2026 Volume 95 Issue 2 Pages 179-189
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 of differentially methylated genes (DMGs) were identified between cultivars, only a small subset overlapped with differentially expressed genes (DEGs), suggesting that the influence of DNA methylation on gene expression patterns is limited. Among 190 nucleotide-binding leucine-rich repeat (NLR) genes known for their role in disease resistance, 33 overlapped with DMRs. Notably, two NLR genes exhibited higher expression levels in the resistant cultivar ‘Nanane’ than in the susceptible cultivar ‘Misugi’, with higher DNA methylation in their gene regions observed in ‘Nanane’, suggesting that differences in DNA methylation affect the expression of particular NLR genes and may play an important role in resistance to pathogens. Our findings indicate that DNA methylation contributes to cultivar-specific epigenetic states. Since most differences were found in TEs, such variation may also be involved in differences in disease resistance and other traits between cultivars. Further studies are needed to assess whether variation in DNA methylation at specific loci contributes to resistance phenotypes in B. rapa.
