Deep-space conditions exert severe stress on plant genome stability, gene expression, epigenetic modification, and cell differentiation. In this study, multiomics analysis is used to observe changes in rice at the molecular and cellular levels after deep-space flight, including an increase in the frequency and types of mutations. While overall DNA methylation levels do not significantly change, CHG methylation levels present an increase that is correlated with DNA methylation responses. RNA presents significantly elevated m6A modification levels, which positively regulate gene expression. The proportion of mesophyll cells decreases, and 188 genes are identified as affecting the differentiation of mesophyll cells. Integrated multiomics analysis supports a hypothesis that the NAC family transcription factor suppressor of variation transmission 1 (SVT1) negatively regulates MAPK pathway genes, potentially influencing differentiation of cells harbouring mutations. Overall, this study comprehensively describes the molecular map of rice after deep-space flight and proposes a putative mechanism through which SVT1 may adapt to deep-space flight by inhibiting the differentiation of cells harbouring mutations.
