Differential methylation patterns in diverse rice accessions in response to abiotic stresses

Cytosine DNA methylation is a dynamic process that can regulate gene expression under different environmental conditions.  Oryza sativa, Asian cultivated rice, embodies a vast amount of natural variation, which allows different accessions to perform better in different environments.  Our study is focused on determining if variation in performance of rice accessions under different environmental conditions can be traced back to differences in the methylation patterns observed in these accessions.  In order to accomplish this, we are investigating methylation differences at CpG sites among accessions in our rice diversity panel by looking for differences among accessions as well as  within organs of specific genotypes in response to several abiotic stresses, including metal toxicities (Al, Cd), and temperature  stress.  First a methylation baseline is being established by looking at methylation patterns in two rice accessions, Nipponbare (a japonica), and IR64 (an indica), in two different tissues (roots and shoots).  Next, eleven different rice accessions, representing the different subpopulations in O. sativa as well as an O. rufipogon accession, will be grown under control and the different stress conditions in a hydroponics system to determine if the methylation patterns in the same two tissues, change in response to a specific stress.  Samples will be analyzed using several methods, including a chip-based assay targeting HpaII methylation targets, by GBS using a methyl-sensitive enzyme, and through bisulfate sequencing.  Preliminary results showing differences in methylation patterns in different genotypes and tissues under both control conditions and in response to specific abiotic stresses will be presented.