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

Reference	BB/N005007/1
Principal Investigator / Supervisor	Dr Christopher Ridout
Co-Investigators / Co-Supervisors	Dr Henk-jan Schoonbeek
Institution	John Innes Centre
Department	Crop Genetics
Funding type	Research
Value (£)	466,516
Status	Completed
Type	Research Grant
Start date	01/09/2015
End date	31/12/2018
Duration	40 months

Abstract

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.

Summary

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 relatesto 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.

Impact Summary

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.

Committee	Not funded via Committee
Research Topics	Crop Science, Microbiology, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	ERA-NET on Coordinating Action in Plant Sciences (ERA-CAPS) [2013-2014]
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/N005112/1 14 ERA-CAPS Mechanistic Analysis of Quantitative Disease Resistance in Brassica by Associative Transcriptomics

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