*4.6. MeDIP-Seq and Data Analysis*

MeDIP-seq for this study was performed by KangChen Bio-tech, Shanghai, China. Sequencing library preparation and data analysis were as performed described by Ding et al. [67]. The available data were aligned to the reference genome of *Oryza\_sativa. Japonica* IRGSP-1.0 using BOWTIE software (V2.1.0) [68]. MeDIP peaks were identified by MACS2 [69], and statistically significant MeDIP-enriched regions (peaks) were identified by comparison to a Poisson background model (cut-off q-value = 10–2). DMRs in MeDIP dataset was identified by diffReps [70] (*p* < 0.0001).
