Oryza Map Alignment Project

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This project will map and align twelve wild genomes of rice to the public finished rice genome sequences. These genome sequences were derived from Oryza sativa ssp. japonica and ssp. indica, the major cultivated rice varieties grown throughout Asia and India. The Oryza Map Alignment Project (OMAP) resource will contain representatives of all extant wild rice genomes, making it possible to describe the genome rearrangements that happened as wild rice underwent domestication to yield the cultivated rice grown today. The OMAP resource will also make it possible to explore the evolution of gene clusters across the rice genus to learn about the diversity of genes in a cluster, or the sequences regulating their expression. This kind of research will not only impact rice genomics, but also the ways in which breeders can target and select genes for agronomically important traits present in some wild rice varieties but absent from cultivated rice. The OMAP resource will be the first of its kind, and will be likely to serve as a model for future resources for other plants, and for animals.Specific objectives 1. Construct DNA fingerprint and Bacterial Artificial Chromosome (BAC)-end sequence physical maps from the 12 wild genomes of rice. 2. Align the 12 physical maps with the sequenced reference subspecies japonica and indica. 3. Construct high-resolution physical maps of rice chromosomes 1, 3 and 10 across the 12 wild genomes using a combination of anchoring strategies.4. Provide convenient bioinformatics research and educational tools to rapidly access and explore the integrated rice genome map resource.Availability of project outcomesAll data derived from this project will be placed in public databases as soon as it is produced and checked for quality. 1. All raw fingerprint data will be available in a downloadable format that can be used by researchers on local Fingerprint Contig (FPC) software.2. All assembled FPC contigs will be viewable on the Internet with webFPC and Gramene (www.gramene.org).3. All BAC-end sequences, quality and trace files will be deposited in Genbank at weekly intervals. 4. All global alignment and SNP data with the reference japonica sequence will be available on Gramene. 5. All reconstruction data for chromosomes 1,3 and 10 will be made available on the project web site at Cold Spring Harbor Laboratory, Purdue University and the University of Arizona (www.omap.org).6. All repeat analysis will be made available through the Purdue University and Cold Spring Harbor Laboratory web sites 7. All software developed in the course of the project at Cold Spring Harbor Laboratory, the University of Arizona, and Purdue University will be released to the community under an open source license approved by the Open Source Initiative (www.opensource.org).