ECA-PGR: Dissecting Natural Mechanisms for Genome Content Variation and the Impact on Phenotypic Variation

ECA-PGR：剖析基因组内容变异的自然机制及其对表型变异的影响

• 批准号: 1546727
• 负责人: Candice Hirsch
• 金额: $ 219.88万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546727&HistoricalAwards=false
• 关键词: ECA; PGR; Dissecting; Natural; Mechanisms

The nature of a plant or animal is defined in part by the DNA content in its genome. One might expect that this important role of imparting information is preserved in genomes over generations. In fact, genomes are known to be unstable and the constituent gene and non-gene content can change over time; genes can be copied, lost, or altered slightly, and such variation has significant impact on the appearance and function of an individual. As an example, the change in gene content in a corn plant can affect its growth or important agronomic traits, such as drought resistance, seed size or yield. The variation in gene content in individuals is puzzling to scientists and clearly beneficial to breeders: How and when does gene content change? What impact does it have on the traits, or phenotype, of the plant? And can the process be harnessed to identify new traits for agricultural improvement? This research project uses corn, or maize, as a model crop to answer these questions. The research is possible because the maize genome is remarkably variable in closely related lines, and there are extensive genetic resources that can be used to test how, when and why genome content changes. The project will identify signatures of genome change and will associate these changes to new traits. In the process, new participants will be trained from many educational levels. Specific efforts will focus on attracting young girls and women to scientific careers. Students and teachers will engage in a type of authentic research in plant genomics that has clear connections to outcomes in agriculture. Mentoring and training opportunities for female scientists will also be collated and disseminated through databases and public web portals.Using maize as a model system, this project will systematically characterize the extent of genome content variation among a panel of diverse genotypes, identify the genetic mechanisms responsible for this variation in genome content through genomic signatures, and measure the impact on phenotypic variation. The research plan integrates genomics, metabolomics, quantitative genetics, and statistical genetics to further our understanding of genome content variation and the role mechanistic origin plays in phenotypic outcomes. Specifically, this project will 1) identify genome content variation between maize inbred lines using a combination of de novo genome assemblies and exome capture using a combination of short- and long-read sequencing technologies, 2) identify mechanistic signatures that elucidate the origin of genome content variation on a genome-wide scale, 3) implement Genome Wide Association Studies to identify genome content variation associated with quantitative, qualitative, essential, and dispensable phenotypic and chemotypic (surface lipid profiles and kernel content) classes of traits in a diverse panel of maize inbred lines, and 4) use statistical genetic approaches to determine if there is a relationship between the mechanisms that create genome content variation and phenotypic outcomes. The project also provides mentoring and training opportunities in new tools and technologies in metabolomics, genomics, and statistical genetics for high school, undergraduate and graduate students, postdoctoral associates, and faculty at primarily undergraduate institutions.

植物或动物的性质部分由其基因组中的DNA含量定义。 人们可能会认为，这种传递信息的重要作用在基因组中代代相传。事实上，基因组是不稳定的，组成基因和非基因的内容可以随着时间的推移而改变;基因可以被复制，丢失或轻微改变，这种变化对个体的外观和功能有重大影响。 例如，玉米植物中基因含量的变化可以影响其生长或重要的农艺性状，如抗旱性、种子大小或产量。 个体中基因含量的变化令科学家们感到困惑，而对育种者来说显然是有益的：基因含量是如何以及何时变化的？它对植物的性状或表型有什么影响？这一过程能否被用来识别农业改良的新特征？这个研究项目使用玉米作为模型作物来回答这些问题。这项研究之所以成为可能，是因为玉米基因组在密切相关的品系中具有显著的可变性，并且有广泛的遗传资源可用于测试基因组内容如何，何时以及为什么变化。该项目将识别基因组变化的特征，并将这些变化与新的性状联系起来。在这一过程中，将对来自不同教育层次的新参与者进行培训。具体工作将侧重于吸引年轻女孩和妇女从事科学事业。学生和教师将从事一种真实的植物基因组学研究，与农业成果有明确的联系。还将通过数据库和公共门户网站整理和传播为女科学家提供的指导和培训机会。该项目将以玉米为模式系统，系统地描述一组不同基因型之间基因组含量变异的程度，通过基因组签名确定导致基因组含量变异的遗传机制，并测量对表型变异的影响。该研究计划整合了基因组学，代谢组学，定量遗传学和统计遗传学，以进一步了解基因组含量变化和机械起源在表型结果中的作用。具体而言，该项目将1）使用从头基因组组装和外显子组捕获的组合，使用短读和长读测序技术的组合，鉴定玉米自交系之间的基因组含量变异，2）鉴定在全基因组范围内阐明基因组含量变异起源的机制特征，3）实施全基因组关联研究，以确定与定量、定性、基本以及表型和化学型（表面脂质分布和籽粒含量）不同玉米自交系组中的性状类别，以及4）使用统计遗传学方法来确定在产生基因组含量变异的机制与表型结果之间是否存在关系。该项目还为高中生、本科生和研究生、博士后以及主要本科院校的教师提供代谢组学、基因组学和统计遗传学新工具和技术方面的指导和培训机会。