This action funds an NSF National Plant Genome Initiative Postdoctoral Research Fellowship in Biology for FY 2019. 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 Michelle Stitzer is "Quantifying the impact of transposable elements on maize fitness and adaptation" The host institution for the fellowship is Cornell University and the sponsoring scientists are Drs. Cedric Feschotte and Edward S. Buckler.
Transposable elements are pieces of DNA that can jump to new positions in genomes. Unlike genes which are reliably inherited from generation to generation, transposable elements can move and generate new copies of themselves at novel positions throughout the genome. Originally discovered in maize, they are now known to exist in genomes across the tree of life. They are particularly active in plant genomes, making up 40% of the DNA in the rice genome and over 85% of the DNA in the maize and wheat genomes. Although transposable elements have been hypothesized to produce mutations valuable for adaptation to stressful environments, this has not been comprehensively tested. This project tests the impact of new transposition on maize adaptation and develops computational resources for transposable element annotation in plant genomes with possible implications for non-plant genomes. Broader impacts include the development of workshops focused on the use of statistical programming language R. These workshops will be tailored to undergraduate biology students with a focus on increasing participation from students underrepresented in STEM. Training objectives include obtaining expertise in plant phenotyping, computational, and molecular techniques as well as experience in communicating coding and bioinformatic techniques to diverse audiences.
The majority of plant genomes are comprised of transposable elements, but little is known about how their movement impacts plant fitness and phenotypes. Using maize as a model system, the project will directly investigate the impact of transposable elements on plant fitness and response to selection. Specific objectives are to: 1) develop software to detect and annotate transposable elements in sequenced reference genomes; 2) phenotype a mapping population of maize that varies in copy number of a transposable element to test whether copy number impacts yield and other fitness-related traits; and, 3) activate transposable elements genome-wide by chemical demethylation to test whether novel insertions generate mutations selected for during adaptation to abiotic stress. All project outcomes will be made accessible for use by the broader research community through various public repositories. All data, scripts, and software produced will be publicly available through GitHub, Figshare (https://figshare.com), MaizeGDB, and/or NCBI-SRA. Germplasm generated in this project will be deposited in the Maize Genetics Cooperation Stock Center.
Keywords: transposable elements, maize genetics, adaptation, genome annotation
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.
