Award Abstract #0321685
Gramene: A Platform for Comparative Cereal Genomics

NSF Org:	DBI Division of Biological Infrastructure
Initial Amendment Date:	December 23, 2003
Latest Amendment Date:	January 29, 2009
Award Number:	0321685
Award Instrument:	Continuing grant
Program Manager:	Diane Jofuku Okamuro DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences
Start Date:	December 15, 2003
Expires:	November 30, 2008 (Estimated)
Awarded Amount to Date:	$5600235
Investigator(s):	Doreen Ware ware@cshl.edu (Principal Investigator) Lincoln Stein (Former Principal Investigator) Susan McCouch (Co-Principal Investigator) Edward Buckler (Co-Principal Investigator) Doreen Ware (Former Co-Principal Investigator)
Sponsor:	Cold Spring Harbor Laboratory 1 BUNGTOWN ROAD COLD SPRING HARBOR, NY 11724 516/367-8307
NSF Program(s):	PLANT GENOME RESEARCH RESOURCE, PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):	BIOT, 9109
Program Element Code(s):	7577, 1329

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.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

Doreen H. Ware, Pankaj Jaiswal, Junjian Ni, Immanuel V. Yap, Xioakang Pan, Ken Y. Clark, Leonid Teytelman, Steven C. Schmidt, Wei Zhao, Kuan Chang, Sam Cartinhour, Lincoln D. Stein, and Susan R. McCouch. "Gramene, a Tool for Grass Genomics," Plant Physiology, v.130, 2002, p. 1606.

Doreen Ware, Pankaj Jaiswal1, Junjian Ni, Xiaokang Pan, Kuan Chang, Kenneth Clark, Leonid Teytelman, Steve Schmidt, Wei Zhao, Samuel Cartinhour, Susan McCouch and Lincoln Stein. "Gramene: a resource for comparative grass genomics," Nucleic Acids Research, v.30, 2002, p. 103.

Jaiswal-P, Ware-D, Ni-J, Chang-K, Zhao-W, Schmidt-S, Pan-X, Clark-K, Teytelman-L, Cartinhour-S, Stein-L, McCouch-S. "Gramene: development and integration of trait and gene ontologies for rice," Comparative and Functional Genomics, v.3, 2002, p. 132.

P Jaiswal, J Ni, I Yap, D Ware, W Spooner, K Youens-Clark, L Ren, C Liang, W Zhao, K Ratnapu, B Faga, P Canaran, M Fogleman, C Hebbard, S Avraham, S Schmidt, T Casstevens, E Buckler, L Stein and S McCouch. "Gramene: a bird's eye view of cereal genomes," Nucleic Acids Research, v.23, 2006, p. D717.

Yamakazi Y, Jaiswal P. "Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase," Plant Cell Physiology, v.46, 2005, p. 63.

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