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Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species

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Abstract

Microsatellites, also known as simple sequence repeats (SSRs), are the class of repetitive DNA sequences present throughout the genome of many plant and animal species. Recent advances in molecular genetics had been the introduction of microsatellite markers to investigate the genetic structuring of natural plant populations. We have employed an enrichment strategy for microsatellite isolation by using multi-enzymes digestion, microsatellite oligoprobes, and streptavidin magnetic beads in Sesamum (Sesamum indicum L.). More than 200 SSR motifs were detected (SSR motifs ≥2 repeat units or 6 bp); 80 % of the clones contained SSR motifs. When regarding SSRs with four or more repeat units and a minimum length of 10 bp, 132 of them showed repeats. Eighteen SSR markers were initially characterized for optimum annealing temperature using a gradient PCR technique. Among the 18 SSR markers characterized, five were found to be polymorphic and used to analyze 60 Sesamum germplasm accessions. The maximum number of alleles detected was four with a single primer and the least number of two alleles with three primers with an average PIC value of 0.77. SSRs are a valuable tool for estimating genetic diversity and analyzing the evolutionary and historical development of cultivars at the genomic level in sesame breeding programs.

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References

  1. Ashri, A. (2010). In J. Janick (Ed.), Plant breeding reviews (Vol. 16). Oxford: Wiley.

    Google Scholar 

  2. Bedigian, D., & Harlan, J. (1986). Economic Botany, 40(2), 137–154.

    Article  Google Scholar 

  3. Bedigian, D., Seigler, D. S., & Harlan, J. R. (1985). Biochemical Systematics and Ecology, 13, 133–139.

    Article  CAS  Google Scholar 

  4. Fukuda, Y., Nagata, M., Osawa, T., & Namiki, M. (1986). Journal of the American Oil Chemists’ Society, 63, 1027–1031.

    Article  CAS  Google Scholar 

  5. Cheung, S. C., Szeto, Y. T., & Benzie, I. F. (2007). Plant Foods for Human Nutrition, 62, 39–42.

    Article  CAS  Google Scholar 

  6. Chung, C. H., Yee, Y. J., Kim, D. H., Kim, H. K., & Chung, D. S. (1995). Plant Science, 109, 237–243.

    Article  CAS  Google Scholar 

  7. Liu, C. J. (1997). Euphytica, 98, 21–27.

    Article  CAS  Google Scholar 

  8. Reiter, S. R., Young, M., & Scolnik, P. A. (1993). Methods in Arabidopsis research. Singapore: World Scientific Publishing.

    Google Scholar 

  9. Isshiki, S., & Umezaki, T. (1997). Euphytica, 93, 375–377.

    Article  CAS  Google Scholar 

  10. Bhat, V., Babrekar, P., & Lakhanpaul, S. (1999). Euphytica, 110, 21–33.

    Article  CAS  Google Scholar 

  11. Kim, D., Zur, G., Danin, P., Lee, Y. S., Shim, K., Kang, C., et al. (2002). Plant Breeding, 121, 259–262.

    Article  CAS  Google Scholar 

  12. Uzun, B., Lee, D., Donini, P., & Cagrirgan, M. (2003). Identification of a molecular marker linked to the closed capsule mutant trait in sesame using AFLP. Plant Breeding, 122, 95–97.

    Article  CAS  Google Scholar 

  13. Dixit, A., Jin, M. H., Chung, J. W., Yu, J. W., Chung, H. K., Ma, K. H., et al. (2005). Molecular Ecology Notes, 5, 736–738.

    Article  CAS  Google Scholar 

  14. Wei, L. B., Zhang, H. Y., Zheng, Y. Z., Guo, W. Z., & Zhang, T. Z. (2008). Acta Biochimica et Biophysica Sinica, 34, 2077–2084.

    CAS  Google Scholar 

  15. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., et al. (1996). Molecular Breeding, 2, 225–238.

    Article  CAS  Google Scholar 

  16. Sambrook, J., & David, R. W. (2001). Molecular cloning: a laboratory manual (3rd ed.). Cold Spring Harbor: Cold Spring Harbor Press.

    Google Scholar 

  17. Sambrook, J., Fritsch, E. F., & Maniatis, T. (1989). Molecular cloning: a laboratory manual. Cold Spring Harbor: Cold Spring Harbor Laboratory.

    Google Scholar 

  18. Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., & McCouch, S. (2001). Genome Research, 11, 1441–1452.

    Article  CAS  Google Scholar 

  19. Doyle, J. J., & Doyle, J. L. (1987). Phytochemical Bulletin, 19, 11–15.

    Google Scholar 

  20. Karagyozov, L., Kalcheva, I. D., & Chapman, V. M. (1993). Nucleic Acids Research, 21, 3911–3912.

    Article  CAS  Google Scholar 

  21. Armour, J. A., Neumann, R., Gobert, S., & Jeffreys, A. J. (1994). Human Molecular Genetics, 3, 599–605.

    Article  CAS  Google Scholar 

  22. Kijas, J. M., Fowler, J. C., Garbett, C. A., & Thomas, M. R. (1994). Biotechniques, 16, 656–662.

    CAS  Google Scholar 

  23. Akkaya, M. S., Bhagwat, A. A., & Cregan, P. B. (1992). Genetics, 132, 1131–1139.

    CAS  Google Scholar 

  24. Gautami, B., Ravi, K., Lakshmi Narasu, M., Hoisington, D. A., & Varshney, R. K. (2009). International Journal of Integrative Biology, 7, 100–106.

    CAS  Google Scholar 

  25. Chin, E. C. L., Senior, M. L., Shu, H., & Smith, J. S. C. (1996). Genome, 39, 866–873.

    Article  CAS  Google Scholar 

  26. Reiter, W. D. (2002). Current Opinion in Plant Biology, l5, 536–542.

    Article  Google Scholar 

  27. Finnegan, E. J., Genger, R. K., Peacock, W. J., & Dennis, E. S. (1998). Annual Review of Plant Physiology and Plant Molecular Biology, 49, 223–247.

    Article  CAS  Google Scholar 

  28. Deininger, P. (1983). Analytical Biochemistry, 129, 216–223.

    Article  CAS  Google Scholar 

  29. Kolliker, R., Jones, E. S., Drayton, M. C., Dupal, M. P., & Forster, J. W. (2001). Theoretical and Applied Genetics, 102, 416–424.

    Article  CAS  Google Scholar 

  30. Qi, X. (2001). Biotechniques, 31, 355–362.

    CAS  Google Scholar 

  31. Van de Weil, C., Arens, P., & Vosman, B. (1999). Genome, 42, 139–149.

    Google Scholar 

  32. Milbourne, D., Meyer, R. C., Collins, A. J., Ramsay, L. D., Gebhardt, C., & Waugh, R. (1998). Molecular and General Genetics, 259, 233–245.

    Article  CAS  Google Scholar 

  33. Rivera, R., Edwards, K. J., Barker, J. H. A., Arnold, G. M., Ayad, G., Hodgkin, T., et al. (1999). Genome, 42, 668–675.

    CAS  Google Scholar 

  34. Arens, P., Durka, W., Wernke, J. H., & Smulders, J. M. (2004). Moleculor Ecology Notes, 4, 209–212.

    Article  CAS  Google Scholar 

  35. Gilbert, J. E., Lewis, R. V., Wilkinson, M. J., & Caligar, P. D. F. (1999). Theoretical and Applied Genetics, 98, 1125–1131.

    Article  CAS  Google Scholar 

  36. Bin, L., Zhang, H. Y., Zheng, Y. Z., Miao, H. M., & Zhang, T. Z. (2008). Genes & Genomics, 31, 199–208.

    Google Scholar 

  37. Tautz, D., & Renz, M. (1984). Nucleic Acids Research, 12, 4127–4138.

    Article  CAS  Google Scholar 

  38. Tautz, D., Trick, M., & Dover, G. A. (1986). Nature, 322, 652–656.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Institute of Biotechnology, A.N.G.R.A.U, Rajendranagar, Hyderabad, 500 030, India

    B. Spandana, V. Prathap Reddy, G. Anuradha & S. Sivaramakrishnan

  2. Biotechnology Division, Directorate of Rice Research (D.R.R), Rajendranagar, Hyderabad, 500 030, India

    G. John Prasanna

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  1. B. Spandana
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  2. V. Prathap Reddy
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  3. G. John Prasanna
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  4. G. Anuradha
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  5. S. Sivaramakrishnan
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Correspondence to B. Spandana.

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Spandana, B., Reddy, V.P., Prasanna, G.J. et al. Development and Characterization of Microsatellite Markers (SSR) in Sesamum (Sesamum indicum L.) Species. Appl Biochem Biotechnol 168, 1594–1607 (2012). https://doi.org/10.1007/s12010-012-9881-7

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  • DOI: https://doi.org/10.1007/s12010-012-9881-7

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