1,001 (Epi) Genomes Project

智力优点：植物生物学家需要在每个物种中获得许多完全测序和功能注释的基因组，以充分利用进化的力量，并了解生物体如何发挥作用并适应其环境。该项目将有助于国际努力，旨在从1,000多个拟南芥近交系中产生基因组DNA序列，同时推动DNA测序本身的硬件和软件开发的技术发展，以理解序列数据。具体来说，该项目将产生基因组，转录组和甲基化序列。 基因组序列将为拟南芥的单倍型结构和结构变异提供一个无与伦比的视角。 转录组序列数据将有助于基因组注释和天然剪接异构体的鉴定。 最后，DNA甲基化组测序数据将允许在整个群体水平上鉴定表观等位基因变异。这三个测序数据集（遗传、转录和DNA甲基化组）将很好地相互吻合，以提供拟南芥种群中的一组全面的变体。将群体或物种内不同个体的遗传、表观遗传和转录变异结合起来，将为通过数量性状位点作图或全基因组关联研究分析表型多样性提供潜在的来源。此外，这些数据将使后续的机制研究，通过实验操作的拟南芥菌株，并将补充个人的研究人员谁是使用相同的加入目录表型的数千个性状的努力。更广泛的影响：该项目的影响将在两个广泛的领域。首先，完成计划中的研究将为植物生物学界带来重要的新资源：关于物种内遗传、表观遗传和转录变异的大规模信息。所有的DNA，胞嘧啶甲基化和RNA序列数据将免费提供给研究界。这些使能工具和技术对农业和林业的长期影响预计将是深远的，为构建具有上级农艺性状的新植物品种提供基础知识。该方案的一个同样重要的方面是培训，培训将在各个层次提供，包括向高中、本科和研究生以及博士后指导提供培训。

Intellectual merit: Plant biologists need many completely sequenced and functionally annotated genomes within each species to fully exploit the power of evolution and to understand how an organism functions and adapts to its environment. This project will contribute to an international effort aimed at generating genomic DNA sequences from over 1,000 inbred strains of Arabidopsis thaliana, while driving technology developments in both the hardware for the DNA sequencing itself and in software development to make sense of the sequence data. Specifically, this project will generate genome, transcriptome, and methylome sequences. The genome sequences will provide an unparalleled view of haplotype structure and structural variation for Arabidopsis thaliana. The transcriptome sequence data will assist in genome annotation and identification of naturally occurring splice isoforms. Lastly, the DNA methylome sequencing data will permit identification of epiallelic variation on a population-wide level. These three sequencing data sets (genetic, transcriptional and DNA methylomes) will dovetail nicely with each other to provide a comprehensive set of variants within the Arabidopsis thaliana population. Combining genetic, epigenetic and transcriptional variation from different individuals in a population or within a species will provide a potential source for analyzing phenotypic diversity via quantitative trait loci mapping or genome-wide association studies. Moreover, these data will enable subsequent mechanistic studies through experimental manipulation of Arabidopsis thaliana strains and will complement the efforts of individual investigators who are using the same accessions to catalog phenotypes for thousands of traits. Broader impacts: The 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, epigenetic and transcriptional variation within a species. All of the DNA, cytosine methylation and RNA 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, undergraduate and graduate students as well as postdoctoral mentoring.