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An integrated RNA-Seq and physiological study reveals gene responses involving in the initial imbibition of seed germination in rice


Seeds can activate a series of genes to avoid imbibition-associated stress during seed germination. However, the precise gene responses at the initial imbibition stage (Phase I) of seed germination are not yet fully understood in rice. In this study, a total of 1544 differentially expressed genes (DEGs) with at least 2-fold change were identified in 8 h imbibed seeds (Phase I) compared to dry seeds of rice using RNA-Seq approach. MapMan analysis revealed that the mainly signalling-, cell wall-, abiotic stress-, and antioxidant-related DEGs were associated with stress responses pathway involving in the initial imbibition of rice seed germination. Among them, the signalling-related DEGs were mainly receptor kinases, and the largest number of cell wall-related DEGs were expansins followed by pectinesterases and polygalacturonases. The abiotic stress-related DEGs were mainly cupin domain protein, methyltransferases and SPX domain protein, and the majority of antioxidant-related DEGs were glutathione S-transferases (GSTs) and peroxidases. Further qRT-PCR analysis revealed that the highest expressions of the majority of GST genes occurred at 8 h imbibition stage in rice, which caused the corresponding highest GST activity at that stage. GSTs might prevent the burst of H2O2 accumulation at the initial imbibition stage that contributes to the following successful seed germination. Our results provide further understanding of gene responses at the initial imbibition stage of seed germination in rice. The identified genes provide a foundation for future studies of seed germination in rice.

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Data availability

The RNA sequencing data have been submitted to the Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra/) under accession number PRJNA544406.


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This work was supported by the National Key Research and Development Plan (Grant No. 2018YFD0100901), the Guangdong Province Key Research and Development Program (Grant No. 2018B020202012), the National Natural Science Foundation of China (Grant No. 31771889), the Guangdong Province Key Laboratory of Plant Molecular Breeding (Grant No. GPKLPMB201903), and the Major Scientific Research Projects of General Colleges and Universities of Guangdong Province (Grant No. 2017KTSCX024).

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Correspondence to Jifeng Ying or Zhoufei Wang.

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Zhao, J., He, Y., Li, X. et al. An integrated RNA-Seq and physiological study reveals gene responses involving in the initial imbibition of seed germination in rice. Plant Growth Regul 90, 249–263 (2020). https://doi.org/10.1007/s10725-019-00567-2

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  • Rice
  • Seed imbibition
  • Stress response
  • Signalling response
  • Cell wall
  • Antioxidant enzyme