14 ERA-CAPS: Mechanistic Analysis of Quantitative Disease Resistance in Brassica by Associative Transcriptomics

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics

Abstract

Brassica napus, a major world-wide crop, comprises a range of crop types including oilseed rape (OSR), grown for edible and industrial oil, biodiesel, protein for animal feed as well as leaf and root vegetables. Diseases are a major factor limiting production, a threat increasing due to climate change and the imminent withdrawal of agrochemicals in Europe. Improved disease control is an urgent priority and breeders are increasingly using quantitative disease resistance (QDR), which is considered broad-spectrum and durable.

This research will identify the most useful QDR genes for OSR breeding and understand the mechanisms behind this to enable predictions of their effectiveness and durability. Our consortium combines the leading expertise on the major OSR pathogens, the latest research on defence mechanisms of resistance and expertise in association genetics to identify effective QDR genes. Our industrial partner, KWS, will provide expertise on deployment of QDR in the field and on the development of genetic markers for molecular breeding of improved OSR varieties.

We will identify resistance to the most important pathogens of OSR: Sclerotinia sclerotiorum, Verticillium spp, Leptosphaeria maculans, Alternaria brassicicola, Pyrenopeziza brassicae, and the model pathogens Pseudomonas syringae and Botrytis cinerea. A panel of 192 diverse B. napus lines will be screened for resistance against these pathogens in controlled environments and at KWS field trial sites. Schools will contribute in a 'citizen science' project and evaluate resistance at locations throughout Europe. In the same lines, we will quantify induced defence responses to conserved pathogen-associated molecular patterns (PAMPs). We will also quantify salicylic acid, lignin, phenylpropanoid, glucosinolate, and indole metabolites that are implicated in resistance mechanisms. Using association transcriptomics, we will identify resistance gene loci against multiple pathogens and understand how this relates to metabolite production and PAMP-triggered immunity.

To test hypotheses about their contribution to resistance, we include studies on specific genes. Whilst glucosinolates contribute to resistance they can reduce the quality of seed. GTR1 and GTR2 are transporters in Arabidopsis that control the allocation of glucosinolates to seeds. We will test gtr1 gtr2 mutants for fitness and create gtr TILLING mutants in Brassica rapa (B. napus A genome) to measure the glucosinolate partitioning between leaves and seed. The work could enable development of OSR with high leaf glucosinolate content for resistance, without compromising seed quality. We will introduce tomato receptor Ve1 into B. napus and assess its ability to mediate resistance against Verticillium wilt.

This research will lead to more sustainable production of OSR, with higher productivity through lower vulnerability to biotic stress and less reliance on chemical inputs.

Technical Summary

Oilseed rape (OSR, Brassica napus) is a major crop worldwide, producing edible oil, biodiesel and protein for animal feed. Diseases are a major factor limiting OSR production and improved control is an urgent priority. Breeders are increasingly using quantitative disease resistance (QDR) which is considered broad-spectrum and durable. This proposal addresses the current gap in our knowledge which is the identification of the most useful QDR for breeding.

The first layer of active defence in plants is based on the perception of pathogen (or microbe) associated molecular patterns (PAMPs/MAMPs) leading to PAMP-triggered immunity (PTI). PAMPs are essential molecules, conserved in entire kingdoms of microbes, and are recognised by pattern recognition receptors (PRRs) in plants. Within ERA-PG (PRR-CROP) we developed methods for studying PTI in Brassica crops.

We will identify gene loci contributing to QDR against the most important pathogens of OSR using the novel method of associative transcriptomics (AT), developed at JIC in B. napus by the Bancroft group. Using a 'B. napus diversity panel' of 192 diverse lines we will quantify resistance to the most important pathogens: Sclerotinia sclerotiorum, Verticillium spp, Leptosphaeria maculans, Alternaria brassicicola, Pyrenopeziza brassicae, Pseudomonas syringae and Botrytis cinerea. We will quantify induced defence responses to PAMPs and measure salicylic acid, lignin, phenylpropanoid, glucosinolate, and indole metabolites that are implicated in resistance mechanisms. Using AT, we will identify resistance gene loci against multiple pathogens and understand how this relates to metabolite production and PAMP-triggered immunity. We will also investigate glucosinolate partitioning between leaves and seed using mutants of GTR1 and GTR2 transporters and introduce tomato receptor Ve1 into B. napus and assess its ability to mediate resistance against Verticillium wilt.

Planned Impact

Production of oilseed rape is rapidly increasing in the EU, where it provides the primary source of edible oil, biodiesel and high-protein animal feed. OSR is at risk from diseases which currently account for losses of 10-20%. With imminent EU restrictions on the use of fungicides, the breakdown of R-genes and climate change, novel approaches to disease control are essential and the aim of this timely project. The economy will benefit because plant breeders will be able to develop new varieties with improved resistance, strengthening Europe's leadership in sustainable agriculture. Farmers will become more competitive with new varieties that they can grow with reduced inputs. Advisors, consultants and levy boards which fund strategic research will benefit through new knowledge about the most appropriate lines to select. The environment will benefit because there will be reduced inputs, and more efficient use of fertilizers and land. This will also benefit policymakers through reducing the carbon footprint and helping governments achieve climate change mitigation (Hughes, et al. 2011). Society will benefit through improved environment and economy and production of safer food. This project stimulates innovation through application of advanced technology to agriculture, contributes to job creation, and provides an exciting training opportunity for the next generation of crop scientists who will further strengthen the European bio-economy.

The consortium is in an exceptional position to achieve impact, with its established strong links with the European breeding industry, farmers, policy makers and the wider agricultural community. We will meet at least annually to review progress and agree knowledge transfer activities. We will regularly present our work at established dissemination events such as the annual OREGIN, Brassica Research Community and Cereals' meetings, where most of the European breeding industry and levy board stakeholders such as HGCA are present. We will disseminate results to industry at the Business Council at the Faculty of Biology and Environmental Protection (Lodz), and at the Polish Federation of Biotechnology. We will write popular articles for the trade press such as Farmers Guardian and Farmers Weekly, publish our research in open-access scientific journals and present our results to academics at international conferences such as the Molecular Plant-Microbe Interactions meeting, Eucarpia and Crucifer Genetics Workshop. We will present our work to the public at events such as the annual Friends of John Innes Centre crop walk and the Fascination of Plants day at Wageningen UR. With a 'Sparking Impact' award, CR is working with the Knowledge Exchange and Commercialisation team at JIC on delivery of scientific output through social media, enabling us to reach and quantify new audiences. We will reach schoolchildren to convey the excitement of plant science as a University and career option. We will work with the Teacher Scientist Network to deliver an impact module in 'citizen science' to augment our research on resistance at locations in each member country. Results from this will be disseminated by TSN and the members of this consortium.

Publications

10 25 50
 
Description This progress summary only reports our role on coordinating the consortium and our own results, not the results of the other six partners.
1) We have organised the kick-off meeting in Norwich, together all participants except WUR. We talked through all work packages and made sure everyone agrees on the distribution of tasks.
2) Together with the computing department at JIC we have put in place a datasharing site, using Office Sharepoint. All information on the consortium and shared material available at JIC has been placed on this website, together with instructions on usage.
3) We have sown, grown, harvested and threshed the first round of bulk up at JIC. Seeds were distributed to all groups. A final selection of 192 lines has been made after feedback from the transcriptome analysis,
4) All 192 lines and 2 references lines were sent to Nottingham for bulk-up, these have been threshed at Elsoms and some have been returned to JIC for distribution to all other groups.
5) We have organised the second meeting in Copenhagen, hosted by Barbara Halkier (UC), 13-14 October 2016. The third meeting was held at Lodz, Poland, 4-6 October 2017
6) Field trials have been sown at KWS-Fehnmann and KWS-UK
7) Conditions and settings for PTI assays and Botrytis and Pseudomonas assays have been optimised for high through put. We discovered 2 new PAMP groups with homologs in our pathogens: NLPs and xylanase. Most lines respond to all PAMPs but BnPEP1 and BcNEP2, responses have at least a 100 fold range in response intensity over the 192 lines. NLPs provoke an all or nothing response, only 12 out of 192 lines respond. BnPEP1 doesn't provoke any response in either Brassica or Arabidopsis Col-0.
8) Initiated collaboration with Earlham Institute (formerly TGAC) to map SNPs to 12 NLP responding and non-responding lines to look in Brassica napus for homologues of AtRLP23 for NLP-response specific clustering of SNPS.
9) The methods optimised in this project have been prepared for publication as a book chapter in the edition Plant Pattern Recognition Receptors in the lab protocol series Methods in Molecular Biology by Springer.
10) Methods and results from this project have been used to establish a PhD project mapping PAMP-triggered immunity in Brassica oleracea. The complimentary aspect of these projects facilitate progress in all Brassica spp. Drafts of further publications are in preparation
Exploitation Route We are developing plans to continue the work in collaboration with others
Sectors Agriculture, Food and Drink,Environment

 
Description the findings have been presented in a number of scientific meetings and public engagement activities. In addition, the research has developed a schools project throughout Europe which is continuing for a second year
First Year Of Impact 2015
Sector Agriculture, Food and Drink,Education
 
Description Consultancy in Plant Pathology 
Organisation RAGT Seeds
Country United Kingdom 
Sector Learned Society 
PI Contribution consultancy
Collaborator Contribution Knowledge and facilities
Impact the consultancy led to the award of the FLIP grant
Start Year 2014
 
Description Plant stimulants to prime plant immunity 
Organisation Arlabion Ltd
PI Contribution We provided our expertise to address a specific research question for the Company
Collaborator Contribution They provided the background and some technical knowledge to the project
Impact A report has been submitted to the company
Start Year 2017
 
Description A taste of Genetic Diversity: demonstration activity for the John Innes Centre open day 
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 Public/other audiences
Results and Impact A demonstration of our research was performed at an open day at the John Innes Centre, involving hands on activities and discussion on the theme of 'a taste of genetic diversity. The activities involved showing how brassicas were used in baby leaf salads, and how heritage barley varieties were used in brewing beer
Year(s) Of Engagement Activity 2017
 
Description Disease resistance and immunity in brassicas: presentation to the Chinese Academy of Agricultural Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of our research on brassica pathology to the Chinese Academy of Agricultural Sciences. The meeting took place at the John Innes Centre
Year(s) Of Engagement Activity 2017
 
Description Disease resistance in Brassicas 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Annual meeting for the BBSRC project Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative transcriptomics
Year(s) Of Engagement Activity 2015,2016
 
Description GCRF visit with Nepalese Researchers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A fact-finding mission to Nepal was undertaken with the aim of developing new collaborations for potential GCRF projects
Year(s) Of Engagement Activity 2017
 
Description Mechanistic Analysis of Quantitative Disease Resistance in Brassica by Associative Transcriptomics 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop on disease resistance in brassicas, leading to further collaborative projects
Year(s) Of Engagement Activity 2015
 
Description Mechanistic Analysis of Quantitative Disease Resistance in Brassica by Associative Transcriptomics ERA-CAPS workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Annual meeting for Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Association Transcriptomics. The meeting was organised at the University of Lodz, Poland, and involved presentations by the members of the consortium
Year(s) Of Engagement Activity 2017
URL http://www.eracaps.org/joint-calls/era-caps-funded-projects/era-caps-second-call-2014/mechanistic-an...
 
Description Mechanistic Analysis of Quantitative Disease Resistance in Brassica by Associative Transcriptomics ERA-CAPS workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at ERA-CAPS meeting, Lisbon
Year(s) Of Engagement Activity 2015
 
Description Oilseed rape genetic improvement network 
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 Attended annual meeting of the oilseed rape genetic improvement network
Year(s) Of Engagement Activity 2016
URL http://www.herts.ac.uk/oregin/about-oregin
 
Description Presentation about crop disease resistance 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact presentation of research activities to ICL speciality fertilizers
Year(s) Of Engagement Activity 2016
 
Description Presentation to Novozymes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact presentation of research to three representatives from Novozymes, a speciality chemicals company based in Denmark
Year(s) Of Engagement Activity 2017
 
Description presentsation to the Flying Farmers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Flying farmers are a group of farmers interested to learn about the latest trends in research. the presentation involved talking to them about our work, and engaging in a discussion with them
Year(s) Of Engagement Activity 2017