Generational Genetic Mechanism of Space Mutagenesis in Rice Based on Multi-Omics

doi:10.1016/j.rsci.2025.03.001

Abstract

Abstract:

Intergenerational inheritance of stress memory plays a crucial role in plant adaptation to environmental changes, particularly in the context of spaceflight, where plants may serve as a food source for humans on long-duration missions. However, the intergenerational genetic effects of spaceflight-induced stress memory in plants remain unclear. In this study, we assessed the cross-generational genetic effects of spaceflight stress memory using the rice mutant B10, identified during the SJ-10 return satellite mission. Our results showed that the oxidative stress effects induced by spaceflight persisted until the M5 generation in rice. We found that the rice genome remained unstable post-spaceflight, leading to alterations in genome methylation levels. Additionally, we observed significant changes in the methylation levels of transposons, suggesting their involvement in the intergenerational inheritance of spaceflight-induced stress memory. Furthermore, we identified thousands of differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes induced by spaceflight stress memory across multiple rice generations. Notably, differentially methylated cytosines were more abundant in non-expressed genes than in DEGs or DAS genes. A substantial number of DEGs and DASs related to oxidative stress were identified, primarily involved in the generation and scavenging of reactive oxygen species. This study also presented report on the response of alternative splicing events in rice to spaceflight stress. Moreover, our findings revealed that genome methylation was associated with gene expression but not with DAS. In conclusion, our study provides comprehensive insights into the intergenerational inheritance of spaceflight-induced stress in rice and may contribute to uncovering novel mechanisms of oxidative stress-induced genomic instability and epigenetic regulation in plant stress inheritance.

Key words: DNA methylation, intergenerational inheritance, rice, SJ-10 return satellite, spaceflight, stress memory

Zeng Deyong, Cui Jie, Yin Yishu, Dai Cuihong, Yu Wencheng, Zhao Haitian, Guan Shuanghong, Cheng Dayou, Sun Yeqing, Lu Weihong. Generational Genetic Mechanism of Space Mutagenesis in Rice Based on Multi-Omics[J]. Rice Science, 2025, 32(3): 400-425.

Figures/Tables 13

Fig. 1. Spaceflight induces phenotypic and physiological changes in different generations (M1-M5) of rice. A-J, Plant height (A), number of tillers per plant (B), H2O2 content (C), malondialdehyde (MDA) content (D), electrolyte leakage rate (E), soluble sugar content (F), superoxide dismutase (SOD) activity (G), ascorbate peroxidase (APX) activity (H), catalase (CAT) activity (I), and peroxidase (POD) activity (J) in different generation of rice. CK, Ground Dongnong 423; B10, Mutant of Dongnong 423 from SJ10 mission. In A and B, data are Mean ± SD (n = 30). In C-J, data are Mean ± SE (n = 3). * and ** indicate significant difference at the 0.05 and 0.01 levels by the Tukey’s test, respectively.

Fig. 2. Spaceflight-induced DNA polymorphisms and base substitution patterns. A, Genome mutation rate of mutant B10 in M1-M5 generations. B, Number of polymorphic loci of mutant B10 in M1-M5 generations. SNP, Single nucleotide polymorphism. C-G, Classification of base substitution mutations of mutant B10 in M1-M5 generations.

Fig. 3. Molecular characteristics of memory-induced single nucleotide polymorphisms under spaceflight stress in different generations of rice. A, M1 generation; B, M2 generation; C, M3 generation; D, M4 generation; E, M5 generation.CDS, Coding sequence; UTR, Untranslated region; Synon, ‌Synonymous mutation; Nonsy, Nonsynonymous mutation.

Fig. 4. Spaceflight induces methylation patterns in M1 (A) and M5 (B) generations of rice. CK, Ground Dongnong 423; B10, Mutant of Dongnong 423 from SJ10 mission.

Fig. 5. Line graph of genome methylation of M1 and M5 generation rice in ground control and spaceflight groups. A-C, CpG methylation (A), CHG methylation (B), and CHH methylation (C) in the M1 generation.D-F, CpG methylation (D), CHG methylation (E), and CHH methylation (F) in the M5 generation.5′ UTR, 5′-Untranslated region; CDS, Coding sequence; 3′ UTR, 3′-Untranslated region; Down2000, 2000 kb downstream of the gene.

Fig. 6. Methylation patterns of transposable element (TE) in different generations of rice induced by spaceflight. A-C, CpG methylation (A), CHG methylation (B), and CHH methylation (C) in the M1 generation.D-F, CpG methylation (D), CHG methylation (E), and CHH methylation (F) in the M5 generation.Up2000, 2000-kb upstream of the gene; TE, Transposable element; Down 2000, 2000-kb downstream of the gene.

Fig. 7. Spaceflight-induced methylation change patterns of different classes of transposable elements in rice. A-C, CpG methylation (A), CHG methylation (B), and CHH methylation (C) in the M1 generation. D-E, CpG methylation (D), CHG methylation (E), and CHH methylation (F) environment in the M5 generation.Up2000, 2000-kb upstream of the gene; DNA, DNA transposon; LINE, Long interspersed nuclear element; SINE, Short interspersed nuclear element; LTR, Long terminal repeat; Down2000, 2000-kb downstream of the gene.

Fig. 8. Spaceflight stress memory induces differentially expressed genes (DEGs) in different rice generations. A and B, Volcano plots of DEGs in M1 (A) and M5 (B) generations. Down, Downregulated DEGs; Up, Upregulated DEGs; NoDif, Genes with no significant differential expression. C, UpSet plot showing unique and shared up- or downregulated DEGs between M1 and M5 generations.D and E, Gene Ontology (GO) analysis of DEGs in M1 (D) and M5 (E) generations. F, Expression changes of genes associated with DNA methylation or demethylation. * and ** represent significant differences at the 0.05 and 0.01 levels, respectively.

Fig. 9. Spaceflight stress memory induces differential expression of reactive oxygen species metabolism-related genes in different generations of rice. * and ** represent significant differences at the 0.05 and 0.01 levels, respectively.

Fig. 10. Spaceflight induces differentially alternative splicing (DAS) in different generations of rice. A, Number of five different types of DAS events identified in M1 and M5 generations. SE, Skipped exon; MXE, Mutually exclusive exons; RI, Retained intron; A3SS, Alternative 3′ splice site; A5SS, Alternative 5′ splice site. B, Venn diagram of unique and shared DAS genes between M1 and M5 generations. C and D, Venn diagrams show the overlap of DAS genes and differentially expressed genes (DEGs) in M1 (C) and M5 (D) generations. E and F, Top 20 enriched Gene Ontology terms of DAS genes in M1 (E) and M5 (F) generations.

Fig. 11. Differentially methylated cytosines (DmCs) are biased among different types of genes. A and B, Comparison of DmC densities between up- or downregulated genes and differential alternative splicing (DAS) genes with randomly selected genes in upstream, body, or downstream regions in M1 (A) and M5 (B) generations. The value in the square is transformed from the P value estimated by Student’s t-test and adjusted by the false discovery rate (FDR) method. If the DmC densities of the differentially expresed gene or DAS gene are larger than those of the randomly selected genes, the value is set as log10(Padj) (minus value). If the densities are less than those of the randomly selected genes, the value is set as -log10(Padj) to distinguish this difference. C and D, Bar plots showing the ratios of different types of genes in the top 10% genes with abundant DmCs in gene body or in two flanking regions in M1 (C) and M5 (D) generations. Up, Upregulated genes; Down, Downregulated genes; NoDiff, Genes with no significant differential expression; Other, Other non-differential genes. Hyper, Hypermethylated density; hypo, Hypomethylated density.

Fig. 12. Correlations among DMRs (differentially methylated regions), DEGs (differentially expressed genes), and DAS (differentially alternative splicing) in different methylation environments. A-C, Correlations among DMRs, DEGs, and DAS in different methylation environments in M1 generation (A, CpG; B, CHG; C, CHH). D-F, Correlations among DMRs, DEGs, and DAS in different methylation environments in M5 generation (D, CpG; E, CHG; F, CHH). Corr represents the coefficient of correlation obtained by Pearson’s. *, **, and *** represent significant differences at the 0.05, 0.01, and 0.001 levels, respectively.

Fig. 13. Overview of metabolism involving differentially expressed genes (DEGs) in M1 (A) and M5 (B) generations. Squares represent DEGs annotated into specific metabolic pathways with red ones for upregulation and blue ones for downregulation. TCA, Tricarboxylic acid cycle; CHO, Carbohydrate; OPP, Oxidative pentose phosphate pathway; misc, Miscellaneous.

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