YIA-PGR: Comparative Genomics of Rice: reconstructing rice chromosome 1 in related species.

YIA-PGR：水稻比较基因组学：重建相关物种中的水稻 1 号染色体。

• 批准号: 0227414
• 负责人: Scott Jackson
• 金额: $ 163.05万
• 依托单位: Purdue University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-10-01 至 2009-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0227414&HistoricalAwards=false
• 关键词: YIA; PGR; Comparative; Genomics; Rice

Encoded in units called "genes" on linear structures known as "chromosomes" present in essentially every cell of every organism is the instruction set for that organism. The purpose of a genome project, such as the nearly complete Rice Genome Project, is to precisely locate and describe each gene. This is not the end of the story however. For the description generated may only hint at the function of a gene and gives little indication as to the interacting role any gene or group of genes plays in the overall functioning of the organism. At this point enters the discipline of genetic mapping-whereby traits may be localized to specific positions on a chromosome. To this end, in genomes related to rice, we will construct physical maps of regions homologous to rice chromosome 1. Libraries of genomes, called BAC libraries, which consist of bacteria containing large pieces of DNA from the genome of interest, will have been constructed for many of the species in the same genus as rice (Oryza). These BAC libraries are the substrate for genome sequencing and, in this case, building sequence-ready comparative maps to compare genomes. Approximately three-quarters of the nearly 5,000 predicted genes on chromosome 1 will be used to isolate and build comparative maps across this group of species. The end result will be the reconstruction of rice chromosome 1 in a group of related species. This will help us to better understand chromosome evolution and more efficiently utilize the rice sequence data for comparative mapping in more distantly related species, such as maize, sorghum and oat. In addition, by using the natural variation that occurs in this group of species, we will be able to begin assigning biological functions to many of the genes predicted to exist in rice based on the sequence data. Deliverables:All information on Overgo sequences, physical location, analysis and reconstruction of chromosome 1 will be available at:http://rice.genomics.purdue.edu Much of the marked up information will be migrated to:http://www.gramene.org. Information on the computational pipeline is also available at:http://rice.genomics.purdue.edu.

编码在称为“基因”的线性结构上的单位称为“染色体”，基本上存在于每个生物体的每个细胞中，是该生物体的指令集。基因组计划的目的，如接近完成的水稻基因组计划，是精确定位和描述每个基因。然而，这并不是故事的结局。因为所产生的描述可能只暗示了一个基因的功能，而很少指出任何基因或基因组在生物体的整体功能中所起的相互作用。这时就进入了遗传图谱的学科，通过遗传图谱可以将性状定位在染色体上的特定位置。为此，在水稻相关基因组中，我们将构建水稻1号染色体同源区域的物理图谱。基因组文库，称为BAC文库，由含有来自感兴趣基因组的大片段DNA的细菌组成，将为与水稻（Oryza）相同属的许多物种构建。这些BAC文库是基因组测序的基础，在这种情况下，构建序列就绪的比较图谱以比较基因组。在1号染色体上的近5,000个预测基因中，约有四分之三将用于分离和构建这组物种的比较图谱。最终结果将是在一组相关物种中重建水稻1号染色体。这将有助于我们更好地理解染色体进化，更有效地利用水稻序列数据在更远的相关物种，如玉米，高粱和燕麦中进行比较作图。此外，通过利用这组物种中发生的自然变异，我们将能够开始根据序列数据为预测存在于水稻中的许多基因分配生物学功能。表格：关于1号染色体的Overgo序列、物理位置、分析和重建的所有信息将在http://rice.genomics.purdue.edu上提供。大部分标记的信息将迁移到http://www.gramene.org。关于计算管道的信息也可在www.example.com上获得。http://rice.genomics.purdue.edu