Genome-Wide Restriction Map of Rice by Optical Mapping

通过光学作图绘制水稻全基因组限制性图谱

• 批准号: 9975606
• 负责人: David Schwartz
• 金额: $ 152.95万
• 依托单位: University of Wisconsin-Madison
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-09-01 至 2005-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9975606&HistoricalAwards=false
• 关键词: Genome; Wide; Restriction; Map; Rice

The grasses provide more than 80% of the world's edible dry matter. Among the grasses, rice has become the model monocot plant, having a relatively small genome (430 Mb), the ability to be transformed, high density genetic maps based on molecular markers, and physical maps from large fragment clones under development. Comparative analysis among the grasses has shown that large grass genomes of important crop plants such as wheat, barley, maize, sorghum, oat and sugarcane share extensive synteny with the genome of rice, thus making detailed study of the rice genome relevant to all grasses. This award supports the construction of an optical restriction map of the genome of rice (O. sativa L. japonica variety Nipponbare) as a first step toward development of a comprehensive understanding of the genome organization of O. sativa L. This variety has been selected by the international plant genome community as the template for a rice genome sequencing effort. Direct restriction mapping of the rice genome will be performed on large, random fragments of genomic DNA, isolated cells, or nuclei mounted on specially prepared surfaces. Ordered restriction maps prepared from individual DNA molecules will be assembled into a continuous map covering the entire genome. Successful application of this approach has already led to the rapid development of optical restriction maps for the genomes of Escherichia coli (4.3 Mb) and Plasmodium falciparum (26 Mb). Efforts are currently underway to map the human genome (3,000 Mb). It is anticipated that a complete optical restriction map of diploid rice can be accomplished in 3 years. The resulting map will be linked to available genetic and physical maps through comparison of restriction fragment patterns of selected BAC clones of Nipponbare DNA, developed elsewhere, and by localization of existing molecular markers in the rice genetic map to these clones. This approach will complement those currently underway by providing critical linking data to fill gaps in BAC contigs as well as a means to organize DNA sequence information generated from a random genome sequencing approach.

牧草提供了世界上80%以上的可食用干物质。在禾本科植物中，水稻已成为模式单子叶植物，其基因组相对较小(430Mb)，具有转化能力，基于分子标记的高密度遗传图谱，以及正在开发的大片段克隆的物理图谱。对禾本科植物的比较分析表明，小麦、大麦、玉米、高粱、燕麦和甘蔗等重要农作物的大型禾本科植物基因组与水稻基因组具有广泛的同源性，从而对与所有禾本科植物相关的水稻基因组进行了详细研究。该奖项支持构建水稻基因组的光学限制图，作为全面了解水稻基因组组织的第一步。该品种已被国际植物基因组社区选为水稻基因组测序工作的模板。水稻基因组的直接限制图谱将在基因组DNA的大而随机的片段、分离的细胞或安装在特殊准备表面上的核上进行。从单个DNA分子准备的有序限制性图谱将被组装成覆盖整个基因组的连续图谱。这种方法的成功应用已经导致了对大肠杆菌(4.3Mb)和恶性疟原虫(26Mb)基因组的光学限制性内切酶图谱的快速开发。目前正在努力绘制人类基因组图(3000 Mb)。二倍体水稻的光学限制性内切酶图谱有望在3年内完成。所得到的图谱将通过比较在其他地方开发的日本晴DNA的选定BAC克隆的限制性片段模式，以及通过将水稻遗传图谱中现有的分子标记定位于这些克隆，将得到的图谱与现有的遗传和物理图谱相关联。这种方法将通过提供关键的连接数据来填补BAC重叠群中的空白，以及一种组织随机基因组测序方法产生的DNA序列信息的手段，来补充目前正在进行的这些方法。