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

PI: Rod a . Wing (University of Arizona)CoPIs: Steven D. Rounsley和Yeisoo Yu （University of Arizona）本项目的目的是生成和分析西非栽培水稻Oryza glaberrima （CG14）的参考基因组序列。参考序列将使用从现有的nsf资助的O. glaberrima物理图谱中选择的细菌人工染色体（BAC）克隆的最小平铺路径生成，该图谱包含整个基因组。这些克隆的DNA将被纯化、汇集并使用454/Roche GSFLX Titanium和配对端焦磷酸测序技术进行测序。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- Oryza sativa的精心整理的注释。此外，针对特定生物学问题的定制分析将被执行。基因组序列及其注释将可通过公共数据库访问，例如GenBank和Gramene （www.gramene.org）。这个项目的广泛影响是双重的。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，水稻育种者面临着在土地和水更少、土壤更贫瘠的情况下将水稻产量翻一番的挑战。获得非洲栽培水稻O. glaberrima的基因组，是了解这两个栽培物种之间差异的第一步，它们是如何适应它们的特定环境的，以及它们如何在更多样化和通常更恶劣的环境中生长而使彼此受益。该研究项目产生的基因组序列将成为生物学家和水稻育种家利用的资源，作为改善全球水稻生产的一个组成部分。本项目还为博士后科学家和各级学生提供若干研究培训机会。首先，学生和博士后研究人员将接受培训，使用尖端基因组学研究技术进行研究，如下一代测序、物理制图、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审查出版物以及在当地和国际会议上传播。项目人员将作为所有培训活动的导师，并定期与每个学生和博士后会面，以确保他们走上正轨，并从他们的研究经历中获得最大的收获。此外，该项目还与皮马社区学院（亚利桑那州图森市）的生物技术、农学和植物科学项目以及亚利桑那大学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BRAVO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、菲律宾和台湾建立了研究伙伴关系，这些地方都适合进行为期10周的国际研究。最后，该项目将参与亚利桑那大学的KEYS项目（K-12青少年参与科学；http://www.bio5.org/training/trainingHigh.php），该项目为高中生提供为期六周的暑期研究实习机会。

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.