Multiomics analysis of the molecular and single-cell responses of rice after deep-space flight on Chang'e-5

Abstract The deep-space environment exerts severe stress on plant genome stability, gene expression, epigenetic modification, and cell differentiation. In this study, through multiomics analysis, changes were observed in rice at molecular and cellular levels after deep-space flight, including an increase in genomic variation frequency and mutations with preferences. While overall DNA methylation levels showed no significant changes, the increase in CHG methylation level was correlated with DNA methylation responses. RNA presented significantly elevated m6A modification levels, which positively regulated gene expression. The proportion of mesophyll cells decreased, and 188 genes were identified as affecting the differentiation of mesophyll cells. Integrated multiomics analysis revealed that the NAC family transcription factor SVT1 negatively regulated MAPK pathway genes to suppress differentiation in cells carrying mutations. Overall, this study comprehensively described the molecular map of rice after deep-space flight, and proposed a new mechanism for SVT1 to adapt to deep-space flight by inhibiting the differentiation of mutant cells.