Award details

Bioinformatics tools for plant genetic resources

Reference	BBS/E/J/000CA284
Principal Investigator / Supervisor	Dr Joanne Dicks
Co-Investigators / Co-Supervisors	Mr Michael Ambrose, Professor Thomas Ellis
Institution	John Innes Centre
Department	John Innes Centre Department
Funding type	Research
Value (£)	90,687
Status	Completed
Type	Institute Project
Start date	01/09/2007
End date	31/08/2009
Duration	24 months

Abstract

Efficient utilisation of plant genetic resources (gene banks) requires versatile, powerful databases for storing, accessing and combining the wide variety of data that are becoming available in rapidly increasing amounts. We have developed a functioning database, GERMINATE, which can accommodate a wide variety of data types, from descriptive (morphology, geography) to molecular (DNA sequence, marker scores, map position etc.). We now seek funds to complete its development into an integrated data and analytical resource for the World's plant genetic resource community. Currently, the GERMINATE database stores passport and multi-crop descriptor data for every popular molecular marker type except SNP. We propose to extend this capability to include SNP data, in a format that is acceptable to the World's plant genetic resources and genomics communities. We will also deploy an ontology module, which will provide standard nomenclatures for phenotypes, developmental stages and mutant or disease ontologies for crop plants, allowing rational searching for these previously inaccessible characters. Additionally, we will increase the functionality of GERMINATE by greatly expanding the number of linked, web-accessible bioinformatic tools, including the existing suites STRUCTURE (for deducing and visualising the population structure of germplasm), TASSEL (for tree drawing and linkage disequilibrium estimation) and DIVA-GIS (for visualising geographical data associated with accessions). Also, a new set of tools will be designed and developed, including GERMANE (managing workflows of multiple, chained analytical routines), CORE (for management of genetic resources, including identification of core collections in response to user requirements), and NETWORK (analysing non-treelike evolution via introgression, using a marker model-based approach). Lastly, the GERMINATE web interfaces will be improved to allow easier and more powerful uploading, retrieving and analysis of the data.

Summary

unavailable

Committee	Closed Committee - Genes & Developmental Biology (GDB)
Research Topics	Plant Science, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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