Featured project


A community resource for wheat functional genomics


A 5-year project funded by the BBSRC’s Bioinformatics and Biological Resources Fund (2008-2013)

Vision

A one stop shop for wheat functional genomics providing UK researchers with authenticated data and biological resources which are freely available without restriction

Summary

UK-based resources for wheat research are currently isolated and tailored to “in-house” needs. As such they are often invisible to or inaccessible by the outside world. With the backing of the wheat community, Monogram (consisting of Rothamsted, IGER, JIC and SCRI), the Wheat Genetic Improvement Network (WGIN) and the Monogram Network we (Bristol University in collaboration with Rothamsted and NIAB) propose to initiate a process which brings together these resources under one umbrella namely the existing Monogram Network and its associated web site. Our approach will organise the UK’s wheat tools and resources such that they become accessible to all, while having a “customer first” approach whereby users of the new Monogram Network site need to perform single searches regardless of the resources’ physical location. With the resources requested the Bristol group will oversee the process whereby both its current biological/bioinformatics’ resources and several new resources become available via the Monogram Network web site. This process will form the initial resource “modules” of the Monogram Network web site to which other members of the community will be encouraged to add to over time in line with BBSRC’s recently launched data sharing policy. Given the global challenges facing all plant scientists we believe that this proposal represents the best opportunity yet for the UK wheat community to work as one and face the future as an integrated community.

Objectives

  • Engage with the UK wheat community to locate further resources and build tools to search for these via the Monogram Network web site portal. Actively promote awareness of the Monogram Network web site and its use as a portal to wheat resources for future projects and new datasets.
  • Redevelop the existing Monogram Network web site to make it fit for purpose as a portal to all the UK’s wheat data and resources.
  • Update the analysis tools, currently within cerealsdb, to incorporate all array-based technologies such as Agilent and Affymetrix GeneChip data.
  • Add genotyping data and analysis tools, including those for the padlock probe technology to the portal facilities.
  • Publicise the TaPMS2-134 and MSH2/MSH6 knockout mutants, offer a TILLING service for these and add sequence information for mutants to the portal as they are screened.
  • Update the digital differential display tool to incorporate libraries other than those generated by the Bristol IGF program (where external library provenance can be guaranteed) and replace the existing simple statistics with pre-cached randomisation tests.
  • In collaboration with Rothamsted, explore ways of linking wheat to Arabidopsis genomics data where homology exists between the two taxa and develop a wheat ENSEMBL database.
  • Expand the facilities currently within wheatbp.net to include more farmer, breeder and end user relevant data.
  • Provide training (practical and bioinformatics) to academic and industrial personnel in the use of technologies developed by the Bristol group.

The project team

University of Bristol Gary Barker, Jane Coghill, Keith Edwards
NIAB Ian Mackay
RRes Nathalie Castells, Chris Rawlings, Paul Verrier


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