Skip to main content

Efficiency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines

Summary

The aim of this study was to investigate the efficiency of ISSR, SSR, and SAMPL marker systems in detecting genetic polymorphism among 30 winter rye inbred lines and to compare the results of cluster analysis performed on data from these marker systems using different statistical methods and coefficients. Each marker system was able to discriminate among the materials analyzed with the lowest value of average genetic similarity (GS) obtained with ISSR markers (0.2888) and the highest with SAMPLs (0.5381). EST-derived SSRs turned out to be less efficient in detecting genetic diversity than those from genomic libraries (average GS values 0.3814 and 0.3221, respectively). The average GS value for combined SSR data was 0.3569. The lack of correlations between similarity and cophenetic matrices obtained with various methods systems suggests that different marker systems should be used simultaneously for a genetic diversity study to exploit as many sources of polymorphisms as possible.

This is a preview of subscription content, access via your institution.

References

  • Blair, M.W., F. Pedraza, H.F. Buenida, E. Gaitán-Solís, S.E. Beebe, P. Gepts & J. Tohme, 2003. Development of a genome-wide anchored microsatellite map for common bean (Phaseolus vulgaris L.). Theor Appl Genet 107: 1362–1374.

    Article  PubMed  CAS  Google Scholar 

  • Cho, Y.G., S. Temnykh, X. Chen, L. Lipovich, S.R. McCouch, N. Ayres & S. Cartinhour, 2000. Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice. Theor Appl Genet 100: 713–722.

    Article  CAS  Google Scholar 

  • Hackauf, B. & P. Wehling, 2002. Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed 121: 17–25.

    Article  CAS  Google Scholar 

  • Jaccard, P., 1908. Nouvelles recherches sur la distribution florale. Bull Soc Vaudoise Sci Nat 44: 223–270.

    Google Scholar 

  • Khlestkina, E.K., M.H.M. Than, E.G. Pestsova, M.S. Röder, S.V. Malyshev, V. Korzun & A. Börner, 2004. Mapping of 99 new microsatellite-derived loci in rye (Secale cereale L.) including 39 expressed sequence tags. Theor Appl Genet 19: 725–732.

    Google Scholar 

  • Morgante, M. & J. Vogel, 1994. Compound Microsatellite Primers for the Detection of Genetic Polymorphism, U.S. Patent Appl. 08/326456.

  • Murray, M.G. & W.F. Thompson, 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8: 4321–4325.

    PubMed  CAS  Google Scholar 

  • Pillen, K., A. Binder, A.B. Kreuzkam, L. Ramsay, R. Waugh, J. Förster & J. Léon, 2000. Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars. Theor Appl Genet 101: 652–660.

    Article  CAS  Google Scholar 

  • Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey & A. Rafalski, 1996. The comparison of RFLP, RAPD, AFLP, and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2: 225–238.

    Article  CAS  Google Scholar 

  • Rakoczy-Trojanowska, M. & H. Bolibok, 2004. Characteristics and comparison of three classes of microsatellite-based markers and their application in plants. Cell Mol Biol Lett 9: 221–238.

    PubMed  CAS  Google Scholar 

  • Rohlf, F.J., 2001. NTSYS-pc Numerical Taxonomy and Multivariate Analysis System, Version 5.1. Exeter, Setauket, NY.

    Google Scholar 

  • Roy, J.K., H.S. Balyan, M. Prasad & P.K. Gupta, 2002. Use of SAMPL for a study of DNA polymorphism, genetic diversity, and possible gene tagging in bread wheat. Theor Appl Genet 104: 465–472.

    Article  PubMed  CAS  Google Scholar 

  • Saal, B. & G. Wricke, 1999. Development of simple sequence repeat markers in rye (Secale cereale L.). Genome 42: 964–972.

    Article  PubMed  CAS  Google Scholar 

  • Singh, A., A. Chaudhury, P.S. Srivastava & M. Lakshmikumaran, 2002. Comparison of AFLP and SAMPL markers for assessment of intra-population genetic variation in Azadirachta indica A. Juss Plant Sci 162: 17–25.

    CAS  Google Scholar 

  • Tosti, N. & V. Negri, 2002. Efficiency of three PCR-based markers in assessing genetic variation among cowpea (Vigna unguiculata subsp. unguiculata) landraces. Genome 45: 268–275.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hanna Bolibok.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bolibok, H., Rakoczy-Trojanowska, M., Hromada, A. et al. Efficiency of different PCR-based marker systems in assessing genetic diversity among winter rye (Secale cereale L.) inbred lines. Euphytica 146, 109–116 (2005). https://doi.org/10.1007/s10681-005-0548-0

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-005-0548-0

Key words

  • genetic diversity
  • ISSR
  • rye
  • SAMPL
  • SSR