NSF Postdoctoral Fellowship in Biology FY 2019: Leveraging Quantitative Genetic Mapping Data for Discovery of Novel Regulatory DNA in Solanum lycopersicum

本行动资助NSF国家植物基因组计划2019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。Grace A. Mason的研究和培训计划的标题是“利用定量基因图谱数据发现茄类植物的新型调控DNA”。该奖学金的主办机构是加州大学戴维斯分校/明尼苏达大学双城分校，赞助科学家是dr。西沃恩·布雷迪和查德·迈尔斯。传统上，作物改良完全依赖于对所需性状的选择性育种。虽然取得了成功，但这种费力的方法降低了育种者基于遗传变异快速预测性状的能力，并改善了可用的育种资源。为了更快、更系统地进行育种，该项目旨在系统地测试番茄基因组中的遗传变异对基因表达和选定的根构型表型的影响。潜在的调控变异将首先测试其影响基因表达的能力，然后测试其对植物根结构表型的影响，这些性状通常研究不足，可能对番茄育种者有潜在的用途。该项目的更广泛影响包括为来自不同背景的当地高中生和大学生提供基础研究方面的实践培训，以及向公众宣传番茄育种以及现代技术如何允许非转基因作物改良。培训目标包括获得在经济相关作物中使用数量遗传学和计算科学以及工具开发的技能。调控DNA的变异被认为是野生物种表型变异以及栽培作物驯化的主要因素。增强子是一种调节性DNA，以时空方式调节靶基因的表达，并且可能相对远于其靶基因，因此难以表征。在动物系统中，数百种增强子已被很好地表征并与靶基因相关联。在植物中，尽管最近努力鉴定全基因组调控元件，但在4种植物物种中只有13个增强子与靶基因直接相关。其中，只有玉米中tb1增强子的变异与驯化和作物改良有明显联系。为了解决这一差异，该项目的总体目标是发现等位基因特异性植物增强子并将其与靶基因联系起来。具体来说，将使用新的计算方法来鉴定番茄（Solanum lycopersicum）中的调控增强子元件，并特别关注根结构性状的遗传定位数据。这项研究将利用几种不同的遗传资源，包括广泛的驯化番茄品种目录，现有的数量性状数据集，以及一组遗传上不同的等基因渗入系。大规模增强子分析技术将用于产生与根结构表型相关的等位基因特异性调控区域。虽然人们一直在努力描述几种栽培植物的调控景观，但这些实验将是第一个使用大规模测序技术直接测试基于植物的关联映射变异的实验。该项目的测序数据将通过国家生物技术信息中心（NCBI） GEO和Probe数据库存档并公开。此外，所有CRISPR-Cas9构建体都将通过非营利性全球质粒库Addgene （https://www.addgene.org/）提供。软件和分析脚本将通过GitHub提供。关键词：番茄，基因表达，遗传变异，调控DNA，增强因子，根结构，定量遗传学该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. 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 Grace A. Mason is "Leveraging Quantitative Genetic Mapping Data for Discovery of Novel Regulatory DNA in Solanum lycopersicum". The host institutions for the fellowship are the University of California, Davis/University of Minnesota, Twin Cities and the sponsoring scientists are Drs. Siobhan Brady and Chad Myers. Traditionally, crop improvement relies solely on selective breeding for desired traits. While successful, this laborious methodology reduces breeders' ability to quickly predict traits based on genetic variation as well as improve available breeding resources. To allow for faster and more systematic breeding, this project aims to systematically test genetic variation within the tomato genome for their effects on gene expression and on selected root architecture phenotypes. Potential regulatory variants will then be tested first for the ability to influence gene expression and then for its effect on plant root architecture phenotypes, traits that are generally understudied and could be of potential use to tomato breeders. The broader impacts of the project include providing hands-on training in basic research for local high school and undergraduate students from diverse backgrounds as well educating the general public about tomato breeding and how modern technologies can allow for non-transgenic crop improvement. Training objectives include acquiring skills in the use of quantitative genetics and computational science and tool development in an economically relevant crop plant.Variation in regulatory DNA is thought to be a major factor for phenotypic variation in wild species as well as domestication of cultivated crop plants. Enhancers, a type of regulatory DNA, regulate target gene expression in a spatiotemporal manner and can be relatively distal to their target genes, thus making them difficult to characterize. In animal systems, hundreds of enhancers are well-characterized and have been linked to target genes. In plants, despite recent efforts to identify genome-wide regulatory elements, only thirteen enhancers in four plant species have been directly linked to target genes. Of these, only variation in the tb1 enhancer in Zea mays (corn) is demonstrably linked to domestication and crop improvement. To address this disparity, the overall goal of this project is to discover allele-specific plant enhancers and link them to their target genes. Specifically, regulatory enhancer elements will be identified in Solanum lycopersicum (tomato) using novel computational methods for genetic mapping data with a specific focus on root architecture traits. The research will take advantage of several diverse genetic resources, including an extensive catalog of domesticated tomato accessions, existing quantitative trait data sets, as well as a genetically divergent set of isogenic introgression lines. Large-scale enhancer assay techniques will be used to yield allele-specific regulatory regions linked to root architecture phenotypes. While there has been intense effort to characterize the regulatory landscape in several cultivated plants, these experiments will be the first to directly test plant-based association mapping variants using large-scale sequencing technologies. Sequencing data from this project will be archived and publicly available through the National Center for Biotechnology Information (NCBI) GEO and Probe databases. Additionally, all CRISPR-Cas9 constructs will be made available by request and through Addgene, the nonprofit global plasmid repository (https://www.addgene.org/). Software and analysis scripts will be made available through GitHub.Keywords: tomato, gene expression, genetic variation, regulatory DNA, enhancer element, root architecture, quantitative geneticsThis 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.