Analysis of Differences in DNA Methylation in Organically and Conventionally Grown Potato Tubers (Solanum tuberosum)

DNA methylation is an epigenetic mark that can be transmitted from one generation to the next. DNA methylation patterns can be specific to environmental conditions. In our ap-proach, differences in DNA methylation pattern were compared among tubers of potato (Solanum tuberosum) grown under organic and conventional farming conditions. These conditions differed in application of fertilizer, herbicides, fungicides and insecticides. Samples grown at two different years under organic and conventional growing conditions in three independent field replicates were analyzed to identify differentially methylated regions (DMRs). Post-bisulfite-adapter tagging whole-genome bisulfite-sequencing (PBAT-WGBS) was performed on the extracted DNA. Only using relaxed selection param-eters revealed sixty shared DMRs were identified among both years analyzed. One of the identified DMR was associated with the StATOX1 gene. StATOX1 is an evolutionarily highly conserved antioxidant copper chaperone, responsible for detoxification of copper in organisms. Copper content of the potato samples was measured by Inductively-Coupled Plasma-Atomic-Emission-Spectrometry (ICP-AES) after high pressure nitric acid oxidation. As organic potato management relies on the application of copper as fungicide, our iden-tified region might be indicative for the application of this specific compound.