Hydrostatic pressure-induced heritable variation in rice is associated with transposon mobilization, DNA methylation changes, and transcriptional reprogramming.

Hydrostatic pressure treatment is associated with persistent phenotypic variation in rice, accompanied by transposon mobilization, DNA methylation changes, and transcriptional reprogramming that remain detectable after nine generations of self-pollination. Environmental stresses can induce genetic and epigenetic changes that contribute to phenotypic variation and, in some cases, may persist across generations. However, whether hydrostatic pressure can generate long-lasting molecular and phenotypic variation in plants remains poorly understood. Here, we investigated a hydrostatic pressure-derived rice lineage (HPM) obtained from pressure-treated seeds and maintained by self-pollination for nine generations. Compared with the wild-type cultivar JL307, HPM plants showed significantly reduced plant height, tiller number, and seed-setting rate. To investigate the molecular basis of these phenotypic differences, we combined analyses of transposon mobilization, DNA methylation, and gene expression. Transposon display showed that the MITE mPing remained mobile, and whole-genome resequencing identified 255 candidate HPM-specific transposable element insertion sites, predominantly in the LTR retrotransposon families Dasheng and Hopi; detected DNA methylation alterations at sampled CCGG sites, in which hypomethylation predominated; and found extensive transcriptional reprogramming involving numerous stress-responsive genes and transcription factor families, including WRKY, MYB, ERF/AP2, NAC, bHLH, and VQ. These molecular changes were accompanied by phenotypic differences that remained detectable in the ninth selfed generation. These findings suggest that hydrostatic pressure treatment can be associated with persistent variation in a selfed rice lineage that remain detectable after nine generations of selfing and was accompanied by transposon mobilization, DNA methylation changes, and transcriptional reprogramming, providing a foundation for further studies of stress-associated heritable variation in plants and its potential applications in crop improvement.