Genome-wide DNA Methylation Profiling Reveals Cultivar-dependent Epigenomic Signatures in <i>Brassica rapa</i>

DNA methylation is a key epigenetic mechanism that regulates gene expression. The level and distribution of DNA methylation have been suggested to contribute to disease resistance and may contribute to differences in disease resistance between cultivars. In this study, we investigated whether inter-cultivar variation in DNA methylation is associated with differences in disease resistance by performing whole-genome bisulfite sequencing (WGBS) on two komatsuna (Brassica rapa var. perviridis) cultivars, ‘Misugi’ (susceptible) and ‘Nanane’ (resistant), under either control or Albugo candida-infected conditions. Cultivar-specific differentially methylated regions (DMRs) were primarily observed in CHG and CHH contexts (where H is A, C, or T) and were enriched in transposable elements (TEs). These DMRs remained largely stable between the control and infected conditions. Although thousands…