Collaborative Research: EDGE CMT: Fractionation of Polyploid Genomes as a Driver of Phenotypic Novelty

Understanding the genetic basis of phenotypic variation remains a grand challenge in biology and holds enormous potential for the bioeconomy, agriculture, and medicine. Achieving this understanding is complicated by genome doubling (polyploidy), which shapes the genomes of most contemporary species by providing extra copies of every gene and plays a role in both cancer and crop development. How genes produce phenotypes can therefore not be understood without considering the impact of polyploidy, a ubiquitous feature of life. Use of cutting-edge biotechnology, including the genome-editing tool CRISPR, will help bridge this genotype-to-phenotype knowledge gap. The flowering plant genus Tragopogon (goatsbeard; sunflower family) includes polyploid species that formed in the last 100 years, providing a unique opportunity to examine the immediate consequences of polyploidy on gene expression and phenotypic variation. Through prior NSF funding, Tragopogon is now a functional genetic model with an established CRISPR system, enabling study of the genetic control of phenotypic innovation. The goal of this project is to better understand the link between genome doubling, gene function, and resulting novel phenotypes in Tragopogon, using cutting-edge biotechnology and AI-driven approaches to gene discovery. Given the prevalence of polyploidy, discoveries in Tragopogon, a model polyploid system, have broad implications, extending across biology to include agriculture, horticulture, and medicine. Broader impacts include educational and training opportunities on team science, the role of collaboration in innovation, plant genomics, lab techniques for gene editing and the genome-phenotype connection, and the role of polyploidy in biology. Breakthrough technologies will be disseminated through workshops at national conferences, and public outreach will include virtual visits to middle and high school classrooms across Florida to share research discoveries. This project will provide insights into a poorly understood research area – the genotype-to-phenotype connection immediately following genome doubling. Given evidence of superior stress response in polyploids in diverse species, including crops, responses to heat and drought stresses were selected as timely and important complex phenotypes to be examined. The genetic basis of environmental stress response in polyploid Tragopogon will be identified through integrated experiments using CRISPR, genomics, and comparisons of gene expression. Objectives include: (1) identify the genetic control of environmental stress response in polyploid Tragopogon through a combination of gene editing, phenotyping, and gene expression network analysis; (2) determine the impact of duplicated genes and gene loss on phenotypes associated with stress response; (3) share biotechnological methods with the research community through an interconnected series of workshops; and (4) introduce topics related to stress response, genomics, and biotechnology to future scientists in middle school, high school, and university. The approaches to be used, which leverage cutting-edge biotechnology, will provide a broadly generalizable framework for studying complex phenotypes in other systems, including other non-models and crops. Identifying the genetic basis of stress response in Tragopogon will facilitate plant breeding, particularly in the sunflower family, which contains many crops and ornamentals. 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.