NSF Postdoctoral Fellowship in Biology FY 2020: Adaptive gene regulation in Mimulus guttatus in locally adapted populations

本行动资助NSF国家植物基因组计划2020财年生物学博士后研究奖学金。该奖学金支持奖学金获得者在主办实验室的研究和培训计划，该奖学金获得者还提出了扩大生物学参与的计划。Leslie M. Kollar的研究和培训计划的标题是“驱动黄猴花（Mimulus guttatus）适应性分化的基因组机制”。该奖学金的主办机构是密歇根州立大学，赞助科学家是David Lowry博士和Chad Niederhuth博士。基因调控的进化长期以来一直被假设在自然界丰富的多样性中发挥关键作用。在短期内，基因表达会随着环境条件的变化而改变。然而，从长远来看，基因调控的进化涉及序列的变化，最终导致多样性和局部适应。本研究的目的是在机制水平上解决关于适应性分化在基因调控进化中的作用的基础重要问题。这种方法只有在具有基因组资源的系统中才有可能，并且在具有良好的局部适应性特征的系统中，例如黄猴花，Mimulus guttatus。阐明进化如何塑造基因调控以响应环境因素，将促进对植物局部适应和胁迫反应机制的理解。了解这些过程对于开发适应更极端气候条件的有弹性的区域适应性作物至关重要。这项研究还将促进对历史上代表性不足的群体的本科研究人员的指导。指导部分将在持续改进模式下运作，该模式将主要侧重于将先前发表的和新开发的方法纳入通用设计中，以指导高等教育中的STEM学生。这些学生将参与分子实验室协议、数据分析和项目开发，直接支持研究目标。培养博士后的目标包括建立转录组学、表观基因组学和基因组学方法，以及增强生物信息学技能。为了了解基因表达如何在适应过程中进化，研究员将研究沿海和内陆黄猴花（Mimulus guttatus）种群之间多种类型的适应性基因调控差异。目标一将评估两国人口在不同发展阶段的监管格局的差异模式。为了确定发育中的局部适应性差异，将评估染色质和转录的变化以及调控序列的变化。目标二将侧重于确定沿海和内陆种群对海洋盐雾耐受性的局部适应性差异的基因调控原因。破坏性盐雾是一种被充分研究的环境胁迫源，这些结果将建立在此基础上，通过确定潜在的调控区域和序列变异。最后，对于目标三，研究员将研究压力记忆如何促进对慢性压力源的不同反应。这种现象被称为“启动效应”或“适应”。研究将集中在M guttatus是否表现出对慢性非生物胁迫，海洋盐雾的启动反应，并确定在什么条件下植物采用这种防御策略。该研究员将在表型水平上建立启动症状，并比较不同长度的盐暴露如何影响沿海和内陆种群的基因调控反应。所有数据、分析和生物标本将通过公共存储库向科学界公开。研究结果将通过期刊出版物和在国家会议上的发言加以传播。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2020. The fellowship supports a research and training plan in a host laboratory for the Fellow who also presents a plan to broaden participation in biology. The title of the research and training plan for this fellowship to Leslie M. Kollar is "Genomic mechanisms driving adaptive divergence in the yellow monkey flower, Mimulus guttatus". The host institution for the fellowship is the Michigan State University and the sponsoring scientists are Dr. David Lowry and Dr. Chad Niederhuth.The evolution of gene regulation has long been hypothesized to play a key role in the rich diversity present in nature. In the short term, gene expression can change as a result of varying environmental conditions. In the long term however, the evolution of gene regulation involves changes in the sequence which ultimately result in diversity and local adaptation. The goal of this research is to address foundationally important questions regarding the role of adaptive divergence in the evolution of gene regulation at a mechanistic level. This approach is only possible in systems with genomic resources and where local adaptation has been well characterized, such as the yellow monkey flower, Mimulus guttatus. Elucidating how evolution shapes gene regulation in response to environmental factors will advance an understanding of the mechanisms of local adaptation and plant stress responses. Understanding these processes will be critical for the development of resilient regionally-adapted crops to more extreme climatic conditions. This research will also promote mentorship for undergraduate researchers from historically underrepresented groups. The mentoring component will operate under a continuous improvement model, which will focus primarily on incorporating previously published and newly developed methods in universal design for mentoring STEM students in higher education. These students will take part in molecular laboratory protocols, data analyses, and project development in direct support of the research aims. Training objectives for the post-doctoral fellow include building on transcriptomic, epigenomic, and genomic methods along with bolstering bioinformatic skills.To understand how gene expression evolves through the process of adaption, the fellow will study multiple types of adaptive gene regulatory divergence between coastal and inland populations of the yellow monkeyflower, Mimulus guttatus. Objective one will evaluate patterns of divergence in the regulatory landscape across developmental stages between the two populations. To establish the locally adaptive differences in development, chromatin and transcriptional changes as well as regulatory sequence variation will be evaluated. Objective two will focus on the identification of the gene regulatory causes of local adaptive differences in tolerance to oceanic salt spray of coastal and inland populations. Damaging salt spray is a well-studied environmental stressor in M. guttatus, and these results will build upon this foundation by identifying underlying regulatory regions and sequence variation. Finally, for objective three, the fellow will examine how stress memory can facilitate differential responses to chronic stressors. This is a phenomenon known as ‘priming’ or ‘acclimation’. The research will focus on whether M guttatus exhibits priming in response to a chronic abiotic stress, oceanic salt spray, and identify under what conditions plants employs this defensive strategy. The fellow will establish the symptoms of priming at the phenotypic level and compare how different lengths of exposure to salt affect gene regulatory responses for the coastal and inland populations. All data, analyses, and biological specimens will be made publicly available to the scientific community through public repositories. Results of the research will be disseminated through journal publications and presentations at national conferences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.