Abstract
Wild sugarcane, Saccharum spontaneum, is a cold-tolerant species, and cultivated S. officinarum is highly sensitive to cold stress. The present study aimed at identifying genes and mechanisms acting in stress conditions using RNA-Seq technique to compare S. spontaneum and the cold-sensitive CP69-1062 cultivar of S. officinarum under non-stress (25 °C), chilling (0 °C), and freezing (− 4 °C) conditions. By studying 347,840,362 reads, the number of 16,088 genes showed a significant expression difference at the 1% probability level. A total of 413 genes with the highest expression changes were selected for the complementary analysis. The results showed the amount and intensity of biological activities of the cold-sensitive cultivar increased at 0 °C. By lowering the temperature to − 4 °C, the catabolic activity of the cold-sensitive cultivar drastically reduced. Reconstruction of the gene co-expression network in sugarcane showed that the LOS1 is a key gene in the chloroplast protein synthesis (elongation factor 2). Its expression profile showed that its expression level in all six samples examined was above 6000 transcript copies. It seems that the SVR3 gene plays a key role in tolerating cold stress in tolerant cultivars. Examination of the expression profile showed that with increasing cold, the SVR3 gene expression decreased in the sensitive cultivar. The expression difference of the SVR3 gene between sensitive and tolerant cultivars exceeded five times at 0 °C, and even more than 13 times at − 4 °C. Given its role in the translation process, the SVR3 gene can be considered a superiority factor of the cold-tolerant cultivar over the sensitive one. It is suggested to study the expression of LOS1 and SVR3 genes in other cold- tolerant plants for a comprehensive view of the action process of these genes. The expression levels of transcripts were validated by RT-qPCR.
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Notes
Biological process.
Molecular function.
Cellular component.
References
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Acknowledgements
We are very grateful to the Sugarcane Research and Training Institute (Tissue Culture Laboratory and Research Greenhouse) related to Khuzestan Sugarcane and By-products Development Company, for helping us in this project.
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MN, and BAF, conceived and designed the manuscript, wrote the manuscript and contributed equally. EE performed the experiments. AE performed the experiments and edited the manuscript. JZ performed the experiments, analyzed the data. MPA performed the experiments.
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Neisi, M., Fakheri, B.A., Ebrahimie, E. et al. RNA-Seq Analyzing Reveals the Key Role of SVR3 Gene in Tolerating the Freezing Stress in Saccharum spontaneum. J Plant Growth Regul 42, 2613–2625 (2023). https://doi.org/10.1007/s00344-022-10731-0
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DOI: https://doi.org/10.1007/s00344-022-10731-0