ARS | Publication request: Plant databases and data analysis tools

Submitted to: Diagnostics in Plant Breeding
Publication Type: Book / Chapter
Publication Acceptance Date: April 16, 2012
Publication Date: N/A

Technical Abstract: It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public databases. For some major crop species, databases exist including GrainGenes (for small grain cereals), Gramene (for rice and related grasses), MaizeGDB (for maize), SoyBase (for soybean), and the Sol Genomics Network (SGN; for tomato, potato, etc.) to name a few. These databases are extensive and useful, but currently require some modifications to accommodate the large volumes of marker information currently being produced. Mechanisms to query such large datasets also are lacking. In addition, public data storage and access to marker data in specialty and new crops remains largely unavailable or is difficult to access and use. This article is devoted to describing tools and resources that are currently available for use and outlines some possibilities for addressing the “big data” and query problems that face both data providers and the plant breeders they seek to serve.