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

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, flower

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.