Epigenomic Variation Among Maize Inbred Lines

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence.  There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences.  Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information.  Genome-wide profiling of DNA methylation in several genotypes of Zea mays (ssp. mays), an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation.  The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs).  Several of these DMRs occur in genomic regions that are identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation.  The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. Further analyses have identified DMRs among other genotypes and tissues of maize.  A subset of the DMRs are correlated with gene expression changes and may contribute to phenotypic variation among maize inbred lines.