NSF Postdoctoral Fellowship in Biology

Padgitt-Cobb, Lillian, Corvallis OR

Investigators

Abstract

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. 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 Lillian Padgitt-Cobb is "Single-cell Study of Gene Expression and Regulatory DNA in the Glandular Trichomes of Hemp (Cannabis sativa) Flowers". The host institution for the fellowship is the Salk Institute for Biological Studies and the sponsoring scientist is Dr. Todd Michael. Hemp (Cannabis sativa) is a plant of cultural and economic significance that is highly valued for the array of molecular compounds it produces. Much of the agronomically-valuable chemistry of hemp occurs in specialized structures of female flowers, called glandular trichomes. Glandular trichomes are multicellular factories that create and store a small number of molecular compounds in large abundance, making it an excellent system to study cell-based chemistry and gene regulation. The key outcomes of this project will focus on determining how molecular compounds are produced in the glandular trichomes, including the location of their production, and the genetic basis controlling the quantity of their production. This is an important area of research for the hemp bioeconomy because growers and stakeholders require hemp plants with a consistent profile of specific molecular compounds, which has implications for cultivation strategies related to how hemp plants are grown. This project includes novel approaches, including the application of single-cell experiments in hemp, which is an opportunity to discover how metabolism is coordinated in glandular trichomes. The first Broader Impacts component of this project will include a collaboration with the San Diego Botanical Garden to develop educational materials for a workshop about principles of plant breeding, focusing on hemp. The workshop will be an opportunity to train the public about the manipulation of plant genetics through breeding. The second Broader Impacts component will include the mentorship of three undergraduate students from local minority-serving universities in San Diego to broaden participation in science. Hemp produces cannabinoid and terpenoid compounds in its glandular trichomes. In contrast to high-THC (tetrahydrocannabinol) cultivars of C. sativa (marijuana), hemp is defined as having a THC content of less than 0.3% by dry weight and is cultivated specifically for its fiber and oil. The regulatory mechanisms that govern biosynthesis, transport, and signaling, and allow C. sativa to devote such a large percentage of its flowering biomass to the synthesis of a few metabolites, remain unclear. The key outcomes of this research project will focus on uncovering mechanistic insights about the regulation of metabolite biosynthesis at a single-cell level, including 1) identification and characterization of cell types in glandular trichomes based on gene expression and accessible chromatin regions from an integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin (scATAC-seq) experiment; 2) identification of de novo and known regulatory motifs, focusing on regulatory motifs in accessible chromatin regions; 3) assessment of sequence variation in accessible chromatin regions and regulatory motifs using genotype and chemotype data available for multiple cultivars of C. sativa; and 4) quantification of a core set of cannabinoids and terpenoids to assess the association between metabolite abundance, regulatory DNA, and expression of key enzymes and co-regulated genes. Sequencing reads from the single-cell experiments will be deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). Scripts and analysis pipelines will be available on GitHub. Results and findings will be shared via peer-reviewed scientific publications. 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.