DNA methylation dynamics in male germline development in Brassica rapa [RNA-seq/Bisulfite-seq]

Cytosine DNA methylation (mC) can silence transposable elements (TEs) and regulate gene expression. However, the mechanism and function of DNA methylation reprogramming during plant development are still largely unknown. To explore the DNA methylation dynamics during the male sexual-lineage development in the Brassicaceae family, we assessed the mC level in meiocyte, microspore and pollen of a Brassica rapa doubled haploid (DH) line by whole genome bisulfite sequencing (WGBS). Analysis of global mC profiles showed that significant reprogramming of CHH methylation occurred in the Brassica rapa male sex cells, similar to that observed in Arabidopsis. Analysis of differential methylation sites identified specific methylation loci in sex cells that can target and possibly regulate gene expression, suggesting a mechanism consistent with that of Arabidopsis. Quite a few long terminal repeat (LTR) transposable elements were activated in meiocyte and microspore, which correlated with reduced DNA methylation. Expression analysis of key genes that affect DNA methylation showed that active methylation and demethylation occurred during male sexual lineage development. These results suggest a conserved DNA methylation reprogramming mechanism during Brassica rapa male sex lineage development. The transcriptome and DNA methylome data obtained will also be useful for other mechanism studies in Brassica rapa. To better understand the DNA methylation reprogramming during male sexual lineage development of Brassica rapa, we analyzed DNA methylome and transcriptome of several male cell types, including meiocyte, microspore and pollen in a DH line ‘K2’ of Non-heading Chinese cabbage (Brassica rapa. ssp. Chinensis), and demonstrated the methylation patterns and the potential influences on transcription across sequence contexts, genic and TEs regions. In addition, we also identified differentially-methylated regions (DMRs), found and analyzed sexual-lineage-specific DNA methylation in Brassica rapa.