Gramene: A Platform for Comparative Cereal Genomics

Gramene：比较谷物基因组学的平台

• 批准号: 0321685
• 负责人: Doreen Ware
• 金额: --
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-12-15 至 2008-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0321685&HistoricalAwards=false
• 关键词: Gramene; Platform; Comparative; Cereal; Genomics

This project will expand and continue the operations of Gramene, a comparative mapping database for rice and other cereals. Gramene is a public resource that leverages the rice genomic sequence to allow researchers working on maize, wheat, sorghum and other cereals to apply knowledge derived from the study of the rice genome to the synteneic regions in their species of interest. We use controlled vocabularies (ontologies) to describe rice genes, mutants and varieties, high throughput analytic techniques to annotate features on the genome, and a combination of automatic and manual annotation to discover relationships between genetic and physical maps. All raw and processed data as well as software, is available on the Gramene web site for unrestricted use.Our specific aims are to:1. Map between the rice and maize genomes.2. Develop an open source genome annotation pipeline.3. Develop tools to manage natural variation in cereal varieties.4. Acquire and maintain quantitative trait loci associations in rice.5. Undertake a pilot project to annotate maize mutants with the Plant Ontology.6. Add advanced query tool and report functionality to the Gramene web site.7. Undertake community outreach to high school students.The broader impact of this project will be to improve the understanding of cereal biology. Rice, maize and wheat are the three most important crops in the world, and improving their yield and stability while decreasing their environmental impact are key to improving world food and environmental security. Due to the shared ancestry of these three crops, it is possible to apply results from one of these species to another. However, to make this cross-species translation possible it is critical that the thousands of researchers working in each of these species can effectively communicate their discoveries across species and community boundaries. The continued development of Gramene will help integrate the genomics investment across the grasses, which will allow genomics researchers to communicate their results effectively. Finally, it will also start providing the informatics infrastructure needed to help bridge the gap between genomics and applied plant improvement.

该项目将扩大和继续Gramene的业务，Gramene是一个稻米和其他谷物比较绘图数据库。Gramene是一种公共资源，利用水稻基因组序列，使研究玉米、小麦、高粱和其他谷物的研究人员能够将从水稻基因组研究中获得的知识应用于其感兴趣物种的同线区。我们使用受控词汇（本体）来描述水稻基因，突变体和品种，高通量分析技术来注释基因组上的功能，并结合自动和手动注释来发现遗传和物理图谱之间的关系。Gramene网站上提供的所有原始和处理过的数据以及软件均可不受限制地使用。我们的具体目标是：1.水稻和玉米基因组之间的图谱。开发一个开源的基因组注释管道.开发管理谷物品种自然变异的工具。获得并保持水稻数量性状位点的关联性.开展一个试点项目，用植物本体注释玉米突变体。在Gramene网站上添加高级查询工具和报告功能。对高中生进行社区外展。该项目的更广泛影响将是提高对谷物生物学的理解。水稻、玉米和小麦是世界上最重要的三种作物，提高其产量和稳定性，同时减少其对环境的影响，是改善世界粮食和环境安全的关键。由于这三种作物的共同祖先，有可能将其中一个物种的结果应用于另一个物种。然而，为了使这种跨物种翻译成为可能，在这些物种中工作的数千名研究人员能够有效地跨物种和社区边界交流他们的发现至关重要。Gramene的持续发展将有助于整合基因组学投资，这将使基因组学研究人员能够有效地交流他们的结果。最后，它还将开始提供帮助弥合基因组学和应用植物改良之间的差距所需的信息学基础设施。