IDRIS- Improving Disease Resistance In Strawberry

Lead Research Organisation: East Malling Research
Department Name: Science

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 So far, resistance has been identified to Phytophthora fragariae, a root disease of strawberry. This is being characterised in further detail.
Exploitation Route For use in marker assisted breeding and diagnostics
Sectors Agriculture, Food and Drink

 
Description Not used yet- grant in progress
Sector Agriculture, Food and Drink
Impact Types Economic

 
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 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 'Disease resistance in Strawberry', specifically talking about the sequencing technologies we are using within the project to determine the genetic basis for pathogen-host interactions, enabling us to provide more durable disease resistance.
Year(s) Of Engagement Activity 2014
URL http://www.emr.ac.uk/press-releases/free-event-dna-technologies-horticulture-industry-held-east-mall...
 
Description Molecular Biology of Plant Pathogens (Bristol, UK) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Molecular Biology of Plant Pathogens provided an excellent forum for networking between junior and senior scientists.

Poster presentation on 'Improving disease resistance in Strawberry', detailing recent advances in the project and future plans.
Year(s) Of Engagement Activity 2015
 
Description Plant and Animal Genome Conference (San Diego) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presented a poster on my genetic mapping program at a major international conference. I won a travel grant on the basis that my program is likely to be useful for studying plant genomes and helpful for plant breeding.
Year(s) Of Engagement Activity 2015
URL http://www.intlpag.org
 
Description RenSeq workshop (John Innes Centre / The Sainsbury Laboratory, Norwich) 
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 Richard Harrison, Charlottle Nellist and Robert Vickerstaff attended a workshop on the novel gene capture technique known as RenSeq, held in Norwich jointly organised/hosted between The Sainsbury Laboratory, The John Innes Centre and The Genome Analysis Centre (now Earlham Institute). The workshop was attended by UK and international researchers. RenSeq involves capturing and sequencing so called NLR genes from plant genomes using synthesised RNA baits. These genes are some of the most important genes involved in plant disease immunity.
Year(s) Of Engagement Activity 2015
URL https://www.jic.ac.uk/directory/brande-wulff/
 
Description Researcher Links Workshop - Latest Technologies for Crop Improvements (Antalya, Turkey) 
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 Early career researchers based in the UK and Turkey participated in a workshop focussing on latest technologies for crop improvement. Richard Harrison gave an oral presentation at the meeting, describing the process of molecular markers for disease resistance and how these can be deployed in an applied breeding program. Andrew Armitage presented a poster titled "Improving disease resistance in strawberry: Effector discovery in Phytophthora pathogens". The workshop fostered face to face discussion between researchers, improving links between UK and Turkish researchers.
Year(s) Of Engagement Activity 2015
URL http://www.worcester.ac.uk/discover/crop-improvement-workshop
 
Description Researcher Links Workshop - Plant-Microbe Interactions (Bangkok, Thailand) 
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 Early career researchers based in the UK and Thailand participated in a workshop on plant-pathogen interactions with an emphasis on studies of pathogen and host diversity, infection and defense mechanisms, as well as disease protection.

Oral presentation on 'Improving disease resistance in Strawberry', detailing recent advances in the project and future plans.

Greater links were fostered between UK and Thai researchers.
Year(s) Of Engagement Activity 2015
URL https://www.britishcouncil.org/education/science/current-opportunities/thailand-workshop-plant-patho...
 
Description Seminar Series (Cardiff university) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Invited talk at the Organisms and Environment seminar series at Cardiff University. This interests of this seminar series focus on biology of whole organisms and their roles and interactions in changing ecosystems, in infection and health and at the genetic level. Andrew Armitage presented a seminar titled "Improving Disease Resistance in Strawberry:
Sequencing fungal & oomycete genomes", this focussed on results from the IDRIS project (BB/K017071/1) but also gave an overview of aims and results from the HAPI-funded project (BB/K020730).

This led to a share with scientific ideas with research leaders at Cardiff University. The most significant impact was exposing undergraduate students to plant pathology and horticulture as future career opportunities.
Year(s) Of Engagement Activity 2016
URL http://www.cardiff.ac.uk/biosciences/research/divisions/organisms-and-environment