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Mining of EST-SSR Markers of Musa and Their Transferability Studies Among the Members of Order the Zingiberales

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Abstract

Expressed sequence tags (ESTs) databases of 11 Musa complementary DNA libraries were retrieved from National Center of Biotechnology Information and used for mining simple sequence repeats (SSRs). Out of 21,056 unique ESTs, SSR regions were found only in 5,158 ESTs. Among these SSR containing ESTs, the occurrence of trinucleotide repeats are the most abundant followed by mono-, di-, tetra-, hexa-, and pentanucleotides. Moreover, this study showed that the rate of class II SSRs (<20 nucleotides) was higher than the class I SSRs (<20 nucleotides), and proportion of class I and II SSRs as abundant for tri-repeats. As a representative sample, primers were synthesized for 24 ESTs, carrying >12 nucleotides of SSR region, and tested among the various genomic group of Musa accessions. The result showed that 88 % of primers were functional primers, and 43 % are showing polymorphism among the Musa accessions. Transferability studies of Musa EST-SSRs among the genera of the order Zingiberales exhibited 100 and 58 % transferability in Musaceae and Zingiberaceae, respectively. The sequence comparison of SSR regions among the different Musa accessions confirmed that polymorphism is mainly due to the variation in repeat length. High percentage of cross-species, cross-genera, and cross-family transferability also suggested that these Musa EST-SSR markers will be a valuable resource for the comparative mapping by developing COS markers, in evolutionary studies and in improvement of the members of Zingiberaceae and Musaceae.

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References

  1. Yu, J., & Kohel, R.J. (1999). Proceedings of the Belt Wise Cotton Research Conferences, National Cotton Council, Memphis, p. 439.

  2. Zane, L., Bargelloni, L., & Patarnello, T. (2002). Molecular Ecology, 11, 1–16.

    Article  CAS  Google Scholar 

  3. Gu, Z., Hillier, L., & Kwok, P. Y. (1998). Human Mutation, 12, 221–225.

    Article  CAS  Google Scholar 

  4. Kantety, R. V., La Rota, M., Matthews, D. E., & Sorrells, M. E. (2002). Plant Molecular Biology, 48, 501–510.

    Article  CAS  Google Scholar 

  5. Picoult-Newberg, L., et al. (1999). Genome Research, 9, 167–174.

    CAS  Google Scholar 

  6. Morgante, M., Hanafey, M., & Powell, W. (2002). Nature Genetics, 30, 194–200.

    Article  CAS  Google Scholar 

  7. Toth, G., Gaspari, Z., & Jurka, J. (2000). Genome Research, 10, 967–981.

    Article  CAS  Google Scholar 

  8. Gupta, P. K., Rustgi, S., Sharma, S., Singh, R., Kumar, N., & Balyan, H. S. (2003). Molecular Genetics Genomics, 270, 315–323.

    Article  CAS  Google Scholar 

  9. Scott, K. D., Eggler, P., Seaton, G., Rossetto, M., Ablett, E. M., Lee, L. S., et al. (2000). Theoretical and Applied Genetics, 100, 723–726.

    Article  CAS  Google Scholar 

  10. Ogundiwin, E. A., Martí, C., Forment, J., Pons, C., Granell, A., Gradziel, T. M., et al. (2009). Plant Molecular Biology, 68, 379–397.

    Article  Google Scholar 

  11. Fouet, O., Allègre, M., Argout, X., Jeanneau, M., Lemainque, A., Pavek, S., et al. (2011). Tree Genetics and Genomics, 74, 799–817.

    Article  Google Scholar 

  12. Gawel, N. J., & Jarret, R. L. (1991). Plant Molecular Biology Reporter, 9(3), 262–266.

    Article  CAS  Google Scholar 

  13. Raji, A., Anderson, J., Kolade, O., Ugwu, C., Dixon, A., & Ingelbrecht, I. (2009). BMC Plant Biology, 9, 118.

    Article  Google Scholar 

  14. Yi, G., Lee, J., Lee, S., Choi, D., & Kim, B. D. (2006). Theoretical and Applied Genetics, 114(1), 113–130.

    Article  CAS  Google Scholar 

  15. Poncet, V., Rondeau, M., Tranchant, C., Cayrel, A., Hamon, S., de Kochko, A., et al. (2006). Molecular Genetics and Genomics, 276(5), 436–449.

    Article  CAS  Google Scholar 

  16. Varshney, R. K., Graner, A., & Sorrells, M. E. (2005). Trends in Biotechnology, 23(1), 48–55.

    Article  CAS  Google Scholar 

  17. Gaudeul, M., Stenøien, H. K., & Agren, J. (2007). American Journal of Botany, 94, 1146–1155.

    Article  Google Scholar 

  18. Sreenu, V. B., Kumar, P., Nagaraju, J., & Nagarajaram, H. A. (2007). Journal of Biosciences, 32, 3–15.

    Article  CAS  Google Scholar 

  19. Varshney, R. K., Thiel, T., Stein, N., Langridge, P., & Graner, A. (2002). Cellular and Molecular Biology Letters, 7(2A), 537–546.

    CAS  Google Scholar 

  20. Eujayl, I., Sledge, M. K., Wang, L., May, G. D., Chekhovskiy, K., Zwonitzer, J. C., et al. (2004). Theoretical and Applied Genetics, 108, 414–422.

    Article  CAS  Google Scholar 

  21. Metzgar, D., Bytof, J., & Wills, C. (2000). Genome Research, 10, 72–80.

    CAS  Google Scholar 

  22. Lescot, M., Piffanelli, P., Ciampi, A. Y., Ruiz, M., et al. (2008). BMC Genomics, 9, 58. doi:10.1186/1471-2164-9-58.

    Article  Google Scholar 

  23. Cheung, F., & Town, C. D. (2007). BMC Plant Biology, 7, 29. doi:10.1186/1471-2229-7-29.

    Article  Google Scholar 

  24. Lothe, R. A., Andersen, S. N., Hofstad, B., Meling, G. I., Peltomäki, P., Heim, S., et al. (1995). Genes Chromosome Cancer, 14(3), 182–188.

    CAS  Google Scholar 

  25. Callen, D. F., Thompson, A. D., Shen, Y., Phillips, H. A., Richards, R. I., Mulley, J. C., et al. (1993). American Journal of Genetics, 52, 922–927.

    CAS  Google Scholar 

  26. Wang, J. Y., Zheng, L. S., Huang, B. Z., Liu, W. L., & WU, Y. T. (2010). Genetic Resources and Crops Evolution, 57(4), 553–563.

    Article  CAS  Google Scholar 

  27. Thiel, T., et al. (2003). Theoretical and Applied Genetics, 106, 411–422.

    CAS  Google Scholar 

  28. Saha, M. C., Mian, M. A. R., Eujayl, I., Zwonitzer, J. C., Wang, L., & May, G. D. (2004). Theoretical and Applied Genetics, 109, 783–791.

    Article  Google Scholar 

  29. Agarwal, R. K., Hendre, P. S., Varshney, R. K., Bhat, P. R., Krishnakumar, V., & Singh, L. (2007). Theoretical and Applied Genetics, 114(2), 359–372.

    Article  Google Scholar 

  30. Gow, C., Noble, J. L., Rollinson, D., & Jones, C. (2005). Genetica, 124(1), 77–83.

    Article  CAS  Google Scholar 

  31. Decroocq, V., Fave, M. G., Hagen, L., Bordenave, L., & Decroocq, S. (2003). Theoretical and Applied Genetics, 106, 912–922.

    CAS  Google Scholar 

  32. Chagne, D., Chaumeil, P., Ramboer, A., Collada, C., Guevara, A., Cervera, M. T., et al. (2004). Theoretical and Applied Genetics, 109, 1204–1214.

    Article  CAS  Google Scholar 

  33. Cordeiro, G. M., Casu, R., McIntyre, C. L., Manners, J. M., & Henry, R. J. (2001). Plant Science, 160, 1115–1123.

    Article  CAS  Google Scholar 

  34. Ellis, J. R., & Burke, J. M. (2007). Heredity, 99, 125–132.

    Article  CAS  Google Scholar 

  35. Gao, L., Tang, J., Li, H., & Jia, J. (2003). Molecular Breeding, 12, 245–261.

    Article  CAS  Google Scholar 

  36. Fatokun, C. A., Menacio-Hautea, D. I., Danesh, D., & Young, N. D. (1992). Genetics, 132, 841–884.

    CAS  Google Scholar 

  37. Bennetzen, J. L., & Freeling, M. (1993). Trends in Genetics, 9, 259–261.

    Article  CAS  Google Scholar 

  38. Gale, M. D., & Devos, K. M. (1998). Proceedings of the National Academy, 95, 1971–1974.

    Article  CAS  Google Scholar 

Download references

Acknowledgment

Authors thankfully acknowledge Dr. M.M. Mustaffa, Director, National Research Centre for Banana, Trichy, for providing facilities to do this part of the work.

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  1. National Research Centre for Banana (ICAR), Thogamalai Road, Thayanur Post, Trichy, 620 102, Tamil Nadu, India

    S. Backiyarani, S. Uma, P. Varatharj & M. S. Saraswathi

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  1. S. Backiyarani
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  2. S. Uma
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  3. P. Varatharj
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  4. M. S. Saraswathi
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Correspondence to S. Backiyarani.

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Backiyarani, S., Uma, S., Varatharj, P. et al. Mining of EST-SSR Markers of Musa and Their Transferability Studies Among the Members of Order the Zingiberales. Appl Biochem Biotechnol 169, 228–238 (2013). https://doi.org/10.1007/s12010-012-9975-2

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  • DOI: https://doi.org/10.1007/s12010-012-9975-2

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