Is Abiotic Stress Tolerance Achieved by Network Restructuring or Invention of New Genetic Modules?

该项目涉及探索植物如何自然适应恶劣环境，以了解胁迫耐受机制，并为更好地耐受变化的环境的粮食和能源作物的发展提供信息。这些结果具有广泛的社会意义，因为作物生产往往受到环境压力的限制，如盐度。这个项目将为不同的团队提供一个学习平台，以设计新的计算和分子工具来研究自然存在的遗传变异。这些团队将由生物和计算机科学研究生、本科生(包括未被充分代表的少数族裔)、高中生和教师以及国际合作者组成。该项目还支持两名初级调查员的职业发展。这个项目产生的数据将被用来设计一个由高中生程序员贡献的交互式可视化数据分析界面。其他活动包括为公众和K-12学生举办的植物营养意识活动，为高中教师和学生举办的关于聚合酶链式反应和DNA指纹识别的暑期讲习班，以及与当地高中生讨论与基因工程相关的伦理问题。该项目产生的DNA序列数据集和生物信息学计划将被公开共享，这将使科学活动从探索遗传和进化机制的基础研究到产生用于作物改良的标记和资源。这个项目将通过分析导致对胁迫的转录反应的基因组签名，然后是有针对性的转基因和分子表型，来研究一个物种如何实现与密切相关的胁迫敏感物种的胁迫适应。总体分析将在一个概念框架中进行测试，该框架强调通过修改现有的核心应激反应系统和/或招募新的遗传成分来实现应激适应。极端植物是理解极端非生物胁迫下植物生存的遗传机制的新兴模型。在已知的十字花科作物野生近缘植物中，两个耐盐性最强的物种--小球藻和盐藻将被作为模式基因组，并将与胁迫敏感的模式甘蓝进行比较，以研究多重盐胁迫的适应性。微小链球藻和碱蓬的基因组都显示出与拟南芥基因组的广泛同源性，这使得比较研究受益于关于拟南芥的丰富遗传信息。物种间比较RNAseq方法被计划用来揭示由过量的Na+、K+或Li+盐引起的非生物胁迫反应基因调控的动态。所有测试物种中的转基因植物都将针对已确定的主要应激反应单位中的代表性基因进行创建。分子水平的表型鉴定将通过从对照和胁迫处理样品中收集的野生型和转基因株系的离子和代谢组谱来实现。最后，将开发描述性遗传模块，将核心数据集与基因组重组联系起来，使已知的和新的胁迫反应途径在胁迫适应和胁迫敏感物种中都能改善胁迫适应。这项工作将提供一个战略性的案例研究，可以扩展到其他生物，通过在转基因植物、转录调控和用于分子表型的代谢体的辅助下进行有针对性的遗传研究来评估基因组组织。该项目由生物科学局分子和细胞生物科学部门的遗传机制簇和NSF EPSCoR计划共同资助。

The project involves exploration of how plants adapt naturally to harsh environments, in order to understand stress tolerance mechanisms and inform development of food and energy crops that can better tolerate changing environments. The outcomes have broad societal relevance, as crop production is frequently constrained by environmental stresses, such as salinity. This project will provide a learning platform for diverse teams to design new computational and molecular tools for studying naturally existing genetic variation. These teams will consist of biological and computer science graduate students, undergraduates, including underrepresented minorities, high school students and instructors, and international collaborators. The project also supports career development for two beginning investigators. Data generated from this project will be used to design an interactive visual data analysis interface with contributions from high school student programmers. Other activities include plant nutrient awareness events for the public and K-12 students, a summer workshop to train high school teachers and students in PCR and DNA fingerprinting, and discussions with local high school students on ethical issues related to genetic engineering. DNA sequence datasets and bioinformatics programs resulting from this project will be shared publicly, which will enable scientific activities ranging from basic research exploring mechanisms in genetics and evolution to generating markers and resources for crop improvement. This project will investigate how a species achieves stress adaptation compared to a closely related stress sensitive species by analyzing genomic signatures that lead to transcriptomic responses to stress, followed by targeted transgenics and molecular phenotyping. The overall analysis will be tested in a conceptual framework that highlights stress adaptation achieved by modifications in existing core stress response systems, and/or recruitment of new genetic components. Extremophile plants represent emerging models for understanding genetic mechanisms governing plant survival under extreme abiotic stresses. Schrenkiella parvula and Eutrema salsugineum, the two most salt-tolerant species among known wild relatives of Brassica crops, will be used as model genomes, and multiple salt stresses will be applied to study adaptation compared to the stress sensitive model A. thaliana. Genomes of both S. parvula and E. salsugineum show extensive overall synteny with the A. thaliana genome, which enables comparative studies benefiting from the wealth of genetic information available on A. thaliana. Inter-species comparative RNAseq methods are planned to uncover the dynamics of abiotic stress responsive gene regulation caused by excessive Na+, K+, or Li+ salts. Transgenic plants in all test species will be created targeting representative genes in major stress responsive units identified. Molecular level phenotyping will be achieved via ionomic and metabolomic profiling of wild-type and transgenic lines collected from control and stress-treated samples. Finally, descriptive genetic modules will be developed with a core data set linking genomic restructuring that enables improved stress adaptation in known and novel stress responsive pathways, in both stress-adapted and stress-sensitive species. The work will provide a strategic case study that can be expanded to other organisms, to evaluate genomic organization via targeted genetic studies assisted by transgenic plants, transcriptomic regulation, and metabolomes used for molecular phenotyping.This project is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate and by the NSF EPSCoR Program.