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

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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.