A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination

Chuanzhong Zhang, Hongru Wang, Xiaojie Tian, Xinyan Lin, Yunfei Han, Zhongmin Han, Hanjing Sha, Jia Liu, Jianfeng Liu, Jian Zhang, Qingyun Bu and Jun Fang ()
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Chuanzhong Zhang: Chinese Academy of Sciences
Hongru Wang: Chinese Academy of Agricultural Sciences
Xiaojie Tian: Chinese Academy of Sciences
Xinyan Lin: Chinese Academy of Sciences
Yunfei Han: Chinese Academy of Sciences
Zhongmin Han: Chinese Academy of Sciences
Hanjing Sha: Chinese Academy of Sciences
Jia Liu: Chinese Academy of Sciences
Jianfeng Liu: Jilin Normal University
Jian Zhang: China National Rice Research Institute
Qingyun Bu: Chinese Academy of Sciences
Jun Fang: Chinese Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-16

Abstract: 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 enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 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. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.

Date: 2024
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DOI: 10.1038/s41467-024-46420-7

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