Gramene: A Platform for Comparative Cereal Genomics

Cold Spring Harbor Laboratory, Cold Spg Hbr NY

Investigators

Abstract

This project will expand and continue the operations of Gramene, a comparative mapping database for rice and other cereals. Gramene is a public resource that leverages the rice genomic sequence to allow researchers working on maize, wheat, sorghum and other cereals to apply knowledge derived from the study of the rice genome to the synteneic regions in their species of interest. We use controlled vocabularies (ontologies) to describe rice genes, mutants and varieties, high throughput analytic techniques to annotate features on the genome, and a combination of automatic and manual annotation to discover relationships between genetic and physical maps. All raw and processed data as well as software, is available on the Gramene web site for unrestricted use. Our specific aims are to: 1. Map between the rice and maize genomes. 2. Develop an open source genome annotation pipeline. 3. Develop tools to manage natural variation in cereal varieties. 4. Acquire and maintain quantitative trait loci associations in rice. 5. Undertake a pilot project to annotate maize mutants with the Plant Ontology. 6. Add advanced query tool and report functionality to the Gramene web site. 7. Undertake community outreach to high school students. The broader impact of this project will be to improve the understanding of cereal biology. Rice, maize and wheat are the three most important crops in the world, and improving their yield and stability while decreasing their environmental impact are key to improving world food and environmental security. Due to the shared ancestry of these three crops, it is possible to apply results from one of these species to another. However, to make this cross-species translation possible it is critical that the thousands of researchers working in each of these species can effectively communicate their discoveries across species and community boundaries. The continued development of Gramene will help integrate the genomics investment across the grasses, which will allow genomics researchers to communicate their results effectively. Finally, it will also start providing the informatics infrastructure needed to help bridge the gap between genomics and applied plant improvement.