A transposon insertion in the OsUBC12 promoter enhances cold tolerance during germination in japonica rice (Oryza sativa)

Abstract Low-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhances its expression. Natural variation analysis revealed transposon insertion in the OsUBC12 promoter mainly in the japonica lineage. Notably, the genomic region carrying the japonica OsUBC12 locus (with the transposon insertion) has been introgressed into the modern elite indica two-line male sterile lines Y58S and J4155S. Further molecular analysis showed that OsUBC12 may negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. In contrast to OsUBC12, OsSnRK1.1 inhibits LTG by enhancing ABA signaling. These findings shed light on the possible genomic contributions of introgressions of the japonica OsUBC12 locus to trait improvements of indica rice cultivars and provide genetic reference points for improving LTG in indica rice.