Genes, Putative Long-Lived mRNAs and Pathways Underlying Genotypic Differences in Rice Seed Storability and Seed Dormancy

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Weak seed dormancy (SD) in rice tends to induce pre-harvest sprouting and impair seed quality and yield pre-harvest, whereas poor seed storability (SS) reduces these traits during post-harvest storage. Although multiple genes associated with these two traits have been cloned, the molecular genetic regulatory relationship between them remains unclear. To dissect the SD-SS correlation, this study compared SD and SS characteristic of 9311 (Xian/Indica) and Nipponbare (NIP, Geng/Japonica) via transcriptomic and metabolomic analyses. Results showed that NIP had strong SD but poor SS, while 9311 exhibited the opposite. Differentially accumulated metabolite (DAM) analysis showed 42 DAMs specific to dormant seeds, 141 to stored seeds, and 93 common to both. Transcriptomic analysis identified 1,334 (13.0%) differentially expressed genes (DEGs) and 11 metabolic pathways (28.9%) commonly associated with SD and SS, including key ones like hormone signaling and secondary metabolism. The biological functions of two core DEGs were further validated using CRISPR/Cas9 technology, among which OsGA2ox8 regulates SD and OsLEA5 (Late embryogenesis abundant protein) affects SS. Validation of DEGs in the gibberellin (GA) pathway demonstrated that knockout of OsGA2ox8 (gibberellin 2-oxidase) significantly reduced SD, whereas its overexpression markedly enhanced SD, confirming the core regulatory role of OsGA2ox8 in SD. Haplotype analysis in natural populations showed that Haplotype 1 of OsGA2ox8 was dominant in Xian subspecies, while Haplotype 2 prevailed in Geng subspecies. Additionally, the analysis of long-lived mRNAs (LLRs) identified 2,938 putative LLRs, of which 309 were associated with both SD and SS. Functional validation of a late embryogenesis abundant protein (OsLEA5) showed that knockout of this gene in NIP significantly decreased SS. This study preliminarily elucidated the differentiation mechanisms of SD and SS, and provided potential targets for breeding rice varieties with enhanced pre-harvest sprouting and superior SS.