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Cold Spring Harbor, OSU Receive $10M from NSF for Grass Genome Resources

NEW YORK (GenomeWeb News) – The National Science Foundation has provided $10 million for two programs at Cold Spring Harbor Laboratory and Oregon State University to develop public data resources containing genomic information about important crop plants, such as corn, rice, wheat, barley, and Arabidopsis.

The bulk of the $10 million will fund continued development of the CSHL-led Gramene project, a resource of plant genomic information. Under a sub-contract, around $2.9 million of the award will go to OSU to develop the Plant Reactome project, a multi-partner portal which houses information about genetic interactions in corn, rice, and Arabidopsis.

OSU also will use its funding to pull together scientific literature about the three plants and include it in the database. Researchers there also will study how hormones are involved in their growth.

Other partners in the Gramene and Plant Reactome projects receiving funding under the NSF award include the Ontario Institute for Cancer Research, the European Bioinformatics Institute, and the American Society of Plant Biologists.

"By honing resources like Gramene, we are bringing to bear the knowledge and hidden insights that leading-edge information technology makes visible in order to serve the needs that plant biologists have in generating ever more sophisticated analyses of experimental data," CSHL Adjunct Professor and lead investigator on the project Doreen Ware said in a statement.

Ware said the funding will help biologists studying these plants, which are relied upon as food staples for billions of people, to integrate valuable but scattered bits of genomic data into the public resource.

The Gramene resource's main objective is to enhance the "mountains of collected data on plant genomes," and it is particularly useful because of the large amount of genomic conservation among the grasses, CSHL said in its statement.

The Gramene project, which was launched in 2001 with funding from the US Department of Agriculture, also houses data on other crops, such as soybean, tomato, and poplar, and it has incorporated genomes of mosses and algae.

The Plant Reactome portal will host the metabolic and regulatory networks of genes and metabolites from corn, Arabadopsis, and rice, each of which has well-annotated genomes, Pankaj Jaiswal, assistant professor of botany and plant pathology at OSU, and co-investigator on the grant, told GenomeWeb Daily News.

The program aims to provide integrated data sets to plant geneticists, molecular and evolutionary biologists, and plant breeders.

"For these three principle plants, we are looking at the genetic diversity across these genomes and fine-mapping the function of these genes, including association mapping, from these genetically diverse lines," Jaiswal said.

"Putting the networks here in the Plant Reactome will actually help us understand if there are certain genetic changes that are happening in that diverse population, and how it is affecting the network interaction and its adaptation to the local area, and phenotype traits, such as flowering time, yield, grain size, nutritional content, and response to various abiotic stresses like drought and salinity, as well as responses to pathogen attacks," he said.

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