Sunday, 24 July 2016

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An innovative 'one stop shop' germplasm potato database resource is now available for scientists online.

The International Potato Center (known by its Spanish acronym CIP) has published a new online database for the potato and sweetpotato.

The database is searchable for more than 90 attributes related to the germplasm held in CIP's extensive genebank collections. The database took more than two years to develop, and is the first of its kind to apply a scheme originally used for housing genomics data to a genebank collection.

"It is the holy grail of the genebank and breeding information managers' community - having a data search facility for different kinds of data," says Reinhard Simon, head of CIP's Research Informatics Unit.

In recent decades, bioinformatics - the application of information technology to better understand biological processes - has been focused primarily on management systems that can deal with the enormous amount of information generated by rapid developments in molecular biology. CIP took one such system, BioMart, and created a novel application allowing integrated searches across a wide range of different data types.

"The kind of information we need is often still housed in specific databases. With this system, potentially all the evaluation data you can think of can be combined; it's a one stop shop," says Simon.

The new database includes what is called passport data, such as the origin and availability of germplasm, compliant with the standard MCPD (multicrop passport descriptor list). With characterisation data organised according to crop specific international standards, users can search for any specific traits they are looking for (e.g., drought tolerance or chipping quality) using morphological characteristics or biotic and abiotic evaluation data. Also included are molecular marker data (SSR), and the entire list of worldwide distributions of CIP held germplasm.

The flexibility of the system allows for a range of information from summary reports to detailed, accession-level information. It has a user-friendly, three-step interface, requiring little or no training. If needed, support is provided on the CIP site and by an online BioMart tutorial. Breeders, scientists, or curators who want to order germplasm from the CIP's genebank can do so via a hyperlink using a 'shopping cart' system, similar to online shopping sites.

The database also provides an important new springboard for further research. The potential is vast, explains Simon, "Curators from other genebanks sometimes need or want to corroborate information, and scientists and other researchers can use all these data for further analysis and for documenting biodiversity."

The database will be updated as new data are released and is available at www.cipotato.org/research/genebank/search

 

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