Gramene: A Platform for Comparative Cereal Genomics

这个项目将扩大和继续Gramene的业务，Gramene是一个稻米和其他谷物的比较性绘图数据库。Gramene是一个公共资源，它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他们感兴趣的物种的合成区域。我们使用受控词汇（本体）来描述水稻基因、突变体和品种，使用高通量分析技术来注释基因组特征，并结合自动和手动注释来发现遗传图谱和物理图谱之间的关系。所有原始和处理过的数据以及软件都可以在Gramene网站上无限制地使用。我们的具体目标是：1。水稻和玉米基因组图谱。开发一个开源的基因组注释管道。开发工具来管理谷物品种的自然变异。获得并维持水稻数量性状位点关联。进行一个试点项目，用植物本体论注释玉米突变体。为Gramene网站添加高级查询工具和报告功能。对高中学生进行社区外展。这个项目更广泛的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，提高它们的产量和稳定性，同时减少它们对环境的影响，是改善世界粮食和环境安全的关键。由于这三种作物具有共同的祖先，因此可以将其中一种作物的结果应用于另一种作物。然而，为了使这种跨物种翻译成为可能，至关重要的是，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群落边界交流他们的发现。Gramene的持续发展将有助于整合整个草地的基因组学投资，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，它还将开始提供所需的信息学基础设施，以帮助弥合基因组学和应用植物改良之间的差距。

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.