BS-Seq reveals major role of differential CHH methylation during leaf rust resistance in wheat (Triticum aestivum L.)

Epigenetic regulation of the activity of defense genes during onset of diseases or resistance against diseases in plants is an active area of research. In the present study, a pair of wheat NILs for leaf rust resistance gene Lr28 (R) in the background of an Indian cultivar HD2329 (S) was used for a study of DNA methylation mediated regulation of gene expression. Leaf samples were collected at 0 h before (S0 and R0) and 96 h after inoculation (S96 and R96). The DNA samples were subjected to BS-Seq and sequencing data were used for identification of differentially methylated/demethylated regions/genes (DMRs and DMGs). Following four pairs of comparisons were used for this purpose: S0 vs S96; S0 vs R0; R0 vs R96; S96 vs R96. Major role of CHH methylation relative to that of CG and CHG methylation was observed. Some important observations include the following: (i) abundance of CHH methylation among DMRs; (ii) predominance of DMRs in intergenic region, relative to other genomic regions (promoters, exons, introns, TSS and TTS); (iii) abundance of transposable elements (TEs) in DMRs with CHH context; (iv) demethylation mediated high expression of genes during susceptible reaction (S0 vs S96) and methylation mediated low expression of genes during resistant reaction (R0 vs R96 and S96 vs R96); (v) major genes under regulation encode proteins, which differ from those encoded by genes regulated during susceptible reaction and (vi) ~ 500 DMGs carried differential binding sites for H3K4/K27me3 marks suggesting joint involvement of DNA and H3 methylation. Thus, CHH methylation either alone or in combination with histone methylation plays a major role in regulating the expression of genes involved in wheat-leaf rust interaction.