Identification of Differential Methylation in Wheat Using Enriched Data

Methylation of the cytosine residues in eukaryote DNA is thought to act as an additional mechanism of gene expression control. It has been reported that methylation levels between members of the same species can differ in response to environmental factors or stresses e.g. temperature (Hashida, S. N. et al., 2006). The potential for differential gene expression of homeologous genes in a polyploidy species such as wheat has also been previously identified (Kermicle, J. L., 1978).

Sodium bisulfite treatment deaminates un-methylated cytosine residues converting them to uracil, allowing, after PCR and sequencing, effective discrimination of the methylation status at every cytosine residue (Darst, R. P. et al., 2010).  This treatment, combined with the use of Agilent’s SureSelect Methyl-Seq Target Enrichment System allows the study of methylation patterns in target regions. In this case a subset of the genic regions of wheat (5Mb) was targeted as a proof of principle. Sequencing reads with a methylation site and a known homeologous SNP allele allow the association of the methylation site with a particular wheat genome.

The study was then used to confirm a number of hypotheses in wheat; firstly, that differential methylation exists between the A, B and D genomes and secondly, using two growth temperatures (12°C and 27 °C), that temperature is capable of altering the methylation state and that this is both genome specific and genome independent. Finally we intend to investigate if it is this underlying methylation that controls both genome specific and temperature dependent changes in gene expression.