Global DNA Methylation Changes in Soybean as a response to Soybean Cyst Nematode (SCN) infection.

Soybean cyst nematode (SCN, Heterodera glycines) is the most damaging pest in soybean production worldwide. The compatible interaction of SCN with susceptible soybean plants is mediated by differential expression of thousands of genes in the infected root cells, leading to the formation of a functional feeding site, the syncytium. During an incompatible interaction of SCN with resistant soybean, the developing syncytium degenerates leading to nematode death. The resistance to SCN in soybean is derived from two major loci, Rhg1 and Rhg4. In this study, the role of genome-wide DNA methylation in regulating gene expression during the compatible interaction was examined using susceptible soybean cultivar ‘Williams 82’. The analysis revealed that SCN induces both hyper- and hypomethylation in thousands of genomic regionsoverlapping with genes. The level and pattern of DNA methylation in various genic regions were found to impact gene transcription. A significant number of the differentially methylated genes was found to overlap with genes known to be significantly differentially expressed in syncytium, providing the first experimental evidence that syncytium transcriptome is epigentically controlled. In addition, the levels and patterns of DNA methylation were compared between the compatible and incompatible interactions using a pair of near-isogenic lines differing in Rhg4 allele. The methylomes of two near isogenic lines, susceptible (TN09-16) and the resistant (TN09-29) were substantially different both under SCN-infected and non-infected conditions. Stably heritable as well as novel non-parental differentially methylated regions in genes with functions related to SCN parasitism of soybean were discovered. Furthermore, differential DNA methylation in microRNA genes was also examined in the susceptible and resistant lines in response to SCN infection. A number of differentially methylated microRNAs were identified specifically in the susceptible lines, Williams 82 and TN09-16, indicating that various components of epigenetic mechanisms are mutually linked. Taken together, profiling DNA methylation at single nucleotide resolution during the susceptible and resistant interactions provided unprecedented insights into the role of this epigenetic mark in determining the compatibility of the interaction between soybean and SCN by impacting the expression of protein-coding and microRNA genes as well as transposable elements located nearby genes.