Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation

During transformation, tissue culture often carries epigenetic and genetic changes underlying somaclonal variations, leading to unpredictable phenotypes. Transformation treatments may individually and jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes have never been examined. Here, we examined the changes in methylomes and transcriptomes associated with each of the components with different combinations of treatments. We found that individual transformation components targeted specific gene sets. When T-DNA was integrated, the pathway of secondary metabolism was activated, whereas primary metabolism was repressed. The transformation treatments resulted in global hypomethylation at CHH sites enriched at promoters highly associated with downregulation. The promoters that colocalized with miniature inverted-repeat TEs (MITEs) were found to be associated with epigenetic responses to stress, and this was not observed at sites without MITEs. Our results demonstrated component-specific epigenetic regulation related to adaptation to the stress response during rice transformation. Overall design: We performed whole-genome bisulfite sequencing (WGBS) and RNA-seq to examine DNA methylation and expression in a total of nine transformation components in TNG67 with two biological replicates of leave samples