Accelerated Breeding for Disease Resistance in Commercial Brassicas by Associative Transcriptomics

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

Abstract

Baby Leaf Kale (BLK) has been popularised as a super food, through the growing health awareness and weight loss movement in the USA and Europe. Consequently, the demand for BLK has increased with global consumption rising by 40% in just one year (2012 - 2013). Diseases caused by mildews and bacteria are a major problem in BLK production. This problem has become even more challenging due to enforced reductions in agrochemical use as a result of changing legislation in early 2015. There are also tight restrictions on the Minimal Residue Level (MRL) of pesticides and fungicides which are defined product by product and frequently reviewed.

CN Seeds is a UK-based commercial seed breeding company specializing in breeding baby leaf salad seeds, including BLK and herb seeds. BLK has been the company's best-selling product over the last two years, accounting for 12% of total revenues. The continual introduction of new varieties that meet and exceed customer needs is a key component of CN Seeds competitive strategy.

This interchange project addresses the challenge of developing disease-resistance with a commercially desirable BLK variety by transferring knowledge between scientists at JIC and CN Seeds. The JIC scientists are working on developing disease resistance in oilseed rape, an important brassica closely related to BLK. The methods that they are using for variety improvement in oilseed rape can be directly applied to BLK, and this interchange aims to transfer that knowledge. The JIC scientists will visit CN Seeds to learn about commercial production of seed for the leaf salad market and the constraints imposed by diseases. This will enable them to tailor their research to address this issue more effectively. A CN Seeds scientist will also work at JIC, learning how to develop disease-resistance screening procedures and about a novel breeding technique known as associative transcriptomics. This genetic technique rapidly identifies gene loci associated with disease resistance which can be used to develop molecular markers for accelerated breeding.

The interchange benefits both JIC and UK science generally through improved understanding of the commercial constraints on seed production; this will enable researchers to target their science to achieve greater impact. The interchange is supported financially by CN Seeds which benefits through improved competitiveness against overseas rivals, increasing exports and revenue for the UK economy.

Technical Summary

This interchange project aims to exchange knowledge between JIC and CN Seeds (CNS) scientists about the commercial and technical improvement of two highly-related brassica species, oilseed rape (B. napus) and baby leaf kale (B. oleracea, BLK). In a related grant (Mechanistic Analysis of Disease resistance in Brassicas by Associative Transcriptomics, MAQBAT), we are undertaking research to develop resistance in B napus. The methods used in MAQBAT can be directly applied to BLK variety improvement.

The first objective enables JIC researchers to experience research in a commercial environment. They will visit customers of CNS to learn about the BLK supply chain and the impact of diseases. Through this objective, the JIC researchers will be able to more effectively target their science to make it relevant to UK industry. The second objective aims to transfer knowledge to CNS so that they can accelerate the breeding of disease-resistant BLK. A CNS scientist will work at JIC, learning about the pathology assays and molecular markers. We will establish and maintain a collection of mildew isolates through the network of growers liaised with CNS and academic partners. We will determine virulence patterns for race differentiation and select the most relevant isolates for agriculture. The isolates will be used for screening disease on the BLK diversity set obtained from the VeGIN network and amplified at CNS.

To develop markers for mildew resistance in BLK, we will follow two strategies: 1) mapping in BLK and 2) transferring results of associative transcriptomics (AT) from B. napus to BLK. For mildew responses in BLK we will use mapping populations and markers established previously within the DEFRA initiatives VeGIN and OReGIN. This will enable CNS to develop their own populations for mapping traits. We will use the B. napus diversity panel from MAQBAT to find loci linked with mildew resistance by AT. These loci can be used by CNS for use in BLK breeding directly.

Planned Impact

This interchange contributes to UK policy makers' efforts, including BBSRC, on enhancing knowledge exchenge and commercialisation. This will create commercial wealth, support economic competitiveness and enhance people's lives as described here.

Who will benefit from this research?
There will be numerous beneficiaries within the global BLK supply chain from this interchange. The supply chain includes growers, seed producers, commercial seed companies, seed merchants and distributors, processors, supermarkets and consumers. This interchange will make the supply chain more secure and competitive in the world market. The management of crop diseases with fewer inputs also drives forward policy to develop sustainable agriculture which benefits consumers and the environment.

How will they benefit?
Growers will become more competitive with new varieties that they can grow with reduced inputs and less impact from crop failure. The economy will benefit because new BLK varieties with improved resistance will be developed in the UK as opposed to the US, strengthening Europe's leadership in sustainable agriculture. 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. Society will benefit through improved environment, economy and production of safer food.

The CNS Group are wholly UK-based, and their main competitors are all based overseas. CNS are contributing financially to the project with the aim of strengthening their competitive position. Development of a mildew-resistant BLK variety could increase CNS market share to over 50%, and enable them to be a dominant player in the market for a number of years. An increase in demand for CNS products would have wider benefits by boosting UK trade for all involved in the seed distribution supply chain; seed production and treating companies, dispatch companies and those involved supplying packaging materials. This interchange 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.

There will be a health benefit to the wider population of consumers. BLK has exceptionally high levels of vitamin A, C and K, calcium and iron content. A number of health benefits have been linked to consuming kale raw, including boosting immunity, reducing the risk of cancer, diabetes, high blood pressure, chronic inflammation, oxidative stress and heart disease. A disease resistant BLK variety will ensure continued production of BLK at a reasonable price for the long-term benefit of the consumer.

Publications

10 25 50
 
Description A pathology lab has been established at CN Seeds. Resistance to downy mildew has been identified in kale which will improve the quality of baby leaf salads. The project has led to a collaboration between JIC, CN Seeds and Sarba Shrestha Seeds in Nepal.
Exploitation Route the findings will enable the development of improve kale varieties for the baby leaf salad market
Sectors Agriculture, Food and Drink

URL https://www.jic.ac.uk/blog/baby-leaf-kale-resistant-to-downy-mildew-disease-created-in-collaboration-between-industry-and-science/
 
Description the research has enabled CN seeds Ltd identify resistance to baby leaf kale which will enable them to develop improved varieties for the market. This is already creating impact by ensuring CN Seeds develops as a leading supplier of seed for the baby leaf market, and other markets. The findings have also been used in further collaborative work with CN Seeds to develop business opportunities with a commercial partner in Nepal. This has led to the successful award of a GCRF/BBSRC-funded 'International Flexible Interchange Project'
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description DTP iCASE
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
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 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 research on brassicas 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Presentations were given to CN Seeds and Clover seeds about research on brassica disease resistance. The work has led to further development of collaborative research with CN Seeds on downy mildew in brassicas for the baby leaf salad market. We also made a successful joint application for GCRF-funded research to develop collaboration between CN Seeds and a seed company in Nepal.
Year(s) Of Engagement Activity 2018
 
Description Genetic analysis of immune responses in brassicas 
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 research results at the 21st Crucifer Genetics Conference, St Malo, France. The audience was comprised of scientific researchers with a wide range of interests in crucifer genetics
Year(s) Of Engagement Activity 2018
URL https://colloque.inra.fr/brassica2018/
 
Description Improving disease control in brassicaas 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Meeting with Prime agriculture to present research and explore potential collaborations in the future. Prime Agriculture are consultants in agriculture, with particular focus on agronomy. The work has led to an application to assess research priorities for disease control research in brassicas
Year(s) Of Engagement Activity 2018
 
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 of FLIP project and New Heritage Barley case study to BBSRC 
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 Policymakers/politicians
Results and Impact Presentation to BBSRC as part of the contribution to 'Excellence with Impact' competition
Year(s) Of Engagement Activity 2016
 
Description Video Blog of collaboration during the flexible interchange project 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I youtube video about the collaborative flexible interchange project was produced and distributed via social media.
Year(s) Of Engagement Activity 2017
 
Description visit to Piccavers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Visit to Piccavers, specialist salad growers, to learn about their business
Year(s) Of Engagement Activity 2016