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WSU to develop national database system for crop genomic research

Washington State University has been awarded a five-year $2 million National Research Support Project grant to build and maintain a national system for sharing digital plant genetic resources. Known as NRSP10, the project is the tenth National Research Support Project in the nation.

Map showing genomic regions of shared ancestral origin of peach and strawberry.  (Sook Jung, WSU).
Map showing genomic regions of shared ancestral origin of peach and strawberry.
(Sook Jung, WSU).

The system will support research for 24 crops grown in all 50 states, collectively valued at $23.6 billion in 2012. However, the concept is flexible enough to have impact on other crops and organisms that are valuable to U.S. agriculture.

“Recent advances in genomic, genetic and breeding technologies have led to a paradigm shift in crop science research,” said Dorrie Main, associate professor of horticulture and the project lead. “The shift is generating petabytes of data that must be organized, stored, analyzed and integrated so that the data are accessible and useful to multiple research communities,” she said.

One petabyte equals one million gigabytes, or one thousand terabytes.

Main explained that many existing genomic databases were developed in isolation using different approaches to the organization of the data for a specific organism. The new system will allow multiple databases to operate under a commonly agreed set of rules using a common language.

An outgrowth of the Genome Database for Rosaceae developed by Main and her colleagues, the system is being built using an open source software platform called TRIPAL. By establishing standards, protocols and applications for data collection, organization, storage, analysis, and curation the system will help standardize crop genetic research.

D.Main by Wilhite 10.3.14IMG_9098crcted
Dorrie Main, WSU Department of Horticulture.

“In Washington State, which grows 300 different crops, only a few can afford to take advantage of new genetic procedures like marker assisted breeding,” said Mike Kahn, associate director of the Washington State Agricultural Experiment Station. “This grant provides the infrastructure and technical support to access the genetic data needed to do genomic research and breeding nationwide.”

Input and feedback over the five-year project from scientists across the nation will ensure a robust system that serves multiple research needs.

The project represents a collaboration among commodity groups for tree fruit, berries, legumes, and cotton; the USDA Agricultural Research Service; and 40 scientists at 12 universities including Clemson University, Cornell University, Michigan State University, North Dakota State University, Oregon State University, Salve Regina University, University of California at Riverside, University of Florida, University of Georgia, University of Minnesota, University of Tennessee and Washington State University.

Media Contacts

Dorrie Main, WSU Department of Horitculture, 509-330-6029