CPGS Oryza Genome Evolution

合作者：O.Panaud(法国佩皮尼昂大学)和D.Weigel(德国马克斯·普朗克发育生物学研究所)，Doreen Ware(冷泉港实验室)，张启发和余思斌(华中农业大学，中国)，韩斌(国家基因研究中心，中国)，Marco Wopeis(非洲水稻中心，华大，中国)，Mathias Lorieux(国际热带农业中心，哥伦比亚)和格鲁吉亚Eizenga(DB NRRC，德国)。亚洲栽培水稻比其他任何作物都能养活更多的人。由于依赖水稻的人口预计将在大约25年内翻一番，育种者面临着在更少的土地、水和肥料以及更贫瘠的土壤上使水稻产量翻一番的艰巨任务。因此，科学界必须团结起来，提供满足未来需求所需的工具和生物学/进化洞察力。该项目的长期目标是利用1500万年来锁定在野生和驯化水稻物种基因组中的进化多样化和适应性，既改善栽培水稻，又解决进化和比较基因组学中的基本问题。为了实现这一目标，该项目将首先为水稻属生成一套公开可用的基因组学资源，包括：i)栽培水稻的三个野生近缘物种和近缘野生稻Leersia perrieri的物理图谱；ii)这些物种3号染色体短臂的完整序列；iii)巴氏野生稻(西非栽培稻的野生祖先)和斑点稻(一种野生物种，将作为八个AA基因组物种的进化群)的完整参考基因组序列；iv)11个野生稻物种和L.perrieri的基因和小RNA表达数据集；以及v)横跨AA基因组系统发育的DNA多态数据集。该项目将把这些新资源与即将到来的5到8个新的水稻参考基因组序列整合起来，为任何植物系统创建最全面的属内比较基因组学平台。该项目将询问这个比较基因组学平台，以发现关键的进化事件，并描述导致10种不同基因组类型的24个水稻物种形成的力量。将涉及的具体研究领域包括：结构变异分析、系统基因组学、种群基因组学、基因组进化和新基因的起源，以及转座元件在基因组进化中的作用。文库、基因组序列及其注释将可通过公共数据库和储存库获取，如AGI BAC/测试资源中心(http://www.genome.arizona.edu/orders/)，NCBI(http://www.ncbi.nlm.nih.gov/)，)和Gramene(www.gram ene.org)。该项目将在几个层面产生广泛影响，包括基础和应用研究社区、博士后/研究生/本科生和高中生培训和指导、社区推广以及K-5儿童及其家庭。对于基础/应用研究社区，该项目将加强和开发属级资源，作为获取植物界无与伦比的新特征和等位基因的平台。这一变革性的平台可以用来解决基本假设驱动的问题，并提供必要的工具来改善世界上最重要的粮食作物。该项目将为对基因组进化、植物育种以及学术和企业科学职业感兴趣的博士后科学家、研究生/本科生和高中生提供培训和指导。最后，该项目将制定一年两次的“植物科学家庭之夜”计划，以K-5年级的学生和家庭为对象，让儿童和他们的家庭对植物以及植物科学在确保地球上安全、可持续和有保障的食品供应中所发挥的作用感到兴奋。

PI: Rod A. Wing (University of Arizona)CoPIs: Scott A. Jackson (Purdue University), Manyuan Long (University of Chicago), Carlos A. Machado (University of Maryland), and Michael J. Sanderson (University of Arizona)Collaborators: O. Panaud (University of Perpignan, France) and D. Weigel (Max Planck Institute for Developmental Biology, Germany), Doreen Ware (Cold Spring Harbor Laboratory), Qifa Zhang and Sibin Yu (Huazhong Agricultural University, China), Bin Han (National Center for Gene Research, China), Marco Wopereis (Africa Rice Center (WARDA), Benin), Mathias Lorieux (International Center for Tropical Agriculture (CIAT), Columbia, and Georgia Eizenga (DB NRRC, Germany.Intellectual merit. Asian cultivated rice (Oryza sativa) feeds more people than any other crop. As the rice-dependent population is expected to double in about 25 years, breeders are faced with the enormous task of doubling rice yields with less land, water, and fertilizers, and on poorer soils. It is therefore critical that the scientific community unites to provide the tools and biological/evolutionary insights required to meet future needs. The project's long-term goal is to exploit 15 million years of evolutionary diversification and adaptation that have been locked in the genomes of wild and domesticated Oryza species, to both improve cultivated rice and address fundamental questions in evolutionary and comparative genomics. To accomplish this goal the project will first generate a set of publicly available genomics resources for the genus Oryza including: i) physical maps for three wild relatives of cultivated rice and the closely related outgoup species Leersia perrieri; ii) complete sequences for the short arms of chromosome 3 of these species; iii) complete reference genome sequences for O. barthii (the wild progenitor of West African cultivated rice), and O. punctata (a wild species that will serve as the evolutionary outgroup the eight AA genome species--the species group containing O. sativa); iv) gene and small RNA expression data sets for 11 Oryza species and L. perrieri; and v) DNA polymorphism data sets across the AA genome phylogeny. The project will integrate these new resources with 5 to 8 forthcoming new Oryza reference genome sequences to create the most comprehensive within-genus comparative genomics platform for any plant system. The project will interrogate this comparative genomics platform to discover key evolutionary events and characterize the forces that led to the formation of 24 Oryza species with 10 different genome types. Specific research areas that will be addressed include: analyses of structural variation, phylogenomics, population genomics, genome evolution and the origin of new genes, and the role of transposable elements in genome evolution. Libraries, genome sequences and their annotations will be accessible via public databases and repositories, such as the AGI BAC/TEST Resource Center (http://www.genome.arizona.edu/orders/), NCBI (http://www.ncbi.nlm.nih.gov/), and Gramene (www.gramene.org).Broader impacts. This project will have broad impacts at several levels, including basic and applied research communities, postdoctoral/graduate/undergraduate and high school student training and mentoring, community outreach, and K-5 children and their families. For basic/applied research communities, the project will enhance and develop a genus-level resource as a platform for accessing new traits and alleles that is unparalleled in the plant world. This transformative platform can be used to address fundamental hypothesis-driven questions as well as provide essential tools to improve the world's most important food crop. The project will provide training and mentoring to postdoctoral scientists, graduate/undergraduate students and high school students interested in genome evolution, plant breeding, and careers in academic and corporate science. Finally, the project will develop a biannual "Plant Science Family Night" program, targeting K-5 students and families, to get children and their families excited about plants and the role plant science plays in ensuring a safe, sustainable, and secure food supply for our planet.