CAREER: Leveraging Conserved Gene Duplications to Improve Plant Regeneration

Plants display extraordinary diversity in form and life history, ranging from small mosses in streams to thousand-year-old trees the size of skyscrapers. Understanding how genetic differences give rise to this diversity enables scientists to better control plant growth and development, facilitating new approaches to crop improvement and engineering through biotechnology. Studying highly diverse plant families provides insight into the genetic mechanisms underlying natural variation. The sunflower family (Asteraceae) is one such group, comprising ~30,000 species (roughly 10% of all flowering plants). Asteraceae share multiple ancient whole genome duplication events, resulting in extra copies of genes that can evolve new or specialized functions. This project will generate genomic sequencing data across Asteraceae, surveying duplicated genes involved in key developmental processes (regulating plant architecture) and then targeting them using genetic analyses to understand their diverse roles in regulating plant growth and development. Novel genes identified in this study will then be tested for their utility in crop improvement using modern biotechnological approaches. In addition to research, this project will support the development of a multi-semester training program ("GrowLab") focused on plant molecular biology. This GrowLab curriculum will provide hands-on training in molecular biology to both undergraduate and graduate students and will facilitate undergraduate placement into research labs where practical, technical skills can be further developed. Gene duplication is a major driver of phenotypic diversification in plants. Following duplication, the most common outcome for paralogous genes is fractionation, leaving only a single functional copy. Occasionally, both paralogs are retained, and their functional divergence can lead to the evolution of novel traits. Understanding paralog divergence, especially of highly conserved developmental regulators, can reveal novel genetic mechanisms in plants while also providing new opportunities for biotechnological innovation. This project will use comparative genomics and functional genetics to identify and functionally validate conserved developmental paralogs in Asteraceae, the most diverse plant family on Earth. With multiple known ancestral whole genome duplications at the base of the family, Asteraceae are an ideal system to study evolutionary outcomes following gene duplication. Focusing specifically on transcription factors, this project will use artificial intelligence (AI)-based analytics to predict and test functional divergence between lineage specific paralogs using genome-scale binding site identification, downstream transcriptional target validation as well as CRISPR-based functional analyses. These data will be the first comprehensive attempt to characterize paralogous gene function across this highly diverse family (representing ~10% of all flowering plants) and will target genes identified as potential developmental regulators to uncover novel functions. Currently, the use of developmental regulators to improve transformation across crop species has remained limited to only a handful of genes (typically derived from model systems). Genes that are identified as having novel developmental roles in Asteraceae species will be tested for broader application as regenerative factors in diverse flowering plant lineages. 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. NSF Award ID: 2541865 | Program: 01003031DB NSF RESEARCH & RELATED ACTIVIT,01002627DB NSF RESEARCH & RELATED ACTIVIT | Principal Investigator: Daniel Jones | Institution: Clemson University, CLEMSON, SC | Award Amount: $1,400,058 View on NSF Award Search: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=2541865 View on Research.gov: https://www.research.gov/awardapi-service/v1/awards/2541865.html