Abstract
Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO3 stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO3 highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (P < 0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response.
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Abbreviations
- ABA:
-
Abscisic acid
- FDR:
-
False discovery rate
- GA:
-
Gibberellin
- Gapdh:
-
Glyceraldehyde-3-phosphate dehydrogenase
- GEO:
-
Gene expression omnibus
- GO:
-
Gene ontology
- MEME:
-
Multiple em for motif elicitation
- MVA:
-
Mevalonic acid
- PLACE:
-
Plant cis-acting regulatory DNA elements
- QRT-PCR:
-
Real-time quantitative RT-PCR
- STEM:
-
Short time-series expression miner
- TFBS:
-
Transcription factor binding sites
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Acknowledgments
We thank the US Department of Energy Joint Genome Institute in collaboration with the user community providing soybean genome sequence data http://www.jgi.doe.gov/.
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This work was supported by the National Natural Science Foundation of China (30570990), the Key Research Plan of Heilongjiang Province (GB05B104), the Innovation Research Group of NEAU (CXT004), and the “863” project (2006AA100104-18).
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ESM 1
Primer sequences of genes in the QRT-PCR assays (XLS 17 kb)
ESM 2
(GIF 71 kb)
ESM 3
Differentially expressed genes between all combinations of time points under NaHCO3 stress (XLS 1515 kb)
ESM 4
(GIF 26 kb)
ESM 5
(GIF 41 kb)
ESM 6
(GIF 46 kb)
ESM 7
(GIF 24 kb)
ESM 8
List of genes in each cluster from STEM clustering (XLS 592 kb)
ESM 9
(GIF 34 kb)
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Ge, Y., Li, Y., Lv, DK. et al. Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. Funct Integr Genomics 11, 369–379 (2011). https://doi.org/10.1007/s10142-010-0191-2
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DOI: https://doi.org/10.1007/s10142-010-0191-2