EDGE: Improving and Streamlining a System for Functional Studies of Polyploidy

Overview: Polyploidy or whole-genome duplication (WGD) is a major force in eukaryotic genome evolution. New polyploids have duplicate gene copies with redundant expression and function. Over time, these duplicates have several possible fates, from retention of both copies with their original function to divergence in expression and/or function to loss or silencing of one copy. However, the rules governing these processes remain unclear, limited largely by a lack of resources and genetic toolkit in organisms that best exemplify WGD. Tragopogon (Asteraceae, sunflower family) is an ideal system for examining the consequences of WGD over time via analyses of gene function, with two well-studied recently (<100 years) formed allotetraploid species, as well as an older (~1 mya) allopolyploid. We propose to optimize a transformation/CRISPR gene editing system in Tragopogon to enable innovative research on WGD and, at a broader scale, gene function in Asteraceae, the largest angiosperm family (25,000 sp.).

Although basal angiosperms represent only 3% of angiosperm species, these basal lineages are key to understanding the origin and subsequent evolution of the flower, as well as other key angiosperm features. However, there are no genetic models for basal angiosperms; furthermore, most basal angiosperms are woody, further limiting genetic manipulation. We therefore propose to continue developing a gene editing system for the phylogenetically pivotal angiosperm Amborella. An Amborella transformation/CRISPR system could be used to address diverse questions about ancestral gene function in the last common ancestor of all extant angiosperms.

Broader Impacts: The methods and tools we develop will be transferable to other systems, not only in Asteraceae and basal angiosperms, but beyond, opening doors for numerous researchers to develop approaches and methods that can be applied to their systems of interest. This alone will have enormous downstream benefits to a large, diverse community of new users.