The ability of plants to adapt their form in response to changing environment is known as phenotypic plasticity. Phenotype plasticity in plants is well documented (e.g. Special Issue, Journal of Experimental Botany, Vol. 57. No. 2, 2006). However, the genetic and genomic mechanisms underlying this phenomenon are poorly understood. Epigenetics is often referred to as the study of mitotically and meiotically changes in gene transcription not associated with changes in DNA sequence. Epigenetic processes that can control gene expression via transcriptional regulation include DNA methylation, in which DNA is modified by the addition of methyl groups to cytosine residues. In plants, DNA methylation is prevalent and variable, and differentially methylated alleles can lead to novel heritable phenotypes. We have initiated a series of experiments to investigate systematically the relationship between DNA methylation and phenotypic plasticity in plants, using a rapid cycling genotype (RO18) of the Brassica rapa ssp. Trilocularis. Among the approaches used is the establishment of a stochastically hypomethylated population via seed treatment with the demethylating agent, 5-Azacytidine, which will serve as a platform for both forward and reverse genetic and genomic analyses. We present the results of an initial dosage response study carried out to determine the range of phenotypic variation that might be sensitive to variations in DNA methylation. A range of strategies to quantify the level and determine the distribution of DNA methylation are being developed. These include the “methylated DNA immunoprecipitation (MeDIP)” technique combined with a macroarray of end-sequenced BACs to determine the genome-wide distribution.