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Identification of microsatellite markers in the rye genome


The rye genomic library, which consists of DNA fragments in the range of 0.5–1.1 kb, was screened for the presence of tri-and tetranucleotide and compound microsatellites. Of the 1,600,000 clones analysed, 102 clones were positive and 41 were suitable for SSR primer pair design. Twenty-six primer pairs amplified specific products, and six of them were capable of detecting polymorphism among 30 rye accessions of different genetic backgrounds. Using a set of Chinese Spring-Imperial wheat-rye addition lines, it was possible to locate 3 newly identified microsatellites on chromosomes 3R, 4R and 7R.



simple sequence repeat


inter-simple sequence repeat


selective amplification of microsatellite polymorphic loci


expressed sequence tags


insert size [bp]


genome size [bp]


genetic similarity


  1. Litt, M. and Luty, J.A. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44 (1989) 397–401.

    PubMed  CAS  Google Scholar 

  2. Tautz, D., Trick, D. and Dover, G. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322 (1986) 652–656.

    Article  PubMed  CAS  Google Scholar 

  3. Gur-Arie, R., Cohen, C.J., Eitan, Y., Shelef, L., Hallerman, E.M. and Kashi, Y. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res. 10 (2000) 62–71.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  6. Korzun, V., Malyshev, S., Voylokov, A.V. and Börner, A. A genetic map of rye (Secale cereale L) combining RFLP, isozyme, protein, microsatellite and gene loci. Theor. Appl. Genet. 102 (2001) 709–717.

    Article  CAS  Google Scholar 

  7. Hackauf, B. and Wehling, P. Identification of microsatellite polymorphisms in an expressed portion of the rye genome. Plant Breed. 121 (2002) 17–25.

    Article  CAS  Google Scholar 

  8. Hackauf, B. and Wehling P. Development of microsatellite markers in rye: map construction. Plant Breed. Seed Sci. 48 (2003) 143–151.

    Google Scholar 

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

    Article  Google Scholar 

  10. Bolibok, H., Rakoczy-Trojanowska, M., Hromada, A. and Pietrzykowski R. Efficiency of different PCR-based marker systems in assessing genetic diversity among rye inbred lines. Euphytica 146 (2005) 109–115.

    Article  CAS  Google Scholar 

  11. Murray, M.G. and Thompson, W.F. Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res. 8 (1980) 4321–4325.

    PubMed  CAS  Google Scholar 

  12. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403–410.

    Article  PubMed  CAS  Google Scholar 

  13. Varshney, R.K., Thiel, T., Stein, N., Langridge, P. and Graner, A. In silico analysis of frequency and distribution of microsatellites in ESTs of some cereals. Cell. Mol. Biol. Lett. 7 (2002) 537–546.

    PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  15. Schlötterer, C. Evolutionary dynamics of microsatellite DNA. Chromosoma 109 (2000) 365–371.

    PubMed  Google Scholar 

  16. Sharopova, N., McMullen, M.D., Schultz, L., Schroeder, S., Sanchez-Villeda, H., Gardiner, J., Bergstrom, D., Houchins, K., Melia-Hancock, S., Musket, T., Duru, N., Polacco, M., Edwards, K., Ruff, T., Register, J.C., Brouwer, C., Thompson, R., Velasco, R., Chin, E., Lee, M., Woodman-Clikeman, W., Long, M.J., Liscum, E., Cone, K., Davis, G. and Coe Jr., E.H. Development and mapping od SSR markers for maize. Plant Mol. Biol. 48 (2002) 463–481.

    Article  PubMed  CAS  Google Scholar 

  17. Röder, M.S., Korzun, V., Wendehakem K., Plaschkem, J., Tixier, M.H., Leroy, P. and Ganal, M.W. A microsatellite map of wheat. Genetics 149 (1998) 2007–2023.

    PubMed  Google Scholar 

  18. Pestsova, E., Ganal, M.W. and Röder, M.S. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43 (2000) 689–697.

    Article  PubMed  CAS  Google Scholar 

  19. Ma, X.F., Wanous, M.K., Houchins, K., Rodriguez Milla, M.A., Goicoechea, P.G., Wang, Z., Xie, M. and Gustafson, J.P. Molecular linkage mapping in rye (Secale cereale L). Theor. Appl. Genet. 102 (2001) 517–523.

    Article  CAS  Google Scholar 

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Correspondence to Monika Rakoczy-Trojanowska.

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Bolibok, H., Rakoczy-Trojanowska, M., Wyrzykowska, M. et al. Identification of microsatellite markers in the rye genome. Cell. Mol. Biol. Lett. 11, 291–298 (2006).

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