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Maize Epigenomic Variation Project

There is a growing interest in understanding how epigenetic variation might contribute to phenotypic variation.  Epigenetic variation, heritable variation that is not due to sequence changes, has been observed in a number of biological phenomena.  However, the prevalence and heritable behavior of epigenetic variation is not well understood.  This project studies epigenetic variation under four specific aims:

Aim 1. Discover epialleles in maize. Previous efforts have identified examples of epigenetic variation among a number of diverse maize inbred varieties. We are identifying and characterizing epialleles in a variety of genotypes including teosinte, doubled haploid plants and plants with novel transposon insertions.

Aim 2. Determine the causes and assess the stability of maize epialleles.We are elucidating the basis for maize epialleles through genomic and genetic analyses and are characterizing the stability of these epialleles through generations and in response to environmental stress.

 Aim 3. Determine the contribution of epigenetics to phenotypic variation. The impact of epigenetic variation on gene expression phenotypes is being diserned in a variety of materials. More importantly, we are characterizing how epialleles contribute to morphological variation in maize populations.

Aim 4. Develop and maintain a Zea epigenomics database (ZED). We are in the process of , updating and annotating a collection of maize epigenomic data derived from this project and from other groups. This information will be kept current with reference genome updates and genome annotations and will be publicly available in through iPlant. 

Whole genome profiling of DNA methylation, histone H3 lysine 9 dimethylation and histone H3 lysine 27 trimethylation will be performed on several tissues of the maize inbred line B73 and on a set of 50 additional inbred lines that capture much of the diversity of maize.  By focusing on this population it is possible to add epigenomic data to a wealth of existing data on genetic and phenotypic information.  This will provide the potential to identify examples of epigenetic variation that contribute to phenotypic variation within a species.

The project will also study how epigenetic differences are inherited in hybrids and in recombinant inbred lines that will provide the opportunity to assess the stability of epigenetic variation over multiple generations, critical to understanding the heritability of epigenetic variation and how it might be relevant to heritable phenotypic variation.  In addition, relatively little is known about the role of epigenetics in natural variation.  In order to provide a more detailed understanding of the role of epigenetics, it is critical to understand how this behavior is inherited and how this variation arises within a species.  

Experimental Microarray

This project will develop tools that will enable epigenomic research in maize and will provide a framework for considering the frequency and stability of epigenetic variation among maize inbred lines and may provide a framework for integrating both genetic and epigenetic variation into plant breeding and improvement projects.

The research project provides a series of excellent training opportunities for scientists at various stages of their careers.  Undergraduate students from the University of Minnesota and Hamline University will be involved with the primary research and will receive mentoring from post-doctoral scientists and principal investigators.  Postdoctoral scientists and a graduate student perform hypothesis-based research that provide experience with genomics and bioinformatics.  In addition, the principal investigators have both shown a commitment to general outreach.  Outreach efforts will include public education and K-12 teacher training.  All data produced by this project will be made publicly available through established databases such as GEO , Gramene ( and MaizeGDB as well as through our project website.  The proposed project will also have broader impacts on other research.  The information obtained in this project will influence studies of breeding and evolution.  A greater understanding of the sources of variation within a species will influence the view of many fields.