Arabidopsis 2010: 1,001 Genomes Project

拟南芥 2010：1,001 基因组计划

• 批准号: 0929402
• 负责人: Joseph Ecker
• 金额: $ 160万
• 依托单位: The Salk Institute for Biological Studies
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2011-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0929402&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; 001; Genomes; Project

Plant biologists need many completely sequenced and functionally annotated genomes within each species in order to fully exploit the power of evolution to understand how an organism functions and adapts to its environment. Researchers interested in natural variation in Arabidopsis propose to generate genomic DNA sequences from over 1000 inbred strains, driving technology developments in both hardware for the DNA sequencing itself and in software development to make sense of the DNA sequence data. The goal of this research project is to record the genetic variation in the entire genome of many strains of the reference plant Arabidopsis thaliana. We will develop and apply cutting edge DNA sequencing approaches using the reference plant A. thaliana to address questions of fundamental importance about plant evolution and gene function. The complete genome sequences for 200 accessions, produced as a result of this project, will provide the first complete view of haplotype structure for Arabidopsis thaliana and will allow future studies of epigenetic variation among different individuals in a population or within a species, a potential source of phenotypic diversity. The patterns of sequence and structural variation will reveal important insights into the dynamics of genome change and pinpoint potentially functionally important sources of genetic and epigenetic variation. Moreover, these data will enable subsequent mechanistic studies through experimental manipulation of Arabidopsis strains. The 1001 Arabidopsis Genomes Project (http://1001genomes.org) will provide detailed genotyping data of wild strains that will complement the efforts of individual investigators to phenotype these same accessions for thousands of traits of interest. For example, this research has the potential for rapid advancement toward the mechanisms by which plants adapt to various climates, utilize soil nutrients and resist pathogen infection. The knowledgebase produced from the 1,001 Arabidopsis Genomes Project will yield direct and measurable outcomes for deployment of similar traits in economically important crops for a changing global environment.Broader Impacts of the Proposed ResearchThe impact of this project will be in two broad areas. First, the completion of the planned research will result in important new resources for the plant biology community: large-scale information on genetic variation among closely related genotypes. The very limited availability of whole genome sequence variation information has negatively impacted a variety of research endeavors such as the understanding of adaptive evolution or the development of association mapping. All of the DNA sequence data will be made freely and easily accessible to the research community. The long-term impact of these enabling tools and technologies on agriculture and forestry is expected to be profound, providing fundamental knowledge for the construction of new plant varieties with superior agronomic traits. An equally important aspect of this program is training, which will be provided at a variety of levels, including outreach to high school and undergraduate students as well as postdoctoral mentoring.

植物生物学家需要在每个物种中有许多完全测序和功能注释的基因组，以便充分利用进化的力量来了解有机体如何运作和适应其环境。对拟南芥自然变异感兴趣的研究人员提议从1000多个近交系产生基因组DNA序列，推动DNA测序硬件和软件开发的技术发展，以理解DNA序列数据。这项研究项目的目的是记录参比植物拟南芥许多品系的整个基因组中的遗传变异。我们将开发和应用先进的DNA测序方法，使用参考植物A.thaliana来解决关于植物进化和基因功能的基本重要问题。该项目产生的200份材料的完整基因组序列将提供第一个关于拟南芥单倍型结构的完整视图，并将使未来能够研究群体中或物种内不同个体之间的表观遗传变异，这是表型多样性的潜在来源。序列和结构变异的模式将揭示对基因组变化动态的重要见解，并精确定位潜在的重要遗传和表观遗传变异来源。此外，这些数据将使随后通过对拟南芥品系进行实验操作的机制研究成为可能。1001拟南芥基因组计划(http://1001genomes.org))将提供野生菌株的详细基因分型数据，这些数据将补充单个研究人员为数千个感兴趣的性状对这些相同的材料进行表型的努力。例如，这项研究有可能在植物适应各种气候、利用土壤养分和抵御病原体感染的机制方面取得快速进展。由1,001个拟南芥基因组项目产生的知识库将产生直接和可测量的结果，用于在不断变化的全球环境中部署类似的经济性状。拟议研究的广泛影响该项目的影响将在两个广泛的领域。首先，计划中的研究的完成将为植物生物界带来重要的新资源：关于密切相关的基因类型之间遗传变异的大规模信息。全基因组序列变异信息非常有限，已经对各种研究工作产生了负面影响，例如对适应性进化的理解或关联图谱的发展。所有DNA序列数据都将免费提供给研究界使用。这些使能工具和技术对农林的长期影响预计将是深远的，为构建具有优越农艺性状的植物新品种提供基础知识。这一计划的另一个同样重要的方面是培训，培训将在不同级别提供，包括面向高中生和本科生的培训，以及博士后指导。