NATURAL EPIGENETIC VARIATION IN MAIZE

Phenotypic variation results from the interaction between genetic variation and environment but it is even more evident that epigenetics acts as an additional component contributing to phenotypic variation. In fact, despite the complexity and sophistication of maize breeding, in some cases the large degree of the phenotypic variation unexplained by allelic variation has been unravelled by epigenetic variation, even if its contribution is still enigmatic due to the relatively few characterized natural epigenetic alleles (epialleles). In plants, one of the epigenetic marks is cytosine methylation (mC) and it occurs in symmetric (CG and CHG, where H is A, C, or T) as well as asymmetric (CHH) contexts. Changes in mC can occur in a spontaneous or induced manner, producing new epialleles that might lead to aberrant gene expression and phenotypic variation. Increasing evidence suggests that epigenetic variation may also arise in a genetic-independent manner, i.e. pure epigenetic variation, providing a mechanism for phenotypic variation in the absence of DNA mutations. Within this context, maize represents a good model to study epigenetic variation because it exhibits different phenomena like transposon silencing, gene imprinting and paramutation. To estimate the extent of pure epigenetic variation in maize and to identify the DNA regions targeted, we developed two maize lines derived from the highly inbred line Mo17. These lines had been separately propagated in a natural environment by single-seed descent for 6 generations. For each line, we assayed gene expression and methylation genome-wide by using RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS) analysis, respectively. The latter method combines restriction enzymes and bisulfite sequencing avoiding the analysis of the entire genome, thus, reducing the costs and computational needs for analyzing the 2 Gb maize genome. Differentially expressed genes and differentially methylated regions were identified between the two groups as well as between single individual plants.