IDRIS- Improving Disease Resistance In Strawberry
Lead Research Organisation:
National Institute 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 a 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.
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 a 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.
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).
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).
Organisations
- National Institute of Agricultural Botany (Lead Research Organisation)
- James Hutton Institute (Collaboration)
- Oregon State University (Collaboration)
- Scion (Collaboration)
- Norwegian Institute of Bioeconomy Research (Collaboration)
- Norwegian Institute for Agricultural and Environmental Research (Collaboration)
- Nanjing Agricultural University (Collaboration)
- UNIVERSITY OF BRITISH COLUMBIA (Collaboration)
Publications
Adams TM
(2020)
Genomic Investigation of the Strawberry Pathogen Phytophthora fragariae Indicates Pathogenicity Is Associated With Transcriptional Variation in Three Key Races.
in Frontiers in microbiology
Armitage AD
(2018)
Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum.
in PloS one
Armitage AD
(2020)
Draft Genome Sequence of the Strawberry Anthracnose Pathogen Colletotrichum fructicola.
in Microbiology resource announcements
He JQ
(2017)
A novel 3D imaging system for strawberry phenotyping.
in Plant methods
Kronmiller BA
(2023)
Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer.
in Molecular plant-microbe interactions : MPMI
Nellist C
(2021)
Comparative Analysis of Host-Associated Variation in Phytophthora cactorum
in Frontiers in Microbiology
Nellist C
(2018)
The Genomes of Rosaceous Berries and Their Wild Relatives
Nellist CF
(2018)
The genomes of Rosaceous berries and their wild relatives
Nellist CF
(2019)
Quantitative trait loci controlling Phytophthora cactorum resistance in the cultivated octoploid strawberry (Fragaria × ananassa).
in Horticulture research
Whitehouse A
(2017)
Progress in strawberry breeding at NIAB-EMR, East Malling, UK
in Acta Horticulturae
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. 2019- varieties from genomic prediction work are advancing through trials by industry partners. Based on the resources generated the industry partners are now carrying out further GWAS on other pathogens (mildew). A former PDRA on this grant is developing her own research programme as a group leader with the project outputs. 2020- varieties are now approaching commercialisation with the genomic predictions from this project. |
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. 2019- varieties now in advanced trials from genomic predictions. Stage in 2021-22 will be farmer trials. Varieties have now been released into the market and are having a significant impact- see attached links to press releases. |
First Year Of Impact | 2020 |
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 | 09/2018 |
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 | Collaboration with JHI on raspberry Phytophthora |
Organisation | James Hutton Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Provided data / knowhow to AHDB studentship between JHI/ NIAB |
Collaborator Contribution | Genome sequences, analysed data, experience |
Impact | Transfer of knowledge from strawberry to rapsberry pathosystem with the objective of identifying disease resistance. |
Start Year | 2018 |
Description | Norway collaboration- P. cactorum |
Organisation | Norwegian Institute for Agricultural and Environmental Research |
Country | Norway |
Sector | Private |
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 |
Country | Norway |
Sector | Public |
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 | Genomic prediction for day neutrality |
Description | This innovation has led to genomic prediction ability for day neutrality at a high level of accuracy. This was underpinned by a number of linked developments in genome sequencing, GWAS population development, phenotyping and statistical genetics. |
IP Reference | |
Protection | Protection not required |
Year Protection Granted | |
Licensed | Commercial In Confidence |
Impact | Day neutrality is a key trait for breeding, which was resolved through analysis of the octoploid genome. This is now being used in rapid combining of resistance and quality traits in breeding programmes, delivering enhanced varieties to market. |
Title | Molecular markers/ genomic prediction for disease resistance |
Description | Resistance has been identified to key oomycete pathogens, Verticillium dahliae and powdery mildew. These are all of the major diseases of strawberry. |
IP Reference | |
Protection | Protection not required |
Year Protection Granted | 2018 |
Licensed | Commercial In Confidence |
Impact | This critical knowhow is now embedded in an industry funded breeding programme which is delivering disease resistant varieties to the market. |
Title | Molecular markers/ genomic prediction for low-input, fruit uniformity and other quality traits |
Description | Molecular markers for key fruit quality traits, along with low input (low P and AMF conlonisation ) were developed as a result of the synthesis of work from multiple projects. |
IP Reference | |
Protection | Protection not required |
Year Protection Granted | |
Licensed | Commercial In Confidence |
Impact | These markers are used in genomic selection pipelines for delivery of enhanced varieties of strawberry to the market, with improvements in fruit quality. |
Title | Crosslink genetic mapping programme |
Description | This is a piece of software for genetic mapping in complex outcrossing polyploids |
Type Of Technology | Software |
Year Produced | 2016 |
Open Source License? | Yes |
Impact | Assembled the first multi-population linkage map for octoploid strawberry |
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 (Malmö, 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 | Talk at Crop Science Society of Zimbabwe |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 40 researchers and industry representatives from Harare, Zimbabwe, which sparked questions and discussion afterwards and the sharing of protocols. |
Year(s) Of Engagement Activity | 2020 |
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 |