This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2023. 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 David Ding is "Tools for engineering plant gene expression". The host institution for the fellowship is UC Berkeley and the sponsoring scientist is Dr. David Savage.
Crop engineering offers a path to address the projected increases in food demand and challenges arising from a changing climate. Recent gene editing tools enable this in principle, but their potential for crop improvement is limited by the lack of understanding of how mutations map to phenotypic outcomes of interest, including increased photosynthetic capacity, drought resistance, or nitrogen-use efficiency. Importantly, tuning the expression of particular target genes can improve such traits, suggesting that understanding and finding genomic mutations that enable rational tuning of protein abundances could be sufficient for crop improvement. Overall, this project develops the missing tools to understand regulatory mutations in plants and could help usher in a new era in which gene editing technology ? in contrast to slow and manual breeding efforts ? could enable the rapid creation of novel crop varieties addressing fundamental food security and sustainability issues for society at large. The training objectives for the Fellow include not just further developing technical, analytical, and synthesis skills, but also communication and teaching skills. The Fellow currently does and will continue to convey the excitement and usefulness of scientific inquiry by participating in volunteering opportunities at Mount Tamalpais College, an organization that provides access to affordable higher education to students incarcerated at San Quentin State Prison.
In this project, a computational pipeline, coupled with high-throughput perturbative experimental assays, will be developed to overcome the inherently slow and low-throughput nature of understanding gene regulatory variants in plants. By focusing on validated sets of genes, the resulting understanding of regulatory mutations could enable simultaneous tuning of multiple target gene abundances with gene editing enzymes, and, since many known target genes participate in orthogonal pathways, could enable additive or synergistic increases in desired traits, as well as an improvement towards multiple traits, in a single step. Findings resulting from this work will be shared through publications, with any generated raw data, and analysis pipelines made available to the general public (through the sequence read archive and GitHub: https://www.ncbi.nlm.nih.gov/sra, www.github.com) for reproducibility and as tools. All created materials will be made available upon request. In this way, everyone will have access to any resources generated from this project.
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.
