The Effect of the Microbiome on the Rice Transcriptome

微生物组对水稻转录组的影响

• 批准号: 0923806
• 负责人: Harsh Bais
• 金额: $ 193.83万
• 依托单位: University of Delaware
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2014-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0923806&HistoricalAwards=false
• 关键词: Effect; Microbiome; Rice; Transcriptome

PI: Harsh P. Bais (University of Delaware)CoPIs: Venkatesan Sundaresan and Jonathan A. Eisen (University of California - Davis)Collaborators: Venu Kalavacharla (Delaware State University) and Gurdev Khush (University of California - Davis)Plants grow in close association with large communities of microbes collectively called the microbiome. Comparatively little is known about the diversity of microbes that associate with plants and their interactions and effects on performance and crop yields. Specific microbes have been extensively documented to provide beneficial effects to plants, such as those involving well-known symbiotic associations in legumes. Previous studies utilizing a single beneficial bacterial species in the model plant Arabidopsis thaliana demonstrate how plants actively recruit beneficial bacteria under biotic stress regimes. While valuable insights can be gained from studies with single microbial species, preliminary studies show a wide diversity of bacterial species associated with field grown rice (Oryza sativa) plants, whose biological significance is completely unknown. This project will utilize a combination of genomic and metagenomic approaches to dissect the impact of microbial associations on rice. Specifically, a controlled experimental system will be established, in which microbial populations will be characterized by metagenomic rRNA profiling, and plant responses by transcriptomic profiling. The expression profiles for localized and whole plant responses will be analyzed for global changes in gene expression, as well as for changes in the expression of specific functional classes of genes that would reflect changes in nutrient availability, or establishment of plant immunity. The proposed research will provide the foundations for future investigations into the impact of the microbiome on plant performance. All sequence and mapping data generated in this project will be accessible through a genome browser that will be developed specifically for this project. Allsequence data will be deposited for long-term dissemination in GenBank, GreenGenes (http://greengenes.lbl.gov), the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/), and NCBI's Short Read Archive (SRA; http://www.ncbi.nlm.nih.gov/Traces/home/). The broader impacts of this project stem, in part, from the interdisciplinary nature of the research. Training for students and postdoctoral associates will integrate quantitative approaches with applications to experimental biology. The project will also have broader impacts in the professional development and educational arenas. Professionally, the students and postdoctoral researcher involved in this project will benefit from experimental design training, the acquisition of technical expertise and interdisciplinary communication. In addition, the project will conduct a robust internship program for outstanding students from Delaware State University (DSU), an 1890 Historically Black University, and Delaware Technical & Community College (DTCC), a two-year institution with substantial numbers of first-generation college and minority students. The "Field to Lab" program will involve training in agricultural sampling, gene expression, metabolic profiling studies and bioinformatics.

PI：Harsh P. Bais（特拉华州大学）CoPI：Venkatesan Sundaresan和Jonathan A.合作者：Venu Kalavacharla（特拉华州州立大学）和Gurdev Khush（加州大学戴维斯分校）植物生长与统称为微生物组的大型微生物群落密切相关。 相对而言，人们对与植物相关的微生物的多样性及其相互作用以及对作物性能和产量的影响知之甚少。特定的微生物已被广泛记录，以提供有益的影响，植物，如那些涉及众所周知的共生协会在豆类。 以前的研究利用模式植物拟南芥中的单一有益细菌物种证明了植物如何在生物胁迫制度下积极招募有益细菌。 虽然可以从单一微生物物种的研究中获得有价值的见解，但初步研究表明，与田间生长的水稻（Oryza sativa）植物相关的细菌物种具有广泛的多样性，其生物学意义完全未知。 该项目将利用基因组学和宏基因组学方法的组合来剖析微生物协会对水稻的影响。 具体地说，将建立一个受控的实验系统，其中微生物种群将通过宏基因组rRNA分析来表征，植物响应通过转录组分析来表征。将分析局部和整个植物反应的表达谱，以了解基因表达的总体变化，以及反映营养物质可用性变化或植物免疫力建立的特定功能类基因表达的变化。拟议的研究将为未来研究微生物组对植物性能的影响提供基础。 该项目中生成的所有序列和映射数据将通过专门为此项目开发的基因组浏览器访问。 所有序列数据将保存在GenBank、GreenGenes（http：//www.example.com）、基因表达综合（GEO）数据库（www.ncbi.nlm.nih.gov/geo/）和NCBI的短读档案（SRA; http：//www.ncbi.nlm.nih.gov/Traces/home/）中以供长期传播。greengenes.lbl.gov 这个项目的更广泛的影响部分源于研究的跨学科性质。 对学生和博士后的培训将把定量方法与实验生物学的应用相结合。该项目还将在专业发展和教育领域产生更广泛的影响。此外，参与该项目的学生和博士后研究人员将受益于实验设计培训，获得技术专业知识和跨学科交流。此外，该项目还将为来自特拉华州州立大学（DSU）（一所1890年历史上的黑人大学）和特拉华州技术社区学院（DTCC）（一所拥有大量第一代大学生和少数民族学生的两年制院校）的优秀学生开展一项强有力的实习计划。“从实地到实验室”方案将包括农业取样、基因表达、代谢特征分析研究和生物信息学方面的培训。