Oryza Map Alignment Project

该项目将绘制和比对12个野生水稻基因组与公开完成的水稻基因组序列。这些基因组序列来源于Oryza sativa ssp。粳稻和粳稻。印度是亚洲和印度的主要栽培水稻品种。Oryza Map Alignment Project （OMAP）资源将包含所有现存野生水稻基因组的代表，从而有可能描述野生水稻经过驯化以产生今天种植的栽培水稻时发生的基因组重排。OMAP资源还将使探索整个水稻属基因簇的进化成为可能，以了解基因簇中的基因多样性，或调节其表达的序列。这类研究不仅将影响水稻基因组学，而且还将影响育种者定位和选择一些在野生水稻品种中存在但在栽培水稻中不存在的重要农艺性状的基因的方法。OMAP资源将是此类资源中的第一个，并可能成为未来其他植物和动物资源的典范。1.具体目标构建水稻12个野生基因组的DNA指纹图谱和细菌人工染色体末端序列物理图谱。2. 将12张物理图谱与测序的参考亚种粳稻和籼稻进行比对。3. 3 .结合锚定策略，在12个野生基因组中构建水稻染色体1、3和10的高分辨率物理图谱。提供方便的生物信息学研究和教育工具，以快速访问和探索整合的水稻基因组图谱资源。项目成果的可用性本项目产生的所有数据一经产生并进行质量检查，将立即存入公共数据库。1. 所有原始指纹数据将以可下载的格式提供，供研究人员在本地指纹配置（FPC）软件上使用。所有组装好的FPC组件都可以通过webFPC和Gramene （www.gramene.org）在互联网上查看。所有bac端序列、质量和跟踪文件将每隔一周存入基因库。4. 所有与参考粳稻序列的全球比对和SNP数据将在Gramene上提供。所有1、3和10号染色体的重建数据将在冷泉港实验室、普渡大学和亚利桑那大学的项目网站上提供（www.omap.org）。所有的重复分析将通过普渡大学和冷泉港实验室的网站提供。冷泉港实验室、亚利桑那大学和普渡大学在项目过程中开发的所有软件将在开源倡议（www.opensource.org）批准的开源许可下发布给社区。

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).