CoPIs: Damon Lisch (University of California, Berkeley), Matt Vaughn (Texas Advanced Computing Center, University of Texas - Austin), and Irina Makarevitch (Hamline University)

While it is clear that genetic changes play a major role in controlling phenotypic variation there is increasing evidence that epigenetic changes may also play an important role. There is considerable excitement about the existence of epigenetic variation because it raises the possibility that a memory of environmental or genetic conditions can be encoded and propagated independent of changes in DNA sequence. This possibility has obvious and important implications for both evolutionary biologists and plant breeders, but the relative role of epigenetic variation in conditioning phenotypic variation, particularly in crop species, remains poorly understood. This project will develop an understanding of the prevalence, origin and effects of epialleles in maize, an agronomically important species that is likely to be rich in epigenetic variation. This work will provide an extensive catalogue of epigenetic variation in maize and teosinte genotypes and will explore the extent to which processes such as generation of doubled haploids or silencing of transposons can contribute to that variation. Several experiments will also probe the mechanisms that underlie the creation and maintenance of epigenetic variation. Others will be aimed at determining the extent to which epigenetic variation can affect plant phenotypes. Collectively, the experiments are designed to provide a comprehensive view of epigenetic regulation in a key crop species. The genomic datasets developed in this project will be publicly available through a project website (accessible via www.cbs.umn.edu/labs/springer/) and at public repositories such as NCBI (www.ncbi.nlm.nih.gov/), Gramene (http://gramene.org), and MaizeGDB (www.maizegdb.org). Curated datasets and data analysis tools will also be publicly available at iPlant and biological materials will be available at public stock centers.

The research will provide a much more substantial understanding of the prevalence and effects of epigenetic variation in populations of maize. It will also help in determining the extent to which that variation contributes to quantitative trait variation in this species, which may have a significant impact on selection of ideal genotypes (or epigenotypes) during plant breeding. In a more general sense, this work will inform the current understanding of the role that epigenetic variation has played in maize domestication and the contribution of epigenetic change to evolutionary change in plants. The project will also develop computational resources that would enable powerful epigenomic studies in maize by centralizing the data and interpretation of complex datasets. Finally, this project will provide training and outreach opportunities for high school, undergraduate and graduate students in a variety of settings. Particular emphasis will be placed on including members of historically under-represented groups and on the incorporation of teacher training into research activities.

Agency
National Science Foundation (NSF)
Institute
Division of Integrative Organismal Systems (IOS)
Application #
1237931
Program Officer
Gerald Schoenknecht
Project Start
Project End
Budget Start
2012-10-01
Budget End
2018-03-31
Support Year
Fiscal Year
2012
Total Cost
$3,424,556
Indirect Cost
Name
University of Minnesota Twin Cities
Department
Type
DUNS #
City
Minneapolis
State
MN
Country
United States
Zip Code
55455