NSF Postdoctoral Fellowship in Biology FY 2019: Deciphering CLE Peptide Signaling Pathways in Sunflower (Helianthus annuus)

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。丹尼尔·斯科特·琼斯博士的研究和培训计划的题目是“破译向日葵（Helianthus annuus） CLE肽信号通路”。该奖学金的主办机构是位于教堂山的北卡罗来纳大学，赞助科学家是扎卡里·尼姆查克博士。与动物不同，植物在其整个生命周期中不断发育并产生新的器官。为了支持这种持续的生长，植物维持了一组功能性的干细胞，这些干细胞可以根据需要分裂成植物内任何其他类型的细胞；产生了茎、叶、根、花和种子中的所有细胞。植物茎部维持的干细胞数量即使有微小的变化，也会直接影响其产生的器官的数量和大小。了解植物中干细胞身份是如何被控制的，直接关系到我们影响重要农学性状的能力，比如果实大小、谷物产量，甚至是整个作物的健康和性能。本项目旨在揭示向日葵这一重要的种子和油料作物中调控干细胞身份的关键基因。在这个项目的过程中，将开发工具，进一步利用向日葵作为研究向日葵科（菊科）物种的模型研究系统，向日葵科是最大的植物科之一，具有巨大的经济意义/潜力。在此奖学金期间提供的支持还将为东道国的第一代大学生提供专门的研究机会。培训目标包括获得比较基因组学、发展、表观遗传学和生物信息学方面的新技能。了解保守的信号通路如何介导细胞间通讯以协调不同的发育形式是生物学中的一个核心问题。CLE （CLAVATA3/胚乳周围区域相关）肽信号在高度分化的物种中代表了一条调节干细胞身份和器官发生的保守途径。本项目的主要目的是：1)鉴定向日葵花序发育过程中表达的CLE信号成分；2)通过RNA-seq和ATAC -seq确定向日葵茎和根分生组织对CLE肽的信号输出；3)在向日葵中实施CRISPR-Cas9诱变，对CLE关键通路组分进行功能分析；4)完成一个密集的科学培训计划，开发比较和大规模基因组学的新技能，同时产生基础数据，以建立一个独立的研究计划。本研究过程中产生的所有基因组数据集将存储在可公开访问的Gene Expression Omnibus-GEO （http://www.ncbi.nlm.nih.gov/geo/）中，并将通过Institut National de la Recherche Aronomique （INRA）向日葵生物信息学资源网站（https://www.heliagene.org/）与向日葵社区免费共享。此外，所有针对向日葵进行优化的CRISPR-Cas9构建体，将根据要求通过非营利性全球质粒库Addgene （https://www.addgene.org/）提供，以便于分发。关键词：向日葵，RNA-seq, ATAC-seq，转录组，干细胞，细胞间信号，花序，花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 Dr. Daniel Scott Jones is "Deciphering CLE peptide signaling pathways in sunflower (Helianthus annuus)". The host institution for the fellowship is the University of North Carolina in Chapel Hill and the sponsoring scientist is Dr. Zachary Nimchuk. Unlike animals, plants continue to develop and generate new organs throughout their lifespan. To support this continual growth, plants maintain a functional set of stem cells that can divide and become any other type of cell within the plant as needed; giving rise to all cells found in stems, leaves, roots, flowers, and seeds. Even slight changes in the number of stem cells maintained in the shoot of a plant can have a direct impact on the number and size of organs it produces. Understanding how stem cell identity is controlled in plants is directly linked with our ability to influence agronomically important traits such as fruit size, grain yield or even overall crop health and performance. This project aims to uncover key genes regulating stem cell identity in sunflower, an important seed and oil crop. During the course of this project, tools will be developed to further the use of sunflower as a model research system for studying species within the sunflower family (Asteraceae), one of the largest plant families with great economic significance/potential. Support provided during this fellowship will also enable research opportunities specifically catered toward first-generation college students at the host institution. Training objectives include acquiring new skills in comparative genomics, development, epigenetics and bioinformatics. Understanding how conserved signaling pathways mediate cell-cell communication to coordinate diverse developmental forms is a central question within the biology. CLE (CLAVATA3/Endosperm surrounding region-related) peptide signaling represents a conserved pathway regulating stem cell identity and organogenesis across highly divergent species. The main objectives of this project are to: 1) identify CLE signaling components expressed during inflorescence development in sunflower; 2) define signaling outputs in sunflower shoot and root meristems in response to CLE peptides via RNA-seq and ATAC -seq; 3) implement CRISPR-Cas9 mutagenesis in sunflower and functionally analyze key CLE pathway components; 4) complete an intensive scientific training program, developing new skills in comparative and large-scale genomics while producing foundational data from which to build an independent research program. All genomic datasets generated during the course of this study will be deposited into the publicly accessible Gene Expression Omnibus-GEO (http://www.ncbi.nlm.nih.gov/geo/) and will be freely shared with the sunflower community via the Institut National de la Recherche Aronomique (INRA) Sunflower Bioinformatics Resource site (https://www.heliagene.org/). Additionally, all CRISPR-Cas9 constructs, optimized for use in sunflower, will be made available by request and through Addgene, the nonprofit global plasmid repository (https://www.addgene.org/), for ease of distribution. Keywords: sunflower, RNA-seq, ATAC-seq, transcriptome, stem cell, intercellular signaling, inflorescence, flowerThis 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.