Article | . 2017 Vol. 29, Issue. 2
Transcriptomic expression profiling of seedlings of wheat (Triticum aestivum L.) under ABA treatment



Department of Biotechnology, Korea University1




2017.. 78:86


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One of the major phytohormones, ABA, is known to play an important role in seed dormancy, germination and response to various stresses. High-throughput sequencing technology was applied to ABA treated wheat seedlings to identify differentially expressed genes (DEGs), and we obtained 65,561,602 raw reads resulting from Illumina sequencing. After quality control and mapping to the draft reference genes of wheat, we identified 2,238 DEGs, and gene ontology (GO) analysis of the DEGs was further conducted. Based on these results, several candidate genes involved in ABA pathways were identified (aldehyde oxidase, β glucosidase and cytochrome P450). The combination of expression pattern analysis of high-throughput sequencing and GO analysis in this study will provide powerful clues and information for investigating the transcriptional changes to understand the transcriptional responses to ABA in wheat.



1. Anders, S., Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol. 11(10):R106. doi:10.1186/gb-2010-11-10-r106.  

2. Assmann, S. M. (2003) OPEN STOMATA1 opens the door to ABA signaling in Arabidopsis guard cells. Trends Plant Sci. 8(4):151-153. doi:http://dx.doi.org/10.1016/S1360-1385(03)00052-9.  

3. Christmann, A., Weiler, E. W., Steudle, E., Grill, E. (2007) A hydraulic signal in root-to-shoot signalling of water shortage. Plant J. 52(1):167-174. doi:10.1111/j.1365-313X.2007.03234.x.  

4. Consortium, T. G. O. (2000) Gene ontologie: Tool for the unification of biology. Nat. Genet. 25(1):25-29. doi:10.1038/75556.Gene.  

5. Cox, M. P., Peterson, D. A., Biggs, P. J. (2010) SolexaQA: At-a-glance quality assessment of Illumina second- generation sequencing data. BMC Bioinformatics 11(1):485. doi:10.1186/1471-2105-11-485.  

6. FAO. (2013) from http://faostat.fao.org/site/567/DesktopDe fault.aspx?PageID=567#ancor  

7. Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., Mitros, T., Dirks, W., Hellsten, U., Putnam, N., Rokhsar, D. S. (2012) Phytozome: A comparative platform for green plant genomics. Nucleic Acids Res. 40(D1):1178-1186. doi:10.1093/nar/gkr944.  

8. Holdsworth, M. J., Bentsink, L., Soppe, W. J. J. (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol. 179(1):33-54. doi:10.1111/j.1469-8137.2008.02437.x.  

9. International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788. doi:10.1126/science.1251788.  

10. Kakumanu, A., Ambavaram, M. M. R., Klumas, C., Krishnan, A., Batlang, U., Myers, E., Grene, R., Pereira, A. (2012) Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq. Plant Physiol. 160(2):846-867. doi:10.1104/pp.112.200444.  

11. Langmead. (2013) Bowtie2. Nat. Methods 9(4):357-359. doi:10.1038/nmeth.1923.Fast.  

12. Lee, K. H., Piao, H. L., Kim, H. Y., Choi, S. M., Jiang, F., Hartung, W., Hwang, I., Kwak, J. M., Lee, I. J., Hwang, I. (2006) Activation of Glucosidase via Stress-Induced Polymerization Rapidly Increases Active Pools of Abscisic Acid. Cell 126(6):1109-1120. doi:10.1016/j.cell.2006.07.034.  

13. Liu, A., Gao, F., Kanno, Y., Jordan, M. C., Kamiya, Y., Seo, M., Ayele, B. T. (2013) Regulation of Wheat Seed Dormancy by After-Ripening Is Mediated by Specific Transcriptional Switches That Induce Changes in Seed Hormone Metabolism and Signaling. PLoS ONE, 8(2). https://doi.org/10.1371/journal.pone.0056570.  

14. Liu, X., Zhang, H., Zhao, Y., Feng, Z., Li, Q., Yang, H. -Q., Luan, S., Li, J., He, Z. -H. (2013) Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 110(38):15485-15490. United States. doi:10.1073/pnas.1304651110.  

15. Lucas, A. (2014) amap: Another Multidimensional Analysis Package.   

16. Mano, Y., Nemoto, K. (2012) The pathway of auxin biosynthesis in plants. J. Exp. Bot. 63(8):2853. doi:10.1093/ jxb/ers091.  

17. Nakashima, K., Yamaguchi-Shinozaki, K. (2013) ABA signaling in stress-response and seed development. Plant Cell Reports, 32(7),959-970. https://doi.org/10.1007/s00299-013-1418-1  

18. Nambara, E., Okamoto, M., Tatematsu, K., Yano, R., Seo, M., Kamiya, Y. (2010) Abscisic acid and the control of seed dormancy and germination. Seed Sci. Res. 20(March 2016):55-67. doi:10.1017/S0960258510000012.  

19. Nonogaki, H. (2014) Seed dormancy and germination-emerging mechanisms and new hypotheses. Front. Plant Sci. 5(May):233. doi:10.3389/fpls.2014.00233.  

20. Pinheiro, C., Chaves, M. M. (2011) Photosynthesis and drought: can we make metabolic connections from available data? J. Exp. Bot. 62(3):869-882. England. doi:10.1093/jxb/erq340.  

21. Saito, S., Hirai, N., Matsumoto, C., Ohigashi, H., Ohta, D. (2004) Arabidopsis CYP707A s Encode ( 1 ) -Abscisic Acid 8 9 -Hydroxylase , a Key Enzyme in the Oxidative Catabolism of Abscisic Acid 1. Plant Physiol. 134(April):1439- 1449. doi:10.1104/pp.103.037614.1.  

22. Seo, M., Koiwai, H., Akaba, S., Komano, T., Oritani, T., Kamiya, Y., Koshiba, T. (2000) Abscisic aldehyde oxidase in leaves of Arabidopsis thaliana. Plant Journal, 23(4):481-488. https://doi.org/10.1046/j.1365-313X.2000.00812.x  

23. Tardieu, F., Parent, B., Simonneau, T. (2010) Control of leaf growth by abscisic acid: Hydraulic or non-hydraulic processes? Plant, Cell Environ. 33(4):636-647. doi:10.1111/j.1365-3040.2009.02091.x.  

24. Teng, K., Li, J., Liu, L., Han, Y., Du, Y., Zhang, J., Sun, H., Zhao, Q. (2014) Exogenous ABA induces drought tolerance in upland rice: the role of chloroplast and ABA biosynthesis-related gene expression on photosystem II during PEG stress. Acta Physiol. Plant. 36(8):2219-2227. doi:10.1007/s11738-014-1599-4.  

25. Wang, Z., Fang, B., Chen, J., Zhang, X., Luo, Z., Huang, L., Chen, X., Li, Y. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics 11(1):726. BioMed Central Ltd. doi:10.1186/1471-2164-11-726.  

26. Warnes, G. R., Bolker, B., Lumley, T. (2012) Gplots: various R programming tools for plotting data. R package version 2.6.0. The R Progect for Statistical Computing, Vienna, Austria.   

27. Zaharia, L. I., Walker-Simmon, M. K., Rodríguez, C. N., Abrams, S. R. (2005) Chemistry of Abscisic Acid, Abscisic Acid Catabolites and Analogs. J. Plant Growth Regul. 24(4):274-284. doi:10.1007/s00344-005-0066-2.  

28. Zhang, G., Guo, G., Hu, X., Zhang, Y., Li, Q., Li, R., Zhuang, R., Lu, Z., He, Z., Fang, X., Chen, L., Tian, W., Tao, Y., Kristiansen, K., Zhang, X., Li, S., Yang, H., Wang, J., Wang, J. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res. 20(5):646-654. doi:10.1101/gr.100677.109.  



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