Bioinformatics tools for plant genetic resources

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office


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.


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