New integrative data portal for brilliant brassicas

12 May 2016

Scientists at the Earlham Institute (EI) have released the first web repository for Brassica (mustard plants) trait data to tackle reproducibility, user controlled data sharing and analysis worldwide.

Scoring the versatile crop’s beneficial traits will assist Brassica breeders in improving their crop yields, increased nutritional benefits and reduce our carbon footprint through biofuel production.

The Brassica Information Portal (BIP), is being developed with a uniquely collaborative Brassica research community. Increasing the visibility of existing research, the open-access Portal will store all data from previous and future pre-breeding trait scoring experiments performed on Brassica species

The BIP presents a standardised, curated data resource for scientists. By matching the characteristics of plants with their genetic background, we can better inform breeding programmes for crop improvement.

The Brassica genus contains versatile vegetable, forage and crop plants that exuberates many valuable attributes for public consumption and the environment. The innovative new data portal hosts information about how, for example, rapeseed responds to different experimental conditions to identify beneficial genetic traits.

Significant to the consumer, these findings will increase the production and quality of the Brassica vegetables, and decrease costs in biofuels through using rapeseed for biodiesel production.

Annemarie Eckes, Research Assistant in the Integrative Genomics Group at EI, said: “Thanks to this database,  traits from pre-breeding trials are made more accessible and can be used for improving existing varieties. Breeding of improved varieties means that we can have very nutritious cabbage / broccoli / swede (all from the Brassica genus) , varieties are resistant to pests, or varieties that need minimum resources.”

Facilitating research projects for population genomics and breeding information, the database will enable scientists to store and analyse large quantities of Brassica trait data. The portal will serve as a gateway for an integrated analysis of phenotypic and genotypic information using methods such as associative transcriptomics and QTL analysis.

Using new traits for marker assisted selection, Brassica breeders will be able to decrease the input of fertiliser and water, increase crop yield, quality and resilience of the plants. High concentrations of industrially important compounds can be selected for in otherwise discarded parts of the plant, adding value to the crop (e.g. lubricants in waste straw).

Additional data that will be collected in the Portal includes information to make rapeseed contain much more oil used for biofuel production. This will reduce our carbon footprint by decreasing the UK’s fossil fuel emissions, and raise energy supplies.

This can all be done with conventional breeding methods, drawing from the list of genetic traits associated with plants in the new Brassica genus database.

With climate change impacting the UK with both droughts and floods, new pests arriving and thriving, old varieties may not be as resilient to these changes in the environment as newly bred ones. It is important to understand and create the diversity of the vegetables we eat to select the best individuals for creating new varieties to ensure these vegetables will also be on our plates in the future.

Annemarie Eckes, added: “The database will be a powerful tool for the breeders to select for new traits important for the future changes. At the same time, they need to produce a reliable amount at appropriate prices for society; to guarantee food and energy security and a healthy diet.”

Dr Wiktor Jurkowski, Project lead and Group Leader at EI, said: “Data sharing today must be extensive, comprehensive, global and long-term. With the BIP, we help the Brassica Community to achieve these objectives.

“With all trait information in one place, and linked with genomics data, many new connections between the plant’s traits and responses in different experiments can be drawn, that was previously not possible. This database can, therefore, encourage integrative, big data analysis, which has become a crucial part of today’s Science.

“At the same time, it is a perfect example of collaborative work across UK and beyond. The Brassica Information Portal is derived from ‘Cropstore’, a database hosting Brassicas and other crops led by Prof Graham King (University of Southern Cross, Australia) and currently supported by the Renewable Industrial Products from Rapeseed (RIPR) project, led by Prof Ian Bancroft at the University of York and by BBSRC.”

The further database design and content curation involved Sarah Ayling, co-lead on BIP project (EI), Tomasz Gubała, Piotr Nowakowski (Spectrum IT), Martin Trick, Judith Irwin and Rachel Wells (John Innes Centre), RIPR, OREGIN 3 consortia and the UK Brassica community, whose feedback is reflected in the user interface and BIP features.

Web-based analytics for the BIP is developed in collaboration with the Clark Group (EI), and Ian Bancroft (University of York). Anil Thanki (Davey Group, EI) and Dan Bolser (EBI) are helping to cross-link BIP with TGAC Browser and Ensembl Plants (http://plants.ensembl.org). The Davey Group will also help with integrating BIP with iPlant and COPO - projects supporting collaborative and open plant science. Finally, Manuel Corpas (EI) and his team will contribute to further development of phenotyping API and oversee implementation of bioinformatics standards developed within the frame of ELIXIR.

See our blog on 'Brilliant Brassica' to find out more about its benefits and the importance of the BIP to science, agriculture, industry and us!

Notes to editors

For more information, please contact:

Hayley London

Marketing & Communications Officer, Earlham Institute (EI)

  • +44 (0)1603 450 107

hayley.london@earlham.ac.uk

The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £6.45M in 2015/2016 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.

www.earlham.ac.uk

The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

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