Identifying Deeply Conserved Patterns of Epigenetic Modification and Imprinting during Seed Development

这项行动资助了2018财年的NSF国家植物基因组计划生物学博士后研究奖学金。该研究金支持研究员在东道实验室的研究和培训计划，研究员还提出了扩大生物学参与的计划。Rebecca Povilus博士的研究和培训计划的标题是“在种子发育过程中识别表观遗传修饰和印记的深度保守模式”。该奖学金的主办机构是怀特黑德生物医学研究所，赞助科学家是玛丽格林博士。种子构成了我们的大部分饮食，是我们所依赖的生态系统的关键部分。了解哪些因素影响种子发育对于改善种子作物是必要的这不仅是为了保护作物（如小麦、玉米、水稻和大豆）的遗传多样性，也是为了确保在将遗传多样性重新引入近交作物品种时能产生有活力的后代。直到最近才有技术和系统来阐明表观遗传修饰（DNA碱基和相关DNA包装蛋白的化学变化）在植物繁殖过程中所起的作用。虽然表观遗传修饰已被证明对少数远亲植物物种的种子发育很重要，但表观遗传修饰的实际模式和影响似乎在物种之间存在很大差异。为了预测基于表观基因组的技术在作物改良和植物育种中的应用范围，必须确定表观遗传修饰的模式，这些模式对所有开花植物都是基本的，或者对特定的谱系是特定的。该项目将为了解表观遗传过程在生殖过程中所发挥的作用如何在开花植物中进化提供一个原本缺乏的基础。要做到这一点，表观遗传修饰及其与种子发育过程中基因表达的关联将在新兴的模式系统睡莲（Nymphaea thermarum）中得到鉴定，睡莲是最古老的开花植物谱系之一。培训目标包括基因组学、表观基因组学和生物信息学。更广泛的影响包括通过Whitehead合作伙伴计划与当地学校教师进行外联，以及开发和分发早期科学教育模块，探讨生物多样性和基础研究对农业和粮食安全的重要性。该模块将作为阿诺德植物园夏季研究所的一部分，并将在www.example.com上提供https://nthermarum.weebly.com/.The该项目的目标是了解表观遗传修饰及其对种子发育过程中基因表达的影响。具体目标包括：（1）确定在生殖发育过程中的表观遗传修饰的动态N。通过甲基化DNA和组蛋白标记的免疫定位、甲基化敏感的DNA测序和染色质谱分析，鉴定热裂菌的基因，以及2）使用杂交和组织特异性基因表达分析鉴定在早期胚胎和胚乳发育过程中具有母本或父本印记的基因。通过比较睡莲属的结果与模式物种的信息，表观遗传修饰和印记基因表达的高度保守模式将与单子叶植物（如谷类作物）或真双子叶植物（如拟南芥）中衍生的模式区分开来。该项目的结果将在开放式预印本服务器和同行评审期刊上发表，信息将在网站https://nthermarum.weebly.com/.Keywords上提供：种子发育，胚胎，胚乳，表观遗传学，睡莲，比较基因组学和表观基因组学该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2018. 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. Rebecca Povilus is "Identifying Deeply Conserved Patterns of Epigenetic Modification and Imprinting during Seed Development". The host institution for the fellowship is the Whitehead Institute for Biomedical Research and the sponsoring scientist is Dr. Mary Gehring.Seeds are important for humans; seeds make up most of our diets and are a key part of the ecosystems that we depend on. Understanding what factors influence seed development is necessary to improve seed crops (such as wheat, corn, rice, and soybean), as well as to ensure the production of viable offspring when re-introducing genetic diversity into inbred crop varieties. Only recently have technologies and systems been available to elucidate the role that epigenetic modifications (chemical changes to DNA bases and to associated DNA-packaging proteins) play during plant reproduction. While epigenetic modifications have been shown to be important for seed development in a small number of distantly related plant species, the actual patterns and effects of epigenetic modification appear to vary substantially between species. To predict how broadly epigenome-based technologies for crop improvement and plant breeding can be applied, the patterns of epigenetic modifications that are fundamental to all flowering plants, or are specific to particular lineages must be determined. This project will provide an otherwise lacking foundation for understanding how the role that epigenetic processes play during reproduction has evolved across flowering plants. To do so, epigenetic modifications and their association with gene expression during seed development will be identified in the emerging model system Nymphaea thermarum, a member of one of the most ancient flowering plant lineages. Training objectives include genomics, epigenomics and bioinformatics. Broader impacts include outreach to local school teachers through the Whitehead Partner program and the development and distribution of a module for early-science education that explores the importance of biodiversity and basic research to agriculture and food security. This module will be presented as part of the Arnold Arboretum Summer Institute, and will be available at https://nthermarum.weebly.com/.The goal of this project is to understand epigenetic modification and its impact on gene expression during seed development. Specific objectives include 1) determining the dynamics of epigenetic modification during reproductive development in N. thermarum through immunolocalization of methylated DNA and histone marks, methylation-sensitive DNA sequencing and chromatin profiling and 2) identifying genes that are maternally- or paternally-imprinted during early embryo and endosperm development using hybrid crosses and tissue specific gene expression analysis. By comparing results from Nymphaea to information from model species, deeply conserved patterns of epigenetic modifications and imprinted gene expression will be distinguished from those that are derived within either monocots (such cereal crops) or eudicots (such as Arabidopsis). Results of this project will be published on open-access pre-print servers and peer-reviewed journals, and information will be available on the website https://nthermarum.weebly.com/.Keywords: seed development, embryo, endosperm, epigenetics, Nymphaea, comparative genomics and epigenomicsThis 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.