Oryza Map Alignment Project

该项目将绘制12个野生水稻基因组图，并将其与公共成品水稻基因组序列进行比对。这些基因组序列来源于水稻SSP。Jumonica和SSP.在亚洲和印度种植的主要栽培水稻品种。Oryza Map Align Project(OMAP)资源将包含所有现存野生稻基因组的代表，这使得描述野生稻经过驯化以获得今天种植的栽培稻时发生的基因组重排成为可能。OMAP资源还将使探索整个水稻属基因簇的进化成为可能，以了解一个簇中基因的多样性，或调控其表达的序列。这类研究不仅会影响水稻基因组学，还会影响育种者针对一些野生稻品种中存在但栽培稻中没有的重要农艺性状的基因进行定位和选择的方式。OMAP资源将是此类资源中的第一个，并可能成为其他植物和动物未来资源的模式。具体目标1.构建来自12个野生水稻基因组的DNA指纹和细菌人工染色体(BAC)末端序列物理图谱。2.将12个物理图谱与已测序的参考亚种水稻和水稻进行比对。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。项目结果的可用性该项目得出的所有数据一旦产生并进行质量检查，将立即放入公共数据库。1.所有原始指纹数据都将以可下载的格式提供，研究人员可以在本地指纹拼接(FPC)软件上使用该格式。所有组装的FPC重叠群将可通过WebFPC和Gramene(www.gram ene.org)在互联网上查看。所有BAC-END序列、质量和跟踪文件将每周保存在Genbank中。4.Gramene上将提供所有全球比对和与参考粳稻序列的SNP数据。5.第1、3和10号染色体的所有重建数据将在项目网站、普渡大学冷泉港实验室和亚利桑那大学(www.omap.org)上公布。所有重复分析将通过普渡大学和冷泉港实验室网站提供7.在冷泉港实验室、亚利桑那大学和普渡大学项目过程中开发的所有软件将根据开放源码倡议(www.opensource.org)批准的开放源码许可证向社区发布。

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).