Oryza Map Alignment Project

Oryza 地图对齐项目

• 批准号: 0321678
• 负责人: Rod Wing
• 金额: --
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-10-01 至 2009-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0321678&HistoricalAwards=false
• 关键词: Oryza; Map; Alignment; Project

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).

该项目将绘制12个野生水稻基因组，并将其与公开的水稻基因组序列进行比对。这些基因组序列来源于水稻（Oryza sativa ssp.）japonica和ssp.籼稻是亚洲和印度的主要栽培水稻品种。水稻图谱比对项目（OMAP）资源将包含所有现存野生稻基因组的代表，从而有可能描述野生稻经过驯化产生今天种植的栽培稻时发生的基因组重排。 OMAP资源还将使探索整个水稻属的基因簇的进化成为可能，以了解簇中基因的多样性或调节其表达的序列。 这种研究不仅会影响水稻基因组学，而且会影响育种者如何靶向和选择一些野生稻品种中存在但栽培稻中不存在的重要农艺性状的基因。 OMAP资源将是同类中的第一个，并且将可能作为其他植物和动物的未来资源的模型。构建12个水稻野生基因组DNA指纹图谱和细菌人工染色体（BAC）末端序列物理图谱。 2.将12张物理图谱与已测序的参考亚种粳稻和籼稻进行比对。 3.结合锚定策略构建水稻1、3、10号染色体在12个野生基因组上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。项目成果的可用性从该项目获得的所有数据将被放置在公共数据库中，一旦产生和检查质量。1.所有原始指纹数据都将以可下载的格式提供，研究人员可以在当地的指纹Contig（FPC）软件上使用。所有组装的FPC重叠群将在互联网上通过webFPC和Gramene（www.gramene.org）可见。所有BAC-末端序列、质量和跟踪文件将每周存入Genbank。4.与参考日本序列的所有全局比对和SNP数据将在Gramene上提供。5.染色体1、3和10的所有重建数据将在普渡大学和亚利桑那大学冷泉港实验室的项目网站上提供（www.omap.org）。所有重复分析将通过普渡大学和冷泉港实验室网站7提供。在冷泉港实验室、亚利桑那大学和普渡大学的项目过程中开发的所有软件将根据开源计划批准的开源许可证向社区发布（www.opensource.org）。