Seed germination and dormancy are complex adaptive traits of higher plants that are influenced by a large number of genes and environmental factors. Studies of genetics and physiology have shown the important roles of the plant hormones abscisic acid (ABA) in the regulation of germination and dormancy. We previously reported a series of regulatory factors controlling rice seed germination and dormancy by screening rice seed germination and dormancy related mutants, and the majority are related to ABA accumulation or signaling.

Optimal rice (Oryza sativa) germination temperature ranges from 25 °C to 35 °C; temperatures below 17 °C cause cold stress, with low germination rates, germination delay, retarded growth and seedling mortality. Moreover, low-temperature germinability is a prerequisite for modern direct-seeding cultivation, an alternative to conventional transplanting that effectively reduces rice production costs. In general, Japonica rice has greater capacity for germination at low temperatures than the indica subpopulation. Hybridization between different rice groups has been a common practice in rice breeding, and genomic loci conferring favorable agronomic traits are often introgressed across different rice subgroups. Which loci in japonica rice can be used to improve the low-temperature germination ability of indica rice? Have they been used in modern breeding?

In this study, we demonstrate that OsUBC12, a gene coding for an E2 ubiquitin-conjugating enzyme, contributes to enhanced germination at low temperatures in japonica rice due to a transposon insertion in its promoter, which boosts its expression. Analysis of natural variation shows that this transposon insertion in the OsUBC12 promoter predominantly appears in the japonica group. Examination of eight typical two-line male sterile rice lines indicates that this allele has been introduced into them through hybridization between indica and japonica rice, with those varieties inheriting the japonica-specific OsUBC12 locus (with transposon insertion) exhibiting superior germinability under cold conditions compared to those lacking this modification. Additional molecular studies reveal that OsUBC12 acts as a suppressor of ABA signaling pathways. The influence of OsUBC12 on seed germination and ABA responses largely hinges on a crucial active site necessary for the function of ubiquitin-conjugating enzymes. Moreover, OsUBC12 interacts directly with the rice enzyme SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), leading to its degradation. OsSnRK1.1 functions to inhibit low-temperature germination (LTG) by amplifying ABA signaling and operates in the pathway following OsUBC12.

Our discoveries highlight the molecular basis of how UBC12 influences LTG and offer genetic insights for the enhancement of LTG in indica rice varieties.

Figure 1. Proposed working model of OsUBC12 in indica and japonica rice.

According to our model (Figure 1), OsSnRK1.1 functions as a downstream key regulator to enhance ABA signaling by up-regulating the expression of ABA signaling-related genes such as OsABI5 and OsRAB21, thus inhibiting LTG. OsUBC12, an E2 enzyme for Lys48-linked polyubiquitination, recruits and degrades OsSnRK1.1. Compared with indica rice, a transposon insertion in the japonica OsUBC12 promoter activates the expression of OsUBC12. Increased OsUBC12 levels further promote the degradation of OsSnRK1.1, thereby weakening OsSnRK1.1-regulated ABA signaling and enhancing low-temperature germinability in japonica rice.