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Expression of MicroRNAs in Cotton

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Abstract

MicroRNAs (miRNAs) are a class of newly identified non-protein-coding small RNAs. miRNAs post-transcriptionally regulate the expression of more than 30% genes, which control many biological and metabolic progresses, including plant growth, development, and response to environmental stresses. However, no studies have been performed on miRNA expression in cotton, one of the most important fiber and economic crops. In this study, we employed quantitative real-time PCR (qRT-PCR) to detect and compare miRNA expressions in eight different cotton organs at different developmental stages. Our results showed that miRNAs were differentially expressed in different cotton organs, with certain classes expressed preferentially in an organ-specific manner. The miR-156 was highly expressed in cotyledon, whereas the miR-172 was highly expressed in young leaves at fruit branch, young flower buds, 0 day post-anthesis (DPA) ovules, and 0 DPA petals. We also found that miR-172 was not highly expressed in all parts of flowers. In contrast, miR-172 was highly expressed in petal but not in stamen and carpel. Interestingly, miR-162 was highly expressed in immature fiber, 2 DPA ovules, and mixtures of 0 DPA stamen and carpel, suggesting miR-162 may play a role in cotton fiber differentiation and development. Our previous study showed that miR-396 may target a fiber-related gene the callose synthase catalytic subunit. In this study, the miR-396 expression was observed in all eight cotton organs. This study identified the expression of miRNAs that may regulate the development of cotton and cotton fiber.

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References

  1. Zhang, B. H., & Feng, R. (2000). Cotton resistance to insect and pest-resistant cotton. Beijing: Chinese Agricultural Science and Technology Press.

    Google Scholar 

  2. Stephens, S. G., & Mosley, M. E. (1974). Early domesticated cottons from archaeological sites in central coastal Peru. American Antiquity, 39, 109–122. doi:10.2307/279225.

    Article  Google Scholar 

  3. IAC (1996). Cotton: Review of world situation, Monogram by International Advisory Committee, (Washington, DC).

  4. Lee, J. J., Woodward, A. W., & Chen, Z. J. (2007). Gene expression changes and early events in cotton fibre development. Annals of Botany, 100, 1391–1401. doi:10.1093/aob/mcm232.

    Article  CAS  Google Scholar 

  5. Taliercio, E. W., & Boykin, D. (2007). Analysis of gene expression in cotton fiber initials. BMC Plant Biology, 7, 22.

    Article  Google Scholar 

  6. Wilkins, T. A., & Arpat, A. B. (2005). The cotton fiber transcriptome. Physiologia Plantarum, 124, 295–300. doi:10.1111/j.1399-3054.2005.00514.x.

    Article  CAS  Google Scholar 

  7. Zhang, B. H., Pan, X. P., Guo, T. L., Wang, Q. L., & Anderson, T. A. (2005). Measuring gene flow in the cultivation of transgenic cotton (Gossypium hirsutum L.). Molecular Biotechnology, 31, 11–20. doi:10.1385/MB:31:1:011.

    Article  CAS  Google Scholar 

  8. Zhang, B. H., Liu, F., Yao, C. B., & Wang, K. B. (2000). Recent progress in cotton biotechnology and genetic engineering in China. Current Science, 79, 37–44.

    CAS  Google Scholar 

  9. Haigler, C. H., Zhang, D., & Wilkerson, C. G. (2005). Biotechnological improvement of cotton fibre maturity. Physiologia Plantarum, 124, 285–294. doi:10.1111/j.1399-3054.2005.00480.x.

    Article  CAS  Google Scholar 

  10. Zhang, B. H., Pan, X. P., Cobb, G. P., & Anderson, T. A. (2006). Plant microRNA: A small regulatory molecule with big impact. Developmental Biology, 289, 3–16. doi:10.1016/j.ydbio.2005.10.036.

    Article  CAS  Google Scholar 

  11. Ambros, V., & Chen, X. M. (2007). The regulation of genes and genomes by small RNAs. Development, 134, 1635–1641. doi:10.1242/dev.002006.

    Article  CAS  Google Scholar 

  12. Kidner, C. A., & Martienssen, R. A. (2005). The developmental role of microRNA in plants. Current Opinion in Plant Biology, 8, 38–44. doi:10.1016/j.pbi.2004.11.008.

    Article  CAS  Google Scholar 

  13. Chen, X. M. (2005). MicroRNA biogenesis and function in plants. FEBS Letters, 579, 5923–5931. doi:10.1016/j.febslet.2005.07.071.

    Article  CAS  Google Scholar 

  14. Chen, X. M. (2004). A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science, 303, 2022–2025. doi:10.1126/science.1088060.

    Article  CAS  Google Scholar 

  15. Aukerman, M. J., & Sakai, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell, 15, 2730–2741. doi:10.1105/tpc.016238.

    Article  CAS  Google Scholar 

  16. Griffiths-Jones, S., Saini, H. K., van Dongen, S., & Enright, A. J. (2008). miRBase: Tools for microRNA genomics. Nucleic Acids Research, 36, D154–D158. doi:10.1093/nar/gkm952.

    Article  CAS  Google Scholar 

  17. Sunkar, R., Girke, T., Jain, P. K., & Zhu, J. K. (2005). Cloning and characterization of microRNAs from rice. The Plant Cell, 17, 1397–1411. doi:10.1105/tpc.105.031682.

    Article  CAS  Google Scholar 

  18. Yao, Y. Y., Guo, G. G., Ni, Z. F., Sunkar, R., Du, J. K., Zhu, J. K., et al. (2007). Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biology, 8, R96.

    Article  Google Scholar 

  19. Zhang, B. H., Pan, X. P., & Anderson, T. A. (2006). Identification of 188 conserved maize microRNAs and their targets. FEBS Letters, 580, 3753–3762. doi:10.1016/j.febslet.2006.05.063.

    Article  CAS  Google Scholar 

  20. Zhang, B. H., Pan, X. P., & Stellwag, E. J. (2008). Identification of soybean microRNAs and their targets. Planta, 229, 161–182. doi:10.1007/s00425-008-0818-x.

    Article  CAS  Google Scholar 

  21. Zhang, B. H., Wang, Q. L., & Pan, X. P. (2007). MicroRNAs and their regulatory roles in animals and plants. Journal of Cellular Physiology, 210, 279–289. doi:10.1002/jcp.20869.

    Article  CAS  Google Scholar 

  22. Zhang, B. H., Pan, X. P., Wang, Q. L., Cobb, G. P., & Anderson, T. A. (2006). Computational identification of microRNAs and their targets. Computational Biology and Chemistry, 30, 395–407. doi:10.1016/j.compbiolchem.2006.08.006.

    Article  CAS  Google Scholar 

  23. Floyd, S. K., & Bowman, J. L. (2004). Gene regulation: Ancient microRNA target sequences in plants. Nature, 428, 485–486. doi:10.1038/428485a.

    Article  CAS  Google Scholar 

  24. Zhang, B. H., Pan, X. P., Cannon, C. H., Cobb, G. P., & Anderson, T. A. (2006). Conservation and divergence of plant microRNA genes. The Plant Journal, 46, 243–259. doi:10.1111/j.1365-313X.2006.02697.x.

    Article  CAS  Google Scholar 

  25. Zhang, B. H., Wang, Q. L., Wang, K. B., Pan, X. P., Liu, F., Guo, T. L., et al. (2007). Identification of cotton microRNAs and their targets. Gene, 397, 26–37. doi:10.1016/j.gene.2007.03.020.

    Article  CAS  Google Scholar 

  26. Zhang, B. H., Pan, X. P., Wang, Q. L., Cobb, G. P., & Anderson, T. A. (2005). Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15, 336–360. doi:10.1038/sj.cr.7290302.

    Article  Google Scholar 

  27. Lauter, N., Kampani, A., Carlson, S., Goebel, M., & Moose, S. P. (2005). microRNA172 down-regulates glossy15 to promote vegetative phase change in maize. Proceedings of the National Academy of Sciences of the United States of America, 102, 9412–9417. doi:10.1073/pnas.0503927102.

    Article  CAS  Google Scholar 

  28. Chen, C. F., Ridzon, D. A., Broomer, A. J., Zhou, Z. H., Lee, D. H., Nguyen, J. T., et al. (2005). Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Research, 33, e179. doi:10.1093/nar/gni178.

    Article  Google Scholar 

  29. Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M., & Weigel, D. (2005). Specific effects of microRNAs on the plant transcriptome. Developmental Cell, 8, 517–527. doi:10.1016/j.devcel.2005.01.018.

    Article  CAS  Google Scholar 

  30. Kurihara, Y., & Watanabe, Y. (2004). Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. Proceedings of the National Academy of Sciences of the United States of America, 101, 12753–12758. doi:10.1073/pnas.0403115101.

    Article  CAS  Google Scholar 

  31. Tang, G. L., Reinhart, B. J., Bartel, D. P., & Zamore, P. D. (2003). A biochemical framework for RNA silencing in plants. Genes & Development, 17, 49–63. doi:10.1101/gad.1048103.

    Article  CAS  Google Scholar 

  32. Park, W., Li, J. J., Song, R. T., Messing, J., & Chen, X. M. (2002). CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology, 12, 1484–1495. doi:10.1016/S0960-9822(02)01017-5.

    Article  CAS  Google Scholar 

  33. Xie, Z. X., Kasschau, K. D., & Carrington, J. C. (2003). Negative feedback regulation of Dicer-like1 in Arabidopsis by microRNA-guided mRNA degradation. Current Biology, 13, 784–789. doi:10.1016/S0960-9822(03)00281-1.

    Article  CAS  Google Scholar 

  34. Liu, B., Li, P. C., Li, X., Liu, C. Y., Cao, S. Y., Chu, C. C., et al. (2005). Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiology, 139, 296–305. doi:10.1104/pp.105.063420.

    Article  CAS  Google Scholar 

  35. Cui, X. J., Shin, H. S., Song, C., Laosinchai, W., Amano, Y., & Brown, R. M. (2001). A putative plant homolog of the yeast beta-1, 3-glucan synthase subunit FKS1 from cotton (Gossypium hirsutum L.) fibers. Planta, 213, 223–230. doi:10.1007/s004250000496.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Biology, East Carolina University, Greenville, NC, 27858, USA

    Baohong Zhang

  2. Department of Chemistry, Western Illinois University, Macomb, IL, 61455, USA

    Xiaoping Pan

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  1. Baohong Zhang
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  2. Xiaoping Pan
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Correspondence to Baohong Zhang.

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Zhang, B., Pan, X. Expression of MicroRNAs in Cotton. Mol Biotechnol 42, 269–274 (2009). https://doi.org/10.1007/s12033-009-9163-y

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  • DOI: https://doi.org/10.1007/s12033-009-9163-y

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