Genome-wide Impact of mPing Transposition on Rice Phenotypic Diversity

PI：Susan R. Wessler（加州大学-滨江分校）CoPI：托马斯布鲁特内尔（博伊斯汤普森研究所），杰森·斯塔吉奇（加州大学-滨江）和孙奇（康奈尔大学）高级人员：乔伊斯·货车·埃克（博伊斯汤普森研究所），詹姆斯伯内特（加州大学-滨江），严文贵（USDA-ARS戴尔邦珀斯国家水稻研究中心）和Yutaka Okumoto（京都大学）本项目的总体目标是了解快速扩增的高拷贝数转座因子（TE）（称为mPing）对水稻产生多样性的影响。这一目标既有应用的方面，也有基础的方面。应用的目标是开发和免费提供新的反向遗传资源的集合，将从基因组到转录组到表型组的特点。其基本目标是首次分析高拷贝TE如何快速使生物体的基因组多样化，并在此过程中改变其对不断变化的环境做出反应的能力。矛盾的是，水稻，具有最稳定的基因组中所描述的作物植物，是主机的最活跃的TE在任何真核生物的特点。 这一幸运的情况将促进下一代测序方法的应用，以测序相关的水稻品种，并调查与非生物胁迫反应相关的基因表达的全球变化。为此，该项目将对五个密切相关的水稻品系进行重测序，其中mPing在过去世纪已扩增到1000多个拷贝，并且仍在积极转座。与密切相关的参考基因组Nipponbare的比较将首次记录任何生物体中独立TE爆发的全球影响。为了评估mPing插入对数量性状的影响，该项目将利用重组近交（RI）群体，其中亲本的mPing插入拷贝数差异很大，许多性状存在显著的表型变异。 将在转基因水稻中测定具有mPing插入的候选基因对表型变异的贡献。为了利用从非常低到非常高的mPing扩增的全范围，该项目将在美国品种中激活mPing，并通过非转基因方法创建多达1500个携带新型mPing插入的品系。 最后，该项目将使用表达谱分析（RNA-seq）来研究mPing在重塑叶片转录组中的作用，以应对非生物胁迫。该项目的预期更广泛的影响包括开发新的非转基因mPing诱变水稻品系，这些品系将从基因组到转录组再到表型组进行表征。生成的所有基因组学数据将保存在GenBank中。将使用内部服务器和Gramene支持数据集的可视化。本项目过程中产生的所有生物材料将在斯图加特（AR）的Dale Bumpers国家水稻研究中心繁殖，非转基因材料的种子将通过USDA-ARS遗传资源-水稻（GSOR）保藏中心免费分发。所有推广活动将通过PI的“动态基因组”课程进行，该课程将在加州大学滨江新建的科学学习设施中教授。 这些课程旨在复制PI的研究实验室，将作为一个管道，将该项目的研究成果与专注于下一代测序方法的大学和高中课堂模块的开发相结合。 因此，这些课程将为本科生、高中生和教师带来下一代技术的兴奋。 最后，项目参与iPlant协作组织的教育推广小组将促进更广泛地传播成功的模块。

PI: Susan R. Wessler (University of California - Riverside)CoPIs: Thomas Brutnell (Boyce Thompson Institute), Jason Stajich (University of California - Riverside) and Qi Sun (Cornell University)Senior Personnel: Joyce Van Eck (Boyce Thompson Institute), James Burnette (University of California - Riverside), Wen-Gui Yan (USDA-ARS Dale Bumpers National Rice Research Center) and Yutaka Okumoto (Kyoto University)The overall goal of this project is to understand the impact of a rapidly amplifying high copy number transposable element (TE) called mPing on generating diversity in rice. This goal has both applied and basic aspects. The applied goal is to develop and make freely available novel collections of reverse genetic resources that will be characterized from genome to transcriptome to phenome. The basic goal is to analyze for the first time how a high copy TE rapidly diversifies the genome of an organism and, in doing so, alters its ability to respond to a changing environment. It is paradoxical that rice, with the most stable genome among characterized crop plants, is host to the most active TE characterized in any eukaryote. This fortunate set of circumstances will facilitate the application of next generation sequencing methodologies to sequence related rice cultivars and survey global changes in gene expression associated with abiotic stress responses. To this end the project will resequence five closely related rice strains where mPing has amplified to over 1000 copies during the past century and where it is still actively transposing. Comparison with the closely related reference genome Nipponbare will document for the first time the global impact of independent TE bursts in any organism. To assess the consequences of mPing insertion(s) on quantitative traits, the project will exploit recombinant inbred (RI) populations where the parents vary widely in their copy number of mPing insertions and where significant phenotypic variation exists for many traits. The contribution of candidate genes with mPing insertions to phenotypic variation will be assayed in transgenic rice. To exploit the full range of mPing amplification, from very low to very high, the project will activate mPing in US cultivars and create up to 1500 lines carrying novel mPing insertions through a non-transgenic approach. Finally, the project will use expression profiling (RNA-seq) to examine the role of mPing in reshaping the leaf transcriptome in response to abiotic stress.The expected broader impact of the project includes the development of novel collections of non-transgenic mPing-mutagenized rice strains that will be characterized from genome to transcriptome to phenome. All genomics data generated will be deposited at GenBank. Visualization of the datasets will be supported using in-house servers and at Gramene. All biological materials generated during the course of this project will be propagated at the Dale Bumpers National Rice Research Center in Stuttgart (AR) and seed stocks of non-transgenic materials will be freely distributed through USDA-ARS Genetic Stocks - Oryza (GSOR) Collection. All outreach activities will be channeled through the PI's "The Dynamic Genome" courses, which will be taught in a newly constructed Science Learning Facility at the University of California - Riverside. These courses, which are designed to replicate the PI's research laboratory, will serve as a conduit that integrates the research output of this project with the development of classroom modules for colleges and high schools focused on next generation sequencing methodologies. As such, these courses will bring the excitement of next-generation technologies to undergraduates and high school students and teachers. Finally, project involvement in the iPlant Collaborative's Education Outreach Team will facilitate the broader dissemination of successful modules.