IDRIS- Improving Disease Resistance In Strawberry

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

Berry crops have been one of the great success stories of British horticulture in recent years. During this century, the retail value of berry sales has increased from £146 million in 2000 to £783m in 2011, now representing 18.4 per cent of total UK fruit sales. Strawberries are 60% of the sector and continue to experience strong growth with sales increasing by 10% between March 2011 and March 2012. These achievements have been driven by scientific and technological advances, including improved cultivars, better control of pests and diseases and innovations allowing more intensive production. Modern cultivars have achieved a significant extension of the season, higher yields per plant, higher percentage of Class 1 fruit and improved eating quality, which has increased demand.

Despite this impressive performance in recent years, the UK strawberry industry now faces some serious challenges, with more variable and unpredictable weather conditions causing problems for growers, and the withdrawal of many fungicides and soil fumigants leading to increased crop losses from soil-borne diseases such as wilt, crown rot and red core, caused by Verticillium dahliae, Phytophthora cactorum and Phytophthora fragariae respectively. Our previous work resulted in a genome sequence for the diploid wild strawberry (through international collaboration) and molecular markers for wilt resistance that are now being deployed at EMR for marker assisted breeding. This is the first programme in the world to develop molecular markers for wilt resistance. Ongoing work aims to provide markers for mildew resistance (a major airborne pathogen), and this proposed work will provide markers which will facilitate more effective selection for resistance to crown rot and red core. This culmination of this work will lead to protection against the major soil and airborne pathogens in the UK.

Moreover, we wish to ask more basic questions about the evolution of plant-pathogen interactions and generate draft genome sequence for the cultivated strawberry (whose genome is four times bigger than the diploid woodland strawberry, as it contains eight copies of each chromosome, rather than two). A genome sequence for the cultivated strawberry is essential for the identification of molecular pathways and processes controlling disease resistance and other agronomic traits, as well as basic studies into how genes have changed throughout evolution. For example, comparisons between the diploid wild strawberry and octoploid cultivated strawberry will improve our understanding of how relationships between plants and their pathogens change between simple and more complex plant genomes. We wish to identify plant resistance genes that recognise conserved, slowly evolving proteins in pathogens, that will allow wide host resistance to many pathogen races and lead to durable resistance.

Industry are enthusiastic to support a targeted pre-breeding programme underpinned by research that leads to a more effective molecular breeding approach, taking advantage of the latest developments in genomics to accelerate the breeding process. Ultimately, improved cultivars would become publicly available, via licensed propagators, to growers throughout the UK and the EU.

Currently, although strawberries are perennial, the standard industry practice is to maintain the plants in the ground for only 8 to 15 months, as cropping for multiple seasons usually results in a build-up of soil diseases that have deleterious effects on both yield and fruit quality. Plants with strong and reliable resistance would allow cropping for multiple years, which would lead to sustainable intensification, reduce production costs and lower fungicide inputs. For consumers this work will lead to strawberries that have had significantly fewer chemicals applied to them and a considerably lowered carbon cost of production because the energy inputs associated with frequent replanting have been reduced.

Technical Summary

This work will apply effectoromics and comparative genomics techniques to identify pathogen effectors and map resistance QTL for the oomycete pathogens, Phytophthora cactorum and Phytophthora fragariae in Fragaria spp. Race specific markers will then be effectively pyramided in parental germplasm along with markers for resistance to Verticillium dahliae and Podosphaera aphanis, and breeding lines crossed to develop a range of pre-breeding material.

To achieve this we will:
Cross multiple cultivars and breeding lines to create populations segregating for race-specific resistances to P. fragariae and resistance to P. cactorum isolates from both crowns and fruit (both P. cactorum) of differing specificities. This work will lead to the creation of a saturated linkage map for the octoploid strawberry using genotyping by sequencing.

Sequencing and transcriptomics of pathogen isolates will allow identification of variable effectors (most likely of the RxLR class). Cloning and transformation of candidate effectors into known resistant and susceptible lines will then allow screening with specific effectors, enabling accurate pyramiding of R-gene loci to improve resistance durability.

Cross infective isolates of P.cactorum from F. x ananassa will be tested on diploid Fragaria vesca to map resistance in F. vesca using GBS. Comparisons between resistance loci in the diploid and the octoploid will be made in order to identify whether the same genomic regions are controlling resistance to P. cactorum as in the octoploid and whether the same, or different effectors are controlling the virulence of the pathogen.

The common parent of the mapping population will be sequenced to high coverage with a range of super-long and shorter read sequencing technologies which can then be effectively scaffolded to yield a draft octoploid genome sequence. This can then be used to further our understanding of resistance at the candidate gene level in the octoploid.

Planned Impact

Completion of this project will attract significant attention from the science, food production, retailing and public communities worldwide; indeed this proposal has already received considerable support from across the UK horticulture industry owing to the potential step-improvement it could make in breeding disease-resistant perennial crops.

Key societal benefits that this project will lead to include:

1) Reduced fungicide applications 2) Decreased carbon cost of production 3) Less pre-harvest waste within crop production 4) Ability to produce crops in a wider range of climate conditions 5) Reduced cost of fruit production 6)Improved UK food security 7) Improved ability to meet EU legislative requirements

Academic beneficiaries

This research will train two PDRAs in a variety of molecular, bioinformatic and genetics techniques that are all of use in academic and industrial settings. These skills are vital to the UK research community as limited consideration towards pre-breeding of perennial food crops is provided by other UK academic institutions. The mapping progeny that will be generated and genotyped will be an important resource for future studies, as it is expected to segregate for a wide range of agronomically important traits (Benefit within 3-5 years). Published research from this project will facilitate the rapid development of cultivars, by international plant breeders, with improved disease resistance (Benefit within 3-5 years).

Commercial beneficiaries - (Soft fruit sector - UK)

This project, leading to disease-resistant strawberries in the UK, will help to protect and enhance the productivity and competitiveness of the UK soft fruit industry through reduced fungicidal inputs and by extending the life of field plantings (reducing production costs as current standard practice is for growers to replant every year - Benefit within 3 years). Disease resistant cultivars will also enable growers to reduce waste, and associated costs, and to produce crops across a wider range of climatic conditions - therefore benefiting the UK food security agenda (Benefit within 5-10 years). UK plant breeders, propagators, marketing companies and grower groups will all benefit from this research though subsequent commercialisation of research (as has been the case with previous research projects feeding into the EMR strawberry breeding programme). Ultimately, cultivars developed downstream form this pre-breeding will be protected by EU Plant Variety Rights to ensure maximum benefit to the UK economy. (Benefit within 2-4 years.)

Public and retail sector (especially supermarkets)

The improved disease-resistant cultivars will be ideally suited to production using integrated pest and disease management systems which are aimed at eliminating residues in fruit. This the public and retailers will have greater access to residue-free produce. More reliable production methods will similarly improve food availability and there is potential to reduce costs in the supply chain (through reduced inputs). Several UK retailers aim to double sales of UK-produced fruit by 2020; this project will assist that aim and improve UK productivity and competitiveness (Benefit within 5-10 years).

Government and policy benefits

The public will benefit through increased food security and sustainability, minimising fungicide residues and minimising the environmental impact from fungicides and soil fumigants on the environment. This feeds in to many UK Government and EU policy agendas including: pesticides (reducing residues), water (ability to grow nearer water courses), climate (growing crops perennially will improve carbon sequestration) and environment (reduced carbon and pesticides). (Benefit within 3-5 years)

Third sector

Environmental lobby groups within the third sector will benefit from this research through reduced fungicide use, less waste and cleaner water courses (Benefit within 2-4 years).

Related Projects

Project Reference Relationship Related To Start End Award Value
BB/K017071/1 01/08/2013 31/01/2016 £748,383
BB/K017071/2 Transfer BB/K017071/1 01/02/2016 31/07/2018 £358,975
 
Description This research grant has had a series of research finding that have uncovered a great deal about phytophthora- strawberry interactions. In short:

1. Resistance QTL to Phytophtora cactorum from a biparental cross
2. Resistance to Phytophthora fragariae races 1-3
3. Sequencing of ~25 genomes of P. fragariae and P. cactorum
4. Full effector identification pipeline developed
5. RNAseq experiments in planta to uncover key effectors
6. Development of transformation and gene editing by CRISPR Cas9 in strawberry
7. GWAS for resistance to P. cactorum in a pre-breeding population
8. Development of a predictive model for breeders for resistance
9. Initial sequencing of the Redgauntlet strawberry genome
10. Validation of verticillium and powdery mildew QTL
11. Sequencing of raspberry genome (outgroups)
12. Sequencing of P. rubi and P. ideae (outgroups)
Exploitation Route The findings in terms of markers have been taken into breeding programmes and published. They are having a significant positive effect on increasing selection intensity for disease resistance.

We are in discussion with AHDB to build on our pathogen effector / diagnostics work/ pipeline.
Sectors Agriculture, Food and Drink

 
Description Markers used in breeding programmes. Predictive model of disease resistance developed from GWAS data allowing greater selection intensity in the breeding programme.
First Year Of Impact 2017
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BBSRC Collaborative Training Partnerships - Fruit Crop Research - Berry Gardens
Amount £90,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 09/2022
 
Title Crosslink- genetic mapping program 
Description Software for genetic mapping 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact High resolution genetic map of octoploid strawberry created 
 
Title Established CRISPR Cas9 gene editing in octoploid strawberry 
Description Established CRISPR Cas9 gene editing in octoploid strawberry through the development of stable Cas9 lines 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact None yet 
 
Description Norway collaboration- P. cactorum 
Organisation Norwegian Institute for Agricultural and Environmental Research
Country Norway 
Sector Public 
PI Contribution Worked jointly on P. cactorum genome assembly and analysis
Collaborator Contribution Analysis of CaZy genes. Contribution of data.
Impact Publication in progress
Start Year 2016
 
Description Phytophthora sequencing consortium 
Organisation Nanjing Agricultural University
Country China 
Sector Academic/University 
PI Contribution Generation of Phytophthora cactorum, Phytophthora idaei, Phytophthora rubi and Phytophthora fragariae genomes and sharing of insights into genome structure and host adaptation in the multinational collaboration through monthly group meetings.
Collaborator Contribution Collaborators from a range of international institutes have contributed genome and transcriptome sequence data to a centralised database for benefit to the Phytophthora community. Gene prediction and effector analysis have been performed on this data to identify trends in Phytophthora evolution across the phylogeny.
Impact Data sharing between institutes. Alignment of research objectives between groups. Expected collaborative publications.
Start Year 2015
 
Description Phytophthora sequencing consortium 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution Generation of Phytophthora cactorum, Phytophthora idaei, Phytophthora rubi and Phytophthora fragariae genomes and sharing of insights into genome structure and host adaptation in the multinational collaboration through monthly group meetings.
Collaborator Contribution Collaborators from a range of international institutes have contributed genome and transcriptome sequence data to a centralised database for benefit to the Phytophthora community. Gene prediction and effector analysis have been performed on this data to identify trends in Phytophthora evolution across the phylogeny.
Impact Data sharing between institutes. Alignment of research objectives between groups. Expected collaborative publications.
Start Year 2015
 
Description Phytophthora sequencing consortium 
Organisation Scion
Country New Zealand 
Sector Public 
PI Contribution Generation of Phytophthora cactorum, Phytophthora idaei, Phytophthora rubi and Phytophthora fragariae genomes and sharing of insights into genome structure and host adaptation in the multinational collaboration through monthly group meetings.
Collaborator Contribution Collaborators from a range of international institutes have contributed genome and transcriptome sequence data to a centralised database for benefit to the Phytophthora community. Gene prediction and effector analysis have been performed on this data to identify trends in Phytophthora evolution across the phylogeny.
Impact Data sharing between institutes. Alignment of research objectives between groups. Expected collaborative publications.
Start Year 2015
 
Description Phytophthora sequencing consortium 
Organisation University of British Columbia
Country Canada 
Sector Academic/University 
PI Contribution Generation of Phytophthora cactorum, Phytophthora idaei, Phytophthora rubi and Phytophthora fragariae genomes and sharing of insights into genome structure and host adaptation in the multinational collaboration through monthly group meetings.
Collaborator Contribution Collaborators from a range of international institutes have contributed genome and transcriptome sequence data to a centralised database for benefit to the Phytophthora community. Gene prediction and effector analysis have been performed on this data to identify trends in Phytophthora evolution across the phylogeny.
Impact Data sharing between institutes. Alignment of research objectives between groups. Expected collaborative publications.
Start Year 2015
 
Description UK - Norwegian collaboration on Phytophthora cactorum 
Organisation Norwegian Institute of Bioeconomy Research
PI Contribution Sequencing of a Norwegian P. cactorum isolate and subsequent identification and analysis of gene complements that may contribute to pathogenicity on strawberry. This collaboration is expected to be maintained through PhD student visits in coming years.
Collaborator Contribution Supply of isolate. Funding for isolate sequencing. Contribution of bioinformatic analysis. Joint writing of final scientific paper. This collaboration is expected to be maintained through PhD student visits in coming years.
Impact Publication of first P. cactorum genome from strawberry and identification of potential genes allowing pathogenicity on strawberry. Collaboration is allowing coordination between institutes on prioritising the functional validation of gene candidates.
Start Year 2014
 
Description Understanding diversity of Phytophthora cactorum 
Organisation Scion
Country New Zealand 
Sector Public 
PI Contribution Sharing early access to Phytophthora cactorum sequencing data from strawberry and apple, advice on analysis and access to pre-publication results.
Collaborator Contribution Sharing early access to Phytophthora cactorum sequencing data from a range of plant hosts, advice on analysis and access to pre-publication results.
Impact Coordination of research objectives. Expected joint publications.
Start Year 2017
 
Title Crosslink genetic mapping software program 
Description Crosslink is a software program able to create genetic maps from genotype data collected from the progeny of a cross between two individuals. The program is suitable for use with an "outcross" where the two parents do not need to be genetically inbred, and there is applicable to a wide range of plants where inbreeding cannot be used. The program is designed to scale efficiently to handle the large number of genetic markers typically being generated by modern and emerging genotyping technologies. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact This tool has allowed us to automate the creation of genetic maps using a larger number of markers, and across multiple mapping families, which would otherwise have been extremely time consuming. Researchers at IBERS, Aberystwyth University, and Earlham Institute have also begun using the tool. Our maps will be used as the basis for constructing the cultivated strawberry genome sequence. 
URL https://github.com/eastmallingresearch/crosslink
 
Description 4th Stustain COST Action 'Pathogen-informed strategies for sustainable broad-spectrum crop resistance' (Bled, Slovenia) 
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 Sustain COST Action is a "European network of scientists and breeders working together to turn breakthroughs in plant-pathogen interaction research into effective breeding strategies for durable disease resistance".

Poster presentation on 'Improving disease resistance in Strawberry', presenting recent updates on resistance quantitative trait loci (QTL) identified against strawberry crown rot disease (Phytophthora cactorum).
Year(s) Of Engagement Activity 2017
URL https://www.cost-sustain.org/Events-and-meetings/4th-Annual-and-Final-Conference-of-the-Sustain-COST...
 
Description 8th International Rosaceae Genomics Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended the eigth International Rosaceae Genomics Conference, presented a poster about progress creating genetic maps and software tools for studying disease resistance in strawberry.
Year(s) Of Engagement Activity 2016
URL https://colloque.inra.fr/rgc8/
 
Description 8th International Rosaceae Genomics Conference (Angers, France) 
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 8th International Rosaceae Genomics Conference focusing on recent updates in the genomics and genetics of Rosaceae species.
Poster presentation on 'Improving disease resistance in Strawberry', detailing our recent updates on resistance to strawberry crown rot disease (Phytophthora cactorum).
Year(s) Of Engagement Activity 2016
URL https://colloque.inra.fr/rgc8/
 
Description Applications of sequencing technology in the horticulture industry (East Malling, UK) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Free event sponsored by Illumina to showcase the benefits and opportunities that DNA technologies can bring to the UK horticulture industry. The event demystified this branch of science and allowed discussions of how the technology works. Oral presentation on 'Developing diagnostics for invasive pathogens', discussing the use of potential for developing new tools identification based upon whole genome sequence data.
Year(s) Of Engagement Activity 2014
URL http://www.emr.ac.uk/press-releases/free-event-dna-technologies-horticulture-industry-held-east-mall...
 
Description BSPP Plant Pathogen Diagnostic Course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Hosted a one day practical course on Plant Pathogen Diagnostics - From symptoms to sequence. We covered a range of pathology skills and knowledge. Collated feedback of the day rated the course very useful, with over 90% of delegates stating they were satisfied or very satisfied with the content, speakers and organisation of the course.
Year(s) Of Engagement Activity 2018
 
Description East Kent Society Soft Fruit Walk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Presentation of project work to members of the East Kent Soft Fruit Society, sparked questions and discussion. Attendees reported increasing their knowledge of key pathogens in strawberry.
Year(s) Of Engagement Activity 2018
 
Description Food secutiry for vulnerable populations: the fungal threat 
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 Oral presentation and group discussion under the Researcher Links scheme. This was a joint meeting funded by the British Council and FAPESP in Ribeirao Preto, Brazil on 11-14 September 2018. The workshop was coordinated by Simon Avery (Univ. Nottingham) and Gustavo Goldman (Univ. Sao Paulo), and had contributions from other experienced researchers. My presentation covered work on Fusarium, Phytophthora, Verticillium and Alternaria at NIAB EMR, raising the profile of the institute and of the funded genomic research that we have been performing. This led to discussions on future research projects and possible new joint-funded grants.
Year(s) Of Engagement Activity 2018
 
Description Fourth International Horticulture Research Conference 
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 Hosted the Fourth International Horticulture Research Conference at NIAB EMR. The conference brought together international researchers conducting basic research on horticultural crops, facilitating them to showcase their latest research findings and to network with colleagues from around the world. The conference allowed us to raise the profile of NIAB EMR and the research we are conducting. A poster was presented specifically detailing the work in this project.
Year(s) Of Engagement Activity 2017
 
Description Fruit Focus 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Fruit Focus is the leading technical event for the soft fruit industry, with ~1,200 attendees. Several posters were produced for the event and were presented throughout the day, which sparked questions and discussion. Attendees reported increased knowledge of strawberry pathogens and the work we are doing to improve resistance to them.
Year(s) Of Engagement Activity 2018
 
Description International Society for Molecular Plant-Microbe Interactions XVII Congress (Portland, USA) 
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 Over 950 delegates from 40 countries attended the congress on Molecular Plant-Microbe Interactions.

Poster presentation on 'Improving disease resistance in Strawberry', detailing recent updates on resistance quantitative trait loci (QTL) identified against strawberry crown rot disease (Phytophthora cactorum).
Year(s) Of Engagement Activity 2016
URL http://www.ismpmi.org/Congress/2016/Pages/default.aspx
 
Description Meeting with Berry Gardens Growers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Met with ~15 growers from Berry Gardens and had informal discussions about progress of the project and future avenues of research.
Year(s) Of Engagement Activity 2018
 
Description Oomycete Molecular Genetics Network (Malm√∂, Sweden) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Work on assembly and annotation of Phytophthora cactorum genome performed by Andrew Armitage at NIAB-EMR was presented by a collaborator (May Bente Brurberg, NIBIO - Norway) to participants of the 2016 meeting of Oomycete Molecular Genetics Network. The presentation was titled "The Phytophthora cactorum genome". This gave exposure of the project to Resaerchers working on Phythophthora and Oomycetes as plant pathogens as well as strengthening ties with NIBIO. A significant outcome of this event was tweets of the presentation's key messages by members of the meeting including Dr. Sophien Kamoun (@KamounLab) who has >7000 followers from science, policymaking and industry.
Year(s) Of Engagement Activity 2016
URL http://www.omgn.org
 
Description The Third International Horticulture Research Conference (Nanjing, China) 
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 I presented a post about my work at the conference.
Year(s) Of Engagement Activity 2016
URL http://www.hortres-conference.org/uploadfiles/The%20Third%20International%20Horticulture%20Research%...
 
Description Third International Horticulture Research Conference (Nanjing, China) 
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 Horticulture Research Conference brought together international researchers conducting basic research on horticultural crops, to showcase the latest research findings.

Oral presentation on 'Improving disease resistance in Strawberry', detailing recent advances in identifying resistance quantitative trait loci (QTL) against strawberry crown rot disease (Phytophthora cactorum).
Year(s) Of Engagement Activity 2016
URL http://www.hortres-conference.org/uploadfiles/hortres2016(2).pdf