Gramene: A Platform for Comparative Plant Genomics

Cold Spring Harbor Laboratory, Cold Spg Hbr NY

Investigators

Abstract

PI: Lincoln Stein (Cold Spring Harbor Laboratory) CoPIs: Doreen Ware (Cold Spring Harbor Laboratory), Susan McCouch, Edward Buckler, and Pankaj Jaiswal (Cornell University; subawardee) The Gramene database (http://www.gramene.org) is an online resource, jointly supported by NSF and the US Department of Agriculture's Agricultural Research Service. It integrates the genomic, genetic and phenotypic information in rice, maize and other cereals, thereby giving scientists and other end-users easy access to this integrated information. This project will provide for the enhancement of Gramene by incorporating biological pathway and genetic diversity information from maize, rice, wheat, sorghum, and other cereals into the resource. Comparative genomics tools will be developed, thereby allowing researchers to use knowledge gained in one plant species to identify and characterize functionally significant genes and other elements in the genomes of other species. Scientists can use the resource to make advances in our fundamental understanding of the plant processes of economic importance such as hybrid vigor, grain development, seed dormancy, drought tolerance, and resistance to diseases. In addition, the tools developed will allow for the estimation of the breeding value of individual genetic variants, thereby providing breeders with the ability to select the ideal combinations of seed stocks to create varieties that have desirable traits such as robustness, the ability to grow in marginal environments, or have high potential as a source for biofuels and other materials of high economic value. Information resources developed, and being developed, through genomics efforts are key elements to advance our fundamental knowledge base for a future bio-based economy and to address the expected need for feeding an expanding world population. Many of the information resource are still underutilized because of the fragmentation of the datasets and the absence of tools to make meaningful connections among them. To fully unlock the potential of plant genome data, the diverse datasets must be integrated so that information is shared both within and between species. It is one of the goals of Gramene to provide that integration. Another goal of the project is to deliver the integrated dataset into the hands of plant geneticists, molecular biologists, evolutionary biologists and breeders by providing compelling, intuitive, user interfaces. Lastly, the project will reach out to students, the public, and to underrepresented minorities via a series of online tutorials and on-site workshops that involves a novel, and cost-effective, public/private partnership. All the information resources generated by Gramene will be available to scientists, breeders, and members of the general public free of charge and without intellectual property restrictions.