Collaborative Research: RESEARCH-PGR: Development of epigenetic editing for crop improvement

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Genome editing tools have revolutionized biology. Scientists are using these tools to connect genes to phenotypes, generate novel phenotypic variation, and for diverse crop improvement applications. This project expands the possibilities for editing in crop plants to include a method for editing gene expression, so called “epigenetic editing”. Epigenetics is a broad term used to describe mechanisms that change gene expression without directly changing the DNA. Epigenetic variability can have profound impacts on an organism’s phenotype, and many important agronomic traits are influenced by gene expression. Broader impacts of the project include the wide dissemination of the method for the improvement of crop plants and other species, plus the training of students via integration with a long running and successful undergraduate internship program. Epigenetic crop improvement strategies will complement existing biotechnology and breeding strategies and may offer opportunities to help maintain crop yields in the face of climate change. This project will directly train the next generation of scientists to use these tools through an effective Research Experiences for Undergraduates (REU) program. All resources generated in this project will be made available for use.This project will expand the possibilities for editing in crop plants to include epigenetic editing. It was recently demonstrated that it is possible to affect gene expression through targeted DNA methylation at MeSWEET10a in the important crop, cassava. MeSWEET10a is not normally expressed in leaf tissue but is ectopically induced by a bacterial pathogen using a transcription activator-like (TAL) effector. De novo methylation of the MeSWEET10a promoter blocked TAL binding and led to decreased disease symptoms. Despite these encouraging results, epigenetic editing is still an immature technology. The goal of this project is to fill specific knowledge gaps related to establishment, maintenance, and inheritance of epigenetic edits and in so doing, lower the entry point for other researchers to adopt this powerful technology. Specifically, aim 1 of this proposal is to develop and distribute epigenetic editing tools in other crop species. The work will leverage and adapt the technologies known to work in cassava to accomplish similar disease outcomes in rice and tomato. Aim 2 will expand on the applications of epigenetic editing in crops. This includes the ability to target multiple loci simultaneously, “fine tune” gene expression and tissue specific editing. Aim 3 is dedicated to characterizing stability and heritability of de novo epialleles. If successful, other research projects and applications in biotechnology will benefit. This work will also provide additional jumping off points for fundamental work on epigenetics in non-model plant systems. Further, an ability to directly edit the epigenome will empower the larger field of epigenetics.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.