14 ERA-CAPS An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Genetics and Breeding

Abstract

EfectaWheat is a partnership of six complementary institutes from the UK (NIAB, FERA), Germany (LFL), Denmark (AARHUS), Norway (NMBU) and Australia (CCDM). The partners form a multidisciplinary team focusing on the economically important wheat leaf spot group (LSG) of necrotrophic pathogens: Parastagonospora nodorum (Pn, cause of Septoria nodorum blotch; SNB), Zymoseptoria tritici (Zt, Septoria tritici blotch; STB) and Pyrenophora tritici-repentis (Ptr, tan spot; TS).

Recently available resources in wheat, including high-resolution genetic mapping populations and high-density genotyping, will be combined with emerging tools and approaches in the pathogens, such as pathogen genome resequencing, and identification of pathogen-produced molecules that mediate infection (termed, 'effectors). These approaches will complement the project partners' expertise in pathogen diagnostics, virulence assessment and field pathotesting across all partner countries. These combine to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions in Europe.

The unique positions of partners at the interface between crop research and translation ensure effective dissemination of project outputs to European agri-industry. This approach has been successfully implemented by CCDM for SNB and TS in Australia. This project will extend the approach to Europe. All resources generated will be made available to the research and industrial communities to facilitate practical exploitation.

Technical Summary

The project partners form a multidisciplinary team focusing on the economically important wheat leaf spot group (LSG) of necrotrophic pathogens: Parastagonospora nodorum (Pn, cause of Septoria nodorum blotch; SNB), Zymoseptoria tritici (Zt, Septoria tritici blotch; STB) and Pyrenophora tritici-repentis (Ptr, tan spot; TS).

High-resolution wheat genetic mapping populations (available at NIAB and LFL) and high-density genotyping will be combined with effector-based tools, pathogen re-sequencing approaches (CCDM), and expertise in pathogen diagnostics, virulence assessment (LFL, AARHUS, FERA), and field pathotesting across all partner countries (NMBU, NIAB, AARHUS, LFL). These combine to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions in Europe.

The unique positions of partners at the interface between crop research and translation ensure effective dissemination of project outputs to European agri-industry. This approach has been successfully implemented by CCDM for SNB and TS in Australia, where it is forecasted to reduce losses by ~EUR100m per annum by 2020. This project will extend the approach to Europe. Specifically, it will:

(1) Establish relative impact of LSG pathogens in target EU countries using molecular approaches.
(2) Identify new TS and SNB effectors.
(3) Determine the effector profile of Pn and Ptr isolates and the sensitivity of cultivars to effectors.
(4) Screen TS, SNB and STB effectors against high-resolution wheat germplasm resources.
(5) Resolve multiple LSG effector and field resistance QTLs at high-resolution.
(6) Establish prevention and management strategies against multiple LSG pathogens.
(7) Deliver tools (effectors and markers) for LSG resistance breeding to EU breeders and researchers.

Planned Impact

please refer to uploaded full ERA-CAPS proposal pdf document
 
Description Since the project start in the last quarter of 2015 we have:

(1) undertaken a series of field trials within 4 countries over two seasons to assess wheat genetic resistance to three necrotrophic pathogens. (2) undertaken QTL analysis across all trials and traits. (3) Sumarised all QTL analyses.
(4) Undertaken pehenotyping and QTL analysis for 4x fungal effectors.
(5) Undertaken a survey of three necrotrophic pathogens in the UK and the EU, finding via molecular investigation that pathogens are infecting wheat even when no visible sign of infection is apparent.
Exploitation Route Identification of genetic markers tagging wheat resistance loci will be available to use in breeding and pre-breeding programmes by wheat breeders.

Informal direct collaboration with one wheat breeding company has been initiated.
Sectors Agriculture, Food and Drink

 
Description Informal interaction with a wheat breeding company has been initiated, with NIAB providing resources for collaborative investigation of wheat resistance.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BBSRC DTP Targeted Studentship, Cambridge University/NIAB
Amount £75,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description BBSRC Travel Award
Amount £30,559 (GBP)
Funding ID BB/N022033/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2016 
End 09/2019
 
Description COST ACTION SUSTAIN - PDRA conference costs
Amount £500 (GBP)
Organisation European Cooperation in Science and Technology (COST) 
Department COST Action
Sector Public
Country Belgium
Start 03/2017 
End 03/2017
 
Description COST ACTION SUSTAIN - PI conference costs
Amount £500 (GBP)
Organisation European Cooperation in Science and Technology (COST) 
Department COST Action
Sector Public
Country Belgium
Start 03/2017 
End 03/2017
 
Description COST SUSTAIN Travel Award
Amount £2,000 (GBP)
Organisation European Cooperation in Science and Technology (COST) 
Department COST Action
Sector Public
Country Belgium
Start 06/2016 
End 06/2016
 
Description Collaboration on the genetic dissection of wheat ear morphology 
Organisation John Innes Centre
Department Department of Crop Genetics
Country United Kingdom 
Sector Private 
PI Contribution Access provided to JIC to 6x of our project trials for collection of phenotypic data. Analysis of resulting phenotype data.
Collaborator Contribution Phenotyping of 3x trials. Training provided in wheat ear phenotyping. Field trial at JIC site, and provision of resulting phenotypic data.
Impact Joint publication in Plant Cell. Talks about future grant possibilities
Start Year 2015
 
Description Collaboration with CCDM, Curtin University, Australia 
Organisation Curtin University
Department Women in Social Economic Research (WiSER)
Country Australia 
Sector Academic/University 
PI Contribution Undertake work providing supporting data for grant proposals. Arrange for Eurasmus EU visiting student placements to help undertake research. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Collaborator Contribution Undertake work providing supporting data for grant proposals. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Impact Joint grant application to ERA-CAPs call. Funded. Joint PhD application to DTP scheme. Funded.
Start Year 2015
 
Description Collaboration with CCDM, Curtin University, Australia 
Organisation Curtin University
Country Australia 
Sector Academic/University 
PI Contribution Undertake work providing supporting data for grant proposals. Arrange for Eurasmus EU visiting student placements to help undertake research. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Collaborator Contribution Undertake work providing supporting data for grant proposals. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Impact Joint grant application to ERA-CAPs call. Funded. Joint PhD application to DTP scheme. Funded.
Start Year 2015
 
Description NIAB-TEAGASC collaborative work on septoria phenotyping of 8-parent MAGIC population 
Organisation Teagasc
Department Teagasc Food Research Centre
Country Ireland 
Sector Academic/University 
PI Contribution Provision of wheat 8-parent population MAGIC seed
Collaborator Contribution preparation, sowing, growth and phenotyping of ~800 MAGIC lines, 2 reps per line, 2015-2016 growth season.
Impact Initiation of collaboration between groups at NIAB and TEAGASC
Start Year 2015
 
Description Abstract and poster at 9th International Symposium on Septoria Diseases of Cereals, Paris, France, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Abstract and poster at 9th International Symposium on Septoria Diseases of Cereals, Paris, France, 2016, titled "Mapping the wheat Snn3 locus conferring sensitivity to the P. nodorum necrotrophic effector SnTox3 using an eight founder MAGIC population"
Year(s) Of Engagement Activity 2016
 
Description Abstract and poster submitted to the COST SUSTAIN conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to the COST SUSTAIN conference 2017, titled "Wheat Effector Assisted Breeding for Resistance to Fungal Pathogens (WEAB)"
Year(s) Of Engagement Activity 2017
 
Description British Science Foundation event: Science Cafe public meeting, 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact British Science Foundation event: Science Cafe public meeting, 2016
Sparked keen interest and discussion amongst the members of the public present.
Year(s) Of Engagement Activity 2016
 
Description Conference abstract and poster submission to COST SUSTAIN 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to COST SUSTAIN 2017, titled "Mapping the wheat Snn3-B1 locus conferring sensitivity to the Parastagonospora nodorum necrotrophic effector SnTox3 using an eight founder multi-parent advanced generation intercross (MAGIC) population and the Avalon x Cadenza doubled haploid population"
Year(s) Of Engagement Activity 2017
 
Description Conference abstract and poster submission to COST SUSTAIN 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to COST SUSTAIN 2017, titled "EfectaWheat: an effector- and genomics-assisted pipeline for necrotrophic plant resistance breeding in whe"
Year(s) Of Engagement Activity 2017
 
Description Conference abstract and poster submission to COST SUSTAIN 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to COST SUSTAIN 2017, titled "Using Multiparent Advanced Generation Inter-Cross (MAGIC) populations to investigate wheat leaf spot group (LSG) host-pathogen interactions in the UK"
Year(s) Of Engagement Activity 2017
 
Description Conference abstract and poster submission to Monogram 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to Monogram 2017, titled "Using MAGIC to dissect the genetics of below- and above-ground phenotypes in wheat"
Year(s) Of Engagement Activity 2017
 
Description Conference abstract and poster submission to Monogram 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submission to Monogram 2017, titled "Mapping the wheat Snn3-B1 locus conferring sensitivity to the Parastagonospora nodorum necrotrophic effector SnTox3 using a variety of mapping populations and elite European germplasm"
Year(s) Of Engagement Activity 2016
 
Description Conference abstract and poster submitted to Monogram 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster submitted to Monogram 2017 meeting, titled "Breeding for resistance to necrotrophic fungal diseases in wheat"
Year(s) Of Engagement Activity 2017
 
Description Conference abstract and poster, at HEZ, Freising, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference abstract and poster, at HEZ, Freising, Germany, titled "MAGIC population in winter wheat: construction and genetic analysis of resistance to fungal pathogens"
Year(s) Of Engagement Activity 2016
 
Description EfectaWheat NIAB Poster Day 2018 
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 Professional Practitioners
Results and Impact EfectaWheat presentation at NIAB Poster Day 2018
Year(s) Of Engagement Activity 2018
 
Description EfectaWheat presentation, Lisbon, Protugal 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk outlining the ERA-CAPs funded project "EfectaWheat". . ERA-CAPS grant holders meeting, 7-8th May Lisbon, Portugal, 2015
Year(s) Of Engagement Activity 2015
 
Description Leyperson article, Landmark 2016 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Article on emerging wheat disease, Tan Spot, published in the NIAB-TAG Network publication Landmark. NIAB-TAG has >2,000 members, which all receive the Landmark publication.
Year(s) Of Engagement Activity 2016
 
Description NIAB Poster Day 2017 
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 Professional Practitioners
Results and Impact Poster and practical demonstrations to disseminate current work
Year(s) Of Engagement Activity 2017
 
Description NIAB-EMR talk 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Talk at NIAB-EMR, March, 2017: overview of my research at NIAB-Cambridge.
Year(s) Of Engagement Activity 2017
 
Description Phytopatological Society Congress Conference poster, Piacenza, Italy, Oct 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Poster presentation of the project work, at the XXIII Italian Phytopatological Society Congress conference, Piacenza, Italy, Oct 2017
Year(s) Of Engagement Activity 2017
 
Description Poster presentation COST SUSTAIN meeting 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact POSTER PRESENTATION: 7. Leburn et al. Wheat effector assisted breeding for resistance to fungal pathogens (WEAB). COST Sustain meeting, Wageningen, 8-10 April 2015.
Year(s) Of Engagement Activity 2015
 
Description Poster presentation COST SUSTAIN meeting Banyuls France 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation: Downie R, Scuderi A, Barber T, Furuki E, Gardner K, Gosman N, Kowalcyzk R, Phan H, Rose G, Tan K-C, Oliver R, Mackay I, Cockram J. Mapping the wheat Snn1 locus to the Parastagonospora nodorum necrotrophic effector SnTox1 using an eight founder mult-parent advanced generation inter-cross population. Third Annual meeting of the COST Action Sustain, 17th - 19th February 2016, Banyuls-sul-Mare, France.
Year(s) Of Engagement Activity 2016
 
Description Poster presentation at COST SUSTAIN meeting France 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster at the COST SUSTAIN conference, Banyuls-sur-Mare, France. EffectaWheat: an effector and genomics assisted pipeline for necrotrophic pathogen resistance breeding in wheat. 3rd Annual meeting of the COST Action Sustain, 17th - 19th February 2016, Banyuls-sul-Mare, France.
Year(s) Of Engagement Activity 2016