Mature dry seeds have a particular mechanism that allows them to survive with loss of >90% of water content called desiccation tolerance (DT). The seed-DT is tightly regulated, being acquired during seed development and lost shortly after germination. The timing of loss of DT after germinated can be extended by exogenous stimuli e.g., a mild osmotic stress (re-induction of the DT to germinated seeds). The molecular processes involved in DT acquisition/loss and re-induction have been well studied at the transcriptomic level, which resulted in identification of DT-associated gene networks. However, our understanding of molecular mechanisms that switch-on/off the genetic networks of seed-DT remains fragmentary, especially from epigenetic aspects. In this study, we identified DT-core genes (a cluster of genes specifically associated with DT re-induction) in root tissues of germinated Medicago by RNA-Seq, followed by analyses to determine the chromatin status of the loci of these DT-core genes. ATAC-Seq revealed that the chromatin state of genomic regions containing the DT-core genes is clearly linked to their expression levels and phenotypes. Additionally, ChIP-Seq for histone repressive marks detected a prominent signal of H3K27me3 on the DT core-gene sequences at the later stage tissue with condensed chromatin, suggesting that silencing of DT in post-germination developmental programs will be mainly due to the H3K27me3 marks by the action of the PRC2 complex. As a result of this investigation, we bioengineer the desiccation process acquired during seed maturation to reinduce this process during seedling establishment allowing an improved seed germination and seedling establishment under extreme drought conditions.