Global Food Initiative
GFI Fellow - Class of 2015
Graduate Student, Population Biology
Lawrence Berkeley National Laboratory/UC Davis
Updating Genomic Annotations of Transposable Elements in Maize
I used computational methods to identify transposable elements in the maize genome. A transposable element is a small piece of DNA that can move itself to another place within its host’s genome. Transposable elements were discovered in maize in the 1940s as unstable loci, apparent when certain genetic crosses yielded kernels with unexpected purple speckles. DNA derived from transposable elements makes up over 85 percent of the corn genome, and transposable elements have been shown to impact the response of plants to environmental stress. My annotation of transposable elements provides novel data for predicting response of plants to agriculturally stressful environments.
The chief outcome of this project is an annotation of transposable elements in the most recent version of the maize genome (AGPv3). This will be released to the community of maize researchers, and will be described in a manuscript summarizing the evolutionary dynamics of transposable element families in the last 15 million years of maize evolution, highlighting how this interplay between transposable elements and their host has predisposed the response of the maize genome to certain types of environmental stress.
My work to date on this fellowship project has focused on describing transposable elements in the maize reference genome, which represents a single inbred line commonly used in agricultural production. This inbred line is a frequent parent of hybrid corn in the United States, but it does not encompass all the genetic diversity present in the species. Projects to sequence and assemble the genomes of other agriculturally important maize inbred lines are underway but have not yet been published. I plan to expand my annotation database to include these genomes as they become available. I am still determining my thesis project, but anticipate including analyses of transposable element-related gene expression and phenotypes of experimentally stressed plants.
Elizabeth Bautista and Kjiersten Fagnan