NSF Postdoctoral Fellowship in Biology

This action funds an NSF Plant Genome Postdoctoral Research Fellowship in Biology for FY 2022. 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 Dr.

Clara Williams is “Coordinated epigenetic changes during regeneration of callus using tomato as a model species.” The host institution for the fellowship is the University of California Berkeley and the sponsoring scientists are Dr. Ben Williams and Dr. Siobhan Brady.

Global food insecurity is a pressing issue that humans face due to an increasing population and is further exacerbated by climate change and war leading to disrupted and reduced supplies. A vast majority of plant improvement efforts involve the propagation of elite cultivars via tissue culture— regardless of whether they were generated by traditional breeding or genetically modified.

Yet, the regeneration of organs and whole plants from tissue culture remains the crux of plant engineering, propagation, and breeding. The research addresses this issue using tomato— the most consumed fruit in the world— as a model species. It will investigate how plants propagated from the same clone can accumulate genetic differences from the parental plant, thereby altering desirable traits.

Furthermore, the research aims to elucidate how genetically similar species can possess remarkably different regeneration capacities. To solve this, the project seeks to determine the genes and protein modifications that enable plasticity under different stages of the regenerative process. Additionally, the research seeks to identify underlying heritable non-genetic differences in the DNA of several tomato varieties and species that help to determine the respective disparities in their regenerative capacity.

Once these differences are determined it will shed light on specific mechanisms that hinder or improve the propagation of plants in tissue culture. Unlocking the ability to regenerate a wider variety of plant cultivars and species would therefore provide a much-needed boost to our ability to improve and innovate crops to meet global challenges. The PI will mentor high school students in the Bay Area, through the program Oakland Serves, providing a positive influence on students to enter and continue with their education in STEM.

While regeneration is usually feasible, the capacity for callus to initiate the growth of new organs and regenerate is strongly influenced by the species, genotype, tissue, and culture conditions. Most recent advances that enhance the regeneration of recalcitrant plants have focused on altering the composition of growth media or ectopic expression of developmental regulators.

However, the precise role of epigenetic information—chemical modifications to DNA or histones that alter gene expression but not the genomic sequence—on regeneration is less understood. To address this, the research will profile how transcriptional expression is driven by changes in chromatin accessibility in cultivated tomato, its wild predecessor, Solanum pimpinellifolium, and a recalcitrant species, Solanum hirsutum.

It will also uncover how DNA damage proliferates during regeneration, a likely cause of somaclonal variation using the in situ DNA-protein complex assay CUT&RUN. The project will generate comprehensive and publicly accessible data sets—on NCBI Sequence Read Archive— profiling DNA damage, chromatin accessibility, and gene expression during regeneration in the commercially relevant crop tomato.

These data sets can be used to understand the temporal and spatial regulation of the chromatin landscape during regeneration in a lineage that possesses both capable regenerators and recalcitrant strains. This will shed light on the effects epigenetic regulation of the genome has on the generation of transgenics, which may be generally applied to all eukaryotes.

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.