Dynamics of the transcriptome and methylome during the regeneration of rice

Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome. Overall design: We studied the transcriptomes (RNA-seq) and methylomes (BS-seq) of TNG67 and IR64 rice in comparisons between the embryonic stage (T0) versus 1. callus induced (T1) 2. callus sub-cultured (T2) 3. failed (TF) and 4. successfully (TS) regenerated calli. The transcription data of IR64 during these stages are represented as I0, I1, I2 IS and IF ad of TNG67 are represented as J0, J1,J2,JS and JF.The methylome data of IR64 during the different stages are represented as i0. i1, i2, iS and iF while TNG67 methylome data at different stages of tissue culture is termed as j0, j1, j2, jS and jF. I0, i0, J0 and j0 correspond to T0; I1, i1, J1 and j1 correspond to T1; I2,i2,J2 and j2 correspond to T2; IS,iS, jS and jS correspond to TS and IF, iF, JF, jF correspond to TF.