The long noncoding RNA VIVIpary promotes seed dormancy release and pre-harvest sprouting through chromatin remodeling in rice.

Abstract

Seed dormancy enables seeds to remain dormant until the environmental conditions are ideal for germination. Understanding the molecular mechanisms that underlie seed dormancy is essential for improving grain quality and preventing pre-harvest sprouting (PHS), a major challenge in global agriculture. Here, we address how long noncoding RNAs (lncRNAs) contribute to the regulation of seed dormancy in rice (Oryza sativa). We identified an lncRNA, VIVIpary, that is specifically expressed in embryos and is associated with shortened seed dormancy. VIVIpary exhibits higher expression in a PHS-sensitive variety, and its overexpression induces PHS, whereas its knockdown delays germination. Mechanistically, VIVIpary promotes the release of seed dormancy by regulating abscisic acid (ABA) signaling. VIVIpary serves as a spatial organizer that shapes chromatin architecture by directly binding to the chromatin adaptor protein OsMSI1 and enhancing its interaction with the histone deacetylase OsHDAC1, thereby reducing chromatin accessibility and fine-tuning ABA signaling. VIVIpary is differentially expressed between wild and cultivated rice, with higher expression in japonica rice, suggesting that it was a target of selection during rice domestication. Together, our findings reveal a domestication-associated lncRNA that modulates ABA signaling and chromatin architecture to regulate seed dormancy and PHS in rice, providing a potential target for improvement of rice agronomic traits.