DNA hypomethylation in tetraploid rice potentiates stress-responsive gene expression for salt tolerance

Significance Polyploidy can stimulate genetic and epigenetic changes that enhance the potential for plant adaptation and fitness under extreme environments, but the molecular basis for this is poorly understood. Here we show that tetraploid rice is more tolerant to salinity than diploid rice. Tetraploidy induces DNA hypomethylation which potentiates genomic loci coexistent with stress-responsive genes including those in jasmonate biosynthesis and signaling pathways for rapid and robust responses under stress. After salt stress, elevated expression of salt-responsive genes can induce hypermethylation and suppress adjacent TEs. This feedback regulation between polyploidy-induced DNA hypomethylation in rapid and strong stress response and stress-induced hypermethylation to repress TEs and/or TE-associated genes may provide evolutionary advantages for selection to enhance adaptation in polyploid plants and crops.