A genome-wide survey of DNA methylation reveals that hypermethylation regulates after-ripening and dormancy of recalcitrant Panax notoginseng seeds

Abstract DNA methylation plays a crucial role in regulating fruit ripening and seed development. The dynamic characteristics of DNA methylation and how it is regulated in morpho-physiological dormancy (MPD)-type seeds during these processes remain unknown. Panax notoginseng seeds are defined by the MPD and are characterized by a strong sensitivity to dehydration during the after-ripening process. We performed DNA methylation analysis, siRNA profiling, and transcriptomics in embryos and endosperm of P. notoginseng seeds at different after-ripening stages. We found hypermethylation in the endosperm compared with the embryo during the after-ripening process, which was caused by increased expression of the DNA methyltransferase PnCMT2 in the seeds. Hypermethylation altered gene transcription to regulate the after-ripening and dormancy of recalcitrant seeds, for example, inhibiting expression of genes in embryo development to maintain seeds in a dormant state. Together, our findings reveal an increase in DNA methylation and its vital driver in gene expression, and thus elucidate how hypermethylation regulates the after-ripening in recalcitrant MPD-typed seeds. This work establishes a key role for epigenetics in regulating the dormancy of MPD-typed seeds with recalcitrant characteristics.