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Identification of microsatellite markers in the rye genome

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Abstract

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.

Abbreviations

SSR:

simple sequence repeat

ISSR:

inter-simple sequence repeat

SAMPL:

selective amplification of microsatellite polymorphic loci

EST:

expressed sequence tags

IS:

insert size [bp]

GmS:

genome size [bp]

GS:

genetic similarity

References

  1. 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.

  2. 2.

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

  3. 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.

  4. 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.

  5. 5.

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

  6. 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.

  7. 7.

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

  8. 8.

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

  9. 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.

  10. 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.

  11. 11.

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

  12. 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.

  13. 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.

  14. 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.

  15. 15.

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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

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Correspondence to Monika Rakoczy-Trojanowska.

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Key words

  • Rye
  • Genomic library
  • SSR
  • Microsatellite
  • Wheat-rye addition lines