Characterization of wheat yellow rust pathogenicity

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

Partial resistance is typically multigenic and characterised genetically as QTLs. The mechanisms of partial resistance are only just beginning to emerge. We will dissect partial resistance of crop species focusing on wheat yellow rust. We will identify and characterise resistance to wheat yellow rust by screening diverse potential sources of resistance, including materials generated and organized through WISP (synthetic wheat lines, wild emmer, alien species), global cereal collections, and mutant lines to provide new sources of partial/durable resistance against yellow rust. High density mapping populations will be generated and the genetic basis of enhanced resistance will be determined. In addition, molecular markers will be developed to enable plant breeders to select advantageous alleles. The results from this objective will enable more rapid deployment of partial resistance in agriculture.

Publications

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Narang D (2019) Fine mapping of Aegilops peregrina co-segregating leaf and stripe rust resistance genes to distal-most end of 5DS. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Arora S (2017) Genome-Wide Association Study of Grain Architecture in Wild Wheat . in Frontiers in plant science

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Ramirez-Gonzalez RH (2015) PolyMarker: A fast polyploid primer design pipeline. in Bioinformatics (Oxford, England)

 
Description We have shown the effectiveness of a partial resistance gene (Yr36) to UK isolates of yellow rust under field conditions. This knowledge has paved the way for breeders to introduce this resistance (which is thought to be durable) into UK varieties.

We have fine mapped a major resistance gene (Yr15) which is of great importance in UK agriculture. We have developed SNP-based markers to accelerate the transfer of this gene into UK germplasm and improve the efficiency of marker assisted selection.

We have discovered the emergence of new yellow rust lineages in the UK. These new isolates represent a wider range of genetic diversity than that present in the UK in the past 25 years.

We have developed a new method to perform RNAseq directly from yellow-rust infected wheat leaves collected in the field (Field Pathogenomics). This has been done in collaboration with NIAB and TGAC and is opening new avenues for pathogen diagnostics directly from the field.
Exploitation Route We are currently working with industrial partners to develop low-cost reliable assays to improve the time of detection of new pathogen isolates.
Sectors Agriculture, Food and Drink

 
Description The develop of new near-diagnostic markers for the Yr15 resistance gene are currently being deployed by two commercial breeders and have been recently published. The knowledge gained from our Yr36 work has also made it an alternative gene for use in UK and is currently being pursued.
Sector Agriculture, Food and Drink
Impact Types Societal,Economic

 
Description UK Global Food Security Science Advisory Board
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
URL https://www.foodsecurity.ac.uk/
 
Description Workshop on Soft Skills, BGRI Meeting
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact Workshop on Soft Skills, BGRI Meeting
 
Description Newton Institutional Links Grant
Amount £299,973 (GBP)
Organisation Newton Fund 
Sector Public
Country United Kingdom
Start 04/2018 
End 03/2020
 
Description Strategic Training Award for Research Skills
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2018 
End 02/2020
 
Title Wheat Expression 
Description The majority of RNA-seq expression studies in plants remain underutilised and inaccessible due to the use of disparate transcriptome references and the lack of skills and resources to analyse and visualise this data. We have developed expVIP, an expression Visualisation and Integration Platform, which allows easy analysis of RNA-seq data combined with an intuitive and interactive interface. Users can analyse public and user-specified datasets with minimal bioinformatics knowledge using the expVIP virtual machine. This generates a custom web browser to visualise, sort and filter the RNA-seq data and provides outputs for differential gene expression analysis. We demonstrate expVIP's suitability for polyploid crops and evaluate its performance across a range of biologically-relevant scenarios. To exemplify its use in crop research we developed a flexible wheat expression browser (www.wheat-expression.com) which can be expanded with user-generated data in a local virtual machine environment. The open-access expVIP platform will facilitate the analysis of gene expression data from a wide variety of species by enabling the easy integration, visualisation and comparison of RNA-seq data across experiments. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact This database provides open access to over 400 RNAseq studies in wheat and the underlying algorithms are all available to adapt to any species with a reference genome. Over 11,000 sessions from >5,000 and >50,000 pageviews 
URL http://www.wheat-expression.com
 
Title Wheat Training 
Description This website provides background information and practical resources to help both budding wheat scientists as well as researchers looking to expand their work into wheat. There is a need to improve crops to feed the world's growing population with the backdrop of climate change. Translation of fundamental plant biology research (e.g. from Arabidopsis thaliana) into crops such as wheat provides a potential route to deal with this challenge. However learning even simple tasks such as growing and crossing wheat plants requires time and effort, while material and methods sections in published articles are often short and cannot substitute teaching aids. This is also true for more complex topics such as the genomics aspect of wheat. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact >4,500 sessions from >2,700 users 
URL http://www.wheat-training.com/
 
Description A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects 
Organisation International Centre for Maize and Wheat Improvement (CIMMYT)
Country Mexico 
Sector Charity/Non Profit 
PI Contribution I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls
Collaborator Contribution See above
Impact This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls
Start Year 2018
 
Description Bayer 
Organisation Bayer
Department Bayer CropScience Ltd
Country United Kingdom 
Sector Private 
PI Contribution Wheat genetics and genomics
Collaborator Contribution Wheat breeding and molecular knowledge
Impact joint projects
Start Year 2012
 
Description KWS 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Genetics and genomics
Collaborator Contribution Breeder know how and germplasm
Impact joint projects
Start Year 2009
 
Description Limagrain 
Organisation Limagrain
Country France 
Sector Private 
PI Contribution Genetics and genomics
Collaborator Contribution Germplasm and breeder know-how
Impact Phd Studentship, field trails, among others
Start Year 2009
 
Description Punjab Agricultural University 
Organisation Punjab Aricultural University
Country India 
Sector Academic/University 
PI Contribution Know how on wheat genomics and genetics, training.
Collaborator Contribution Gernplasm, local knowledge
Impact Have helped partners implement marker technology.
Start Year 2011
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution Genetics and genomics
Collaborator Contribution Wheat germplasm and know how
Impact Shared projects
Start Year 2009
 
Description Australian, UK scientists solve 30-year wheat rust genetics puzzle 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Australian, UK scientists solve 30-year wheat rust genetics puzzle
Year(s) Of Engagement Activity 2018
URL https://www.eurekalert.org/pub_releases/2018-08/uos-aus082418.php
 
Description Daily Mail Online 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Genetic make-up of wheat has been decoded for the first time: Scientists say it could lead to low allergy varieties and crops that need less water
Year(s) Of Engagement Activity 2018
URL https://www.dailymail.co.uk/sciencetech/article-6068177/Genetic-make-wheat-decoded-time.html
 
Description Discussion Norman Lamb, MP 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Discussion Norman Lamb, MP
Year(s) Of Engagement Activity 2017
 
Description Discussion with Gov Office Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Discussion with Gov Office Science
Year(s) Of Engagement Activity 2017
 
Description JIC Open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact JIC Open Day
Year(s) Of Engagement Activity 2018
 
Description Penny Mordaunt, Secretary of State for International Development. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Penny Mordaunt, Secretary of State for International Development.
Year(s) Of Engagement Activity 2018
 
Description Rachel Lambert, Senior Livelihoods Adviser, Agriculture Research DFID 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Rachel Lambert, Senior Livelihoods Adviser, Agriculture Research DFID
Year(s) Of Engagement Activity 2018
 
Description • EPSO-EC Conference at EXPO Milano 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact EU meeting on new breeding technologies
Year(s) Of Engagement Activity 2015