Generation and Analysis of a Reference Sequence for the West African Cultivated Rice - Oryza Glaberrima (CG14)

西非栽培稻 - Oryza Glaberrima (CG14) 参考序列的生成和分析

• 批准号: 0822284
• 负责人: Rod Wing
• 金额: $ 147.78万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-03-01 至 2012-02-29
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0822284&HistoricalAwards=false
• 关键词: Generation; Analysis; Reference; Sequence; West

PI: Rod A. Wing (University of Arizona)CoPIs: Steven D. Rounsley and Yeisoo Yu (University of Arizona)The objective of this project is to generate and analyze a reference genome sequence of the West African cultivated rice Oryza glaberrima (CG14). The reference sequence will be generated using a minimum tiling path of bacterial artificial chromosome (BAC) clones selected from an existing NSF-funded O. glaberrima physical map, which encompasses the entire genome. DNA from these clones will be purified, pooled and sequenced using 454/Roche GSFLX Titanium and paired-end pyrosequencing technologies. A standardized annotation process will be applied across the whole genome taking advantage of the well-curated annotation for the Asian cultivated rice species - Oryza sativa. In addition, customized analyses targeted at specific biological questions will be performed. The genome sequence and its annotation will be accessible via public databases, such as GenBank and Gramene (www.gramene.org). The broader impacts of this project are two-fold. First, since the world's rice-dependent population is expected to double in the next 25 years, rice breeders are faced with the challenge of doubling rice yields with less land and water, and with poorer soils. Obtaining the genome of the African cultivated rice, O. glaberrima, is the first step towards understanding the differences between the two cultivated species, how each has adapted to their particular environments, and how each may benefit the other to be grown in more diverse and often harsh environments. The genome sequence produced by this research project will be a resource utilized by biologists and rice breeders as a component in efforts towards improving worldwide rice production. This project also offers several research training opportunities for postdoctoral scientists and students at all levels. First, students and postdoctoral researchers will be trained to perform research using cutting edge genomics research technologies such as next generation sequencing, physical mapping, de novo assembly of large plant genomes, genome annotation and comparative evolutionary genomics. Their research results will be disseminated through peer review publications and at local and international meetings. Project personnel will serve as mentors for all training activities and will meet regularly with each student and postdoc to ensure they are on track and getting the most out of their research experience. In addition, the project has partnered with Biotechnology, Agronomy and Plant Science programs at Pima Community College (Tucson AZ), and the Life Science Undergraduate Biology Research Program at University of Arizona to provide undergraduate students with summer research internships. These students will also have an opportunity to apply for the BRAVO program (http://www.ubrp.arizona.edu/) which allows them to perform research abroad for a minimum of 10 weeks. The project has research partnerships in Benin (West Africa), China, Colombia, France, Japan, the Philippines, and Taiwan, all suitable locations for a 10 week international research experience.Finally, the project will participate in the University of Arizona's KEYS program (K-12 Engaging Youth in Science; http://www.bio5.org/training/trainingHigh.php) which provides six week summer research internships for advanced high school students.

Pi：Rod A.Wing(亚利桑那大学)Copis：Steven D.Rounsley和Yeiso Yu(亚利桑那大学)这个项目的目标是产生和分析西非栽培水稻Oryza tarberrima(CG14)的参考基因组序列。参考序列将使用细菌人工染色体(BAC)克隆的最小平铺路径来生成，这些克隆是从NSF资助的现有Oangberrima物理图谱中选择的，该图谱包含整个基因组。这些克隆的DNA将使用454/Roche GSFLX钛和配对末端焦磷酸测序技术进行纯化、汇集和测序。一个标准化的注释过程将应用于整个基因组，利用对亚洲栽培水稻物种--水稻--的精心策划的注释。此外，还将针对特定的生物学问题进行定制分析。基因组序列及其注释将通过公共数据库，如GenBank和Gramene(www.gram ene.org)获取。这个项目的更广泛的影响是双重的。首先，由于世界上依赖水稻的人口预计将在未来25年内翻一番，水稻育种者面临着用更少的土地和水以及更贫瘠的土壤将水稻产量翻一番的挑战。获取非洲栽培水稻的基因组是了解这两个栽培物种之间的差异的第一步，每个栽培物种如何适应其特定的环境，以及它们如何使对方受益于在更多样化和往往更恶劣的环境中生长。这一研究项目产生的基因组序列将成为生物学家和水稻育种者利用的一种资源，作为努力改善全球水稻产量的一个组成部分。该项目还为各级博士后科学家和学生提供了几个研究培训机会。首先，将培训学生和博士后研究人员使用尖端基因组研究技术进行研究，如下一代测序、物理图谱、大型植物基因组的从头组装、基因组注释和比较进化基因组学。他们的研究成果将通过同行评议出版物以及在当地和国际会议上传播。项目人员将担任所有培训活动的导师，并将定期与每一名学生和博士后会面，以确保他们走上正轨，并最大限度地利用他们的研究经验。此外，该项目还与皮马社区学院(图森AZ)的生物技术、农学和植物科学项目以及亚利桑那大学的生命科学本科生物学研究项目合作，为本科生提供暑期研究实习机会。这些学生还将有机会申请布拉沃项目(http://www.ubrp.arizona.edu/))，该项目允许他们在国外进行至少10周的研究。该项目在贝宁(西非)、中国、哥伦比亚、法国、日本、菲律宾和台湾都有研究伙伴关系，这些地方都适合进行为期10周的国际研究体验。最后，该项目将参与亚利桑那大学的Key计划(K-12青年参与科学；http://www.bio5.org/training/trainingHigh.php))，该计划为高中生提供为期6周的暑期研究实习机会。