is essential for the strategic planning required to produce high-yielding wheat varieties that will be resistant when deployed in 10 years (considering time between initial crossing and variety release). This may also lead directly to management decisions on how to effectively manage the threat of PST to UK wheat production. This audience will be reached through publications in the farming press. For instance, results from our preliminary study have already been reported in EDP24, the HGCA newsletter, NIAB-TAG bulletin, world-grain.com, Farmers Guardian, Agrii company newsletter, EADT24 and the Crop Production Magazine.
Population geneticists. Where possible new tools and data analysis pipelines generated herein will be integrated into the interactive Galaxy user interface to ensure they are accessible to the widest demographic, that includes bench biologists. All tools and pipelines once verified will be publically released without delay.

The general public will benefit from interactions with the PI and Co-I's, who have given talks to public audiences on a variety of issues such as plant biosecurity. They will specifically focus on further educating the public on genome science and pathogen dispersal in relation to plant pathogens and the crops they infect. They will give at least one talk to a public audience relating to this project, at least once per year.

The PDRA's, programmer and RA recruited for this project will benefit from improved skills, knowledge and experience gained from the research and wider training. This will contribute to their future economic activity in the public and/or private sectors. The innovative nature of the project ensures these individuals will likely develop unique skills that should prove highly attractive in the marketplace. This proposal also brings together an array of disciplines that will provide an exciting training ground for a cadre of excellent young scientists. This will contribute to the next generation of skilled crop scientists, with benefits beyond the immediate outcomes of this project.

Publications

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Related Projects

Project Reference Relationship Related To Start End Award Value
BB/M025519/1 01/07/2015 28/02/2017 £396,173
BB/M025519/2 Transfer BB/M025519/1 01/03/2017 30/06/2018 £132,389
 
Description CGIAR Inspire challenge
Amount $58,500 (USD)
Organisation CGIAR 
Sector Charity/Non Profit
Country Global
Start 10/2017 
End 09/2018
 
Description Horizon 2020
Amount € 176,015 (EUR)
Funding ID 773311-2 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 05/2018 
End 04/2022
 
Title Field pathogenomics web interface 
Description We have formulated a web interface to host all the data that is generated under our "field pathogenomics" pathogen surveillance project in a format that is accessible to a wide audience. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact The web interface is still under development but we are already getting positive responses from our industrial collaborators about the ability to use this to disseminate the data generated within our IPA. 
URL https://wheatis.tgac.ac.uk/yellowrust-map/
 
Title CyVerse UK software stack deployment 
Description The CyVerse (formerly iPlant) UK project at EI provides hardware resources in an easy to use manner through a web interface called the Discovery Environment (DE), as well as developer and bioinformatician access through APIs and software. A series of commands, called a pipeline, is combined into a script and / or a virtualised operating system container image called Docker. The pipeline can run on any hardware available to the implementer, which in this case will be the extensive HTCondor cluster set up at EI. Once a pipeline is running correctly on through the raw scheduler, the app can be registered on the Agave API (http://www.agaveapi.co). This is enabled through constructing JSON files that specify input sources together with user-supplied and default parameters that are necessary for the pipeline to run. Once a pipeline is registered through Agave, it is available as a GUI "app" through the DE, and can be made public after testing. 
Type Of Technology Grid Application 
Year Produced 2016 
Impact The EI CyVerse hardware enables the bioinformatics pipelines developed by the project partners (Univ's. Liverpool, Nottingham, Warwick) to be run on this HPC environment. Once deployed in the CyVerse UK environment, these tools can then be made available globally through the CyVerse Discovery Environment, reaching upwards of 18000 potential users. We have released this infrastructure and are accepting users from the UK research community to start using the hardware. 
URL http://cyverseuk.org/about/cyverse-uk-projects/tgac/
 
Title Field Pathogenomics web service 
Description The Field Pathogenomics service is for tracking the geographical spread of pathogens over time. The method uses new gene sequencing technology to assess the population structure of pathogens directly from infected field samples. It then provides a convenient map-based view of the collected data for easy user access. 
Type Of Technology Webtool/Application 
Year Produced 2016 
Open Source License? Yes  
Impact Field Pathogenomics service is used to allow web-based access to a selection of wheat-based pathogen samples recorded both nationally and globally by a variety of different companies and institutions collaborating together. The Field Pathogenomics service runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/yellowrust-map/
 
Title Grassroots API 
Description The Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Software 
Year Produced 2015 
Open Source License? Yes  
Impact The Grassroots API powers the public BLAST service that runs at TGAC, predominantly for the currently available wheat assemblies including the recently released TGAC v1 w2rap assembly (in preparation). We have served over 4000 unique users with over 6000 BLAST jobs since November 2015. It also underpins the Field Pathgenomics project (BBSRC IPA award 2015, PI - Saunders D., TGAC/JIC fellow), a web portal that represents the detection and subsequent phenotyping and genotyping of the wheat yellow rust pathogen. The site aims to enable researchers and breeders to track rust epidemics over variety and time, allowing for a more proactive approach to wheat crop breeding and farming. Finally, we are working with the CerealsDB group at Univ. Bristol to deploy the Grassroots infrastructure alongside the CerealsDB web portal, allowing a federation of searching, datasets, analysis and dissemination of markers, genotypes and associated feature and literature information. 
URL https://wheatis.tgac.ac.uk/grassroots/api/
 
Title Grassroots Tools Website 
Description This is the website for the Grassroots Infrastructure project aims to create an easily-deployable suite of computing middleware tools to help users and developers gain access to scientific data infrastructure that can easily be interconnected. With the data-generative approaches that are increasingly common in modern life science research, it is vital that the data and metadata produced by these efforts can be shared and reused. The Grassroots Infrastructure project wraps up industry-standard software tools with a consistent API that can be federated on a number of levels. This means institutions and groups can deploy a simple lightweight virtual machine, expose local data, connect up any existing data services, and federate their instance of the Grassroots with others out-of-the-box. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact Too soon to record impact 
URL https://grassroots.tools/
 
Title The Grassroots Infrastructure 
Description The Grassroots software is an open source "as-a-Service" stack that powers a number of data dissemination and analysis activities at EI, and other sites such as CerealsDB at the University of Bristol. We have continued to develop the functionality within the software stack to share crop-related datasets. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact Grassroots has previously been used to host the Field Pathogenomics project website and Yellow Rust map, the EI wheat BLAST service, the CerealsDB federation project, and the multi-scale improvements to the Polymarker marker design software. Recently, Grassroots has been put forward as the main data repository and metadata catalogue for the Designing Future Wheat project, and has started to host data from this project, the Open Wild Wheat Consortium, and 5 new wheat genomes from EI. The Grassroots service runs within the CyVerse UK National Capability infrastructure. 
URL https://grassroots.tools/
 
Description "Building resilience against crop diseases: a global surveillance system (GSS)" 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Rockefeller funded workshop to discuss the development of a global pathogen surveillance system
Year(s) Of Engagement Activity 2018
 
Description Agri-Tech East Pollinator event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Agri-Tech East Pollinator: Rusts and Other Cereal Killers
Year(s) Of Engagement Activity 2016
URL https://www.cambridgenetwork.co.uk/events/pollinator-rusts-and-other-cereal-killers/
 
Description Blog entry about research project (Wheat Side Story) 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Blog post on research project
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/articles/wheat-side-story
 
Description Field pathogenomics video 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We generated a video to explain our "field pathogenomics" pathogen surveillance technique to a wide audience. We also used an innovative book format to showcase the video at conferences and events. The video is available online via youtube and has been exceptionally useful in promoting further engagement with the project.

We are in the process of also activating a campaign to further promote the video on youtube over the next few months.
Year(s) Of Engagement Activity 2015,2016
URL https://www.youtube.com/watch?v=_Ij9PDnSpag
 
Description Grassroots Infrastructure and the Wheat Information System (Genome 10K & Genome Science 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mr Bian and Dr Tyrrell presented a poster at Genome 10K & Genome Science 2017 conference.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description JIC Industry showcase event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact JIC Industry showcase event
Year(s) Of Engagement Activity 2018
 
Description Meeting for collaborators on the Field Pathogenomics project 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact As part of the Field Pathogenomics project, a meeting with the industrial collaborators to discuss what features they would like added to the web-based tool that we created for users to access the data.
Year(s) Of Engagement Activity 2016
URL https://grassroots.tools/yellowrust-map/
 
Description New Phytologist workshop 
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 New Phytologist/DFG SPP1819-funded workshop "Molecular mechanisms underlying the rapid evolution of plant-microbe interactions"
Year(s) Of Engagement Activity 2018
 
Description Royal Norfolk Agricultural Association (RNAA) and Agritech East event 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact The John Innes Centre and The Genome Analysis Centre showcased some of the technologies used in science, as part of Agritech Week. They partnered with the Royal Norfolk Agricultural Association (RNAA) and Agritech East for the event.

We had a stand at the event where we showcased the technology that we have been developing for this grant to improve pathogen surveillance.
Year(s) Of Engagement Activity 2015
 
Description WheatIS Expert Working Grop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The expert working group for the Wheat Information System is developing standards and tools to enable the global wheat science community to share data effectively.
Year(s) Of Engagement Activity 2014,2015,2016,2017,2018
URL http://wheatis.org/
 
Description Women in computing blog series at the EI website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Blog post to promote women in computing
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/articles/women-computing-pilar-corredor-moreno
 
Description Youth STEMM awards 
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 Schools
Results and Impact Youth STEMM awards
Year(s) Of Engagement Activity 2017
 
Description Youth STEMM awards 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The Youth STEM Award event (YSA) at the Norwich Research Park aimed to promote biological sciences, predominantly plant research, to 200 14-16 year old schoolgirls.

We presented our research on pathogen surveillance and was interviewed by the press around this topic.
Year(s) Of Engagement Activity 2016