Plant Molecular Biology

, Volume 27, Issue 4, pp 835–845 | Cite as

Barley microsatellites: allele variation and mapping

  • J. Becker
  • M. Heun
Research Article


Microsatellites have developed into a powerful tool for mapping mammalian genomes and first reports about their use in plants have been published. A database search of 228 barley sequences from GenBank and EMBL was made to determine which simple sequence repeat (SSR) motif prevails in barley. Nearly all types of SSRs were found. The (A)n and (T)n SSRs occurred more often than (C)n and (G)n for n≥10. Among the dinucleotide repeats, the (CG)n SSRs occurred least often. Trinucleotide repeats did not occur with n>7 and there is no correlation between the GC content in the trinucleotide motifs and the number of observed SSRs. Analysing 15 different microsatellites with 11 barleys yielded 2.1 alleles per microsatellite. Sequencing 25 putative microsatellites showed that the resolution capacity of highquality agarose gels was sufficient to determine differences of only three base paris. Five microsatellites were mapped on three different chromosomes of a barley RFLP map.

Key words

barley microsatellites simple sequence repeats mapping sequencing 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Akkaya MS, Bhagwat AA, Cregan PB: Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132: 1131–1139 (1992).PubMedGoogle Scholar
  2. 2.
    Beckmann JS, Soller M: Toward a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites. Bio/technology 8: 930–932. (1990).CrossRefPubMedGoogle Scholar
  3. 3.
    Bell CJ, Ecker JR: Assignment of 30 microsatellite loci to the linkage map of Arabidopsis Genomics 19: 137–144 (1994).CrossRefPubMedGoogle Scholar
  4. 4.
    Brunel D: A microsatellite marker in Helianthus annuus L. Plant Mol Biol 24: 397–400 (1994).PubMedGoogle Scholar
  5. 5.
    Close TJ, Kortt AA, Chandler PM: A cDNA-based comparison of dehydration-induced proteins (dehydrins) in barley and corn. Plant Mol Biol 13: 95–108 (1989).PubMedGoogle Scholar
  6. 6.
    Condit R, Hubbell SP: Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34: 66–71 (1991).PubMedGoogle Scholar
  7. 7.
    Davies K: Of mice and men (and cows and cats). Nature 361: 478 (1993).CrossRefPubMedGoogle Scholar
  8. 8.
    Devereux J, Haeberli P, Smithies O: A comprehensive set of sequence analysis programs for the vax. Nucl Acids Res 12: 387–395 (1984).PubMedGoogle Scholar
  9. 9.
    Dietrich W, Katz H, Lincoln SE, Shin H-S, Friedman J, Dracopoli NC, Lander ES: A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131: 423–447 (1992).PubMedGoogle Scholar
  10. 10.
    Good AG, Pelcher LE, Crosby WL: Nucleotide sequence of a complete barley alcohol dehydrogenase 1 cDNA. Nucl Acids Res 16: 7182 (1988).PubMedGoogle Scholar
  11. 11.
    Goodfellow PN: Variation is now the theme. Nature 359: 777–778 (1992).CrossRefPubMedGoogle Scholar
  12. 12.
    Graner A, Siedler H Jahoor A Herrmann RG, Wenzel G: Assessment of the degree and the type of restriction fragment length polymorphism in barley (Hordeum vulgare). Theor Appl Genet 80: 826–832 (1990).CrossRefGoogle Scholar
  13. 13.
    Graner A, Jahoor A, Schondelmaier J, Siedler H, Pillen K, Fischbeck G, Wenzel G, Hermann RG: Construction of an RFLP map of barley. Theor Appl Genet 83: 250–256 (1991).CrossRefGoogle Scholar
  14. 14.
    Hahn M, Lehnacker H, Knogge W: Unpublished. Data from EMBL, accession number X58566 (1991).Google Scholar
  15. 15.
    Hamada H, Petrino MC, Takugana T A novel repeated element with Z-forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79: 6465–6469 (1982).PubMedGoogle Scholar
  16. 16.
    Hansen L: Unpublished. Data from EMBL, accession number M58753 (1991).Google Scholar
  17. 17.
    Heck GR, Dorsett C, Ho TH: Unpublished. Data from EMBL, accession number M77475 (1992).Google Scholar
  18. 18.
    Heun M, Kennedy AE Anderson JA, Lapitan NLV, Sorrells ME, Tanksley SD: Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare) Genome 34: 437–447 (1991).Google Scholar
  19. 19.
    Kandpal RP, Kandpal G, Weissman SM: Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers. Proc Natl Acad Sci USA 91: 88–92 (1992).Google Scholar
  20. 20.
    Kauppinen S: Structure and expression of the Kas 12 gene encoding a beta-ketoacyl-acyl carrier protein synthase I isozyme from barley. J Biol Chem 267: 23999–24006 (1992).PubMedGoogle Scholar
  21. 21.
    Kleinhofs A, Kilian A, Saghai-Maroof MA, Biyashev RM, Hayes P, Chen FQ, Lapitan N, Fenwick A, Blake TK, Kanazin V, Ananiev E, Dahleen L, Kudrna D; Bollinger J, Knapp SJ, Liu B, Sorrells M, Heun M, Franckowiak JD, Hoffman D, Skadsen R, Steffenson BJ: A molecular, isozyme and morphological map of the barley (Hordeum vulgare) genome. Theor Appl Genet 86: 705–712 (1993).CrossRefGoogle Scholar
  22. 22.
    Kramer HH, Swomley Blander BA: Orienting linkage maps on the chromosomes of barley. Crop Sci 1: 339–342 (1961).Google Scholar
  23. 23.
    Lagercrantz U, Ellegren H, Andersson L: The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucl Acids Res 21: 1111–1115 (1993).PubMedGoogle Scholar
  24. 24.
    Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L: MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174–181 (1987).PubMedGoogle Scholar
  25. 25.
    Litts JC, Simmons CR, Karrer EE, Huang N, Rodriguez RL: The isolation and characterization of a barley 1,3–1,4-β-glucanase gene. Eur J Biochem 194: 831–838 (1990).PubMedGoogle Scholar
  26. 26.
    Manninen I, Schulman AH: Bare-1, a copia-like retro-element in barley (Hordeum vulgare L.). Plant Mol Biol 22: 829–846 (1993).CrossRefPubMedGoogle Scholar
  27. 27.
    Morgante M, Olivieri AM: PCR-amplified microsatellites as markers in plant genetics. Plant J 3: 175–182 (1993).CrossRefPubMedGoogle Scholar
  28. 28.
    Ostrander EA, Jong PM, Rine J, Duyk G: Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences. Proc Natl Acad Sci USA 89: 3419–3423 (1992).PubMedGoogle Scholar
  29. 29.
    Rafalski JA, Tingey SV: Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends Genet 9: 275–280 (1993).CrossRefPubMedGoogle Scholar
  30. 30.
    Rasmussen SK, Johansson A: Nucleotide sequence of a cDNA coding for the barley seed protein CMa: an inhibitor of insect alpha amylase. Plant Mol Biol 18: 423–427 (1992).PubMedGoogle Scholar
  31. 31.
    Robertson M, Close TJ, Cuming AC: Unpublished. Data from EMBL, accession number X71362 (1993).Google Scholar
  32. 32.
    Röder MS, Lapitan NLV, Sorrells ME, Tanksley SD: Genetic and physical mapping of barley telomeres. Mol Gen Genet 238: 294–303 (1993).PubMedGoogle Scholar
  33. 33.
    Rohde W, Becker D, Salamini F: Unpublished. Data from EMBL, accession number X07931 (1988).Google Scholar
  34. 34.
    Rohde W, Doerr S, Salamini F, Becker D: Structure of a chalcone synthase gene from Hordeum vulgare. Plant Mol Biol 16: 1103–1106 (1991).CrossRefPubMedGoogle Scholar
  35. 35.
    Rohrer GA, Leeson JA, Keele JW, Smith TP, Beattie CW: A microsatellite linkage map of the porcine genome. Genetics 136: 231–245 (1994).PubMedGoogle Scholar
  36. 36.
    Rundle SJ, Zielinski RE: Organization and expression of two tandemly oriented genes encoding ribulosebiphosphate carboxylase/oxygenase activase in barley. J Biol Chem 266: 4677–4685 (1991).PubMedGoogle Scholar
  37. 37.
    Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW: Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81: 8014–8018 (1984).PubMedGoogle Scholar
  38. 38.
    Salcedo G, Fra-Mon P, Molina-Cano JL, Aragoncillo C, Garcia-Olmedo F: Genetics of CM-proteins (A-hordeins) in barley. Theor Appl Genet 68: 53–59 (1984).CrossRefGoogle Scholar
  39. 39.
    Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1989).Google Scholar
  40. 40.
    Schnorr KM, Juricek M, Huang C, Culley D, Kleinhofs A: Analysis of barley nitrate reductase cDNA and genomic clones. Mol Gen Genet 227: 411–416 (1991).Google Scholar
  41. 41.
    Senior ML, Heun M: Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeasts using a CT primer. Genome 36: 884–889 (1993).PubMedGoogle Scholar
  42. 42.
    Tautz D: Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl Acids Res 17: 6463–6471 (1989).PubMedGoogle Scholar
  43. 43.
    Tautz D, Renz M: Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucl Acids Res 12: 4127–4138 (1984).PubMedGoogle Scholar
  44. 44.
    Thomas MR, Scott NS: Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86: 985–990 (1993).Google Scholar
  45. 45.
    Wang Z, Weber JL, Zhong G, Tanksley SD: Survey of plant short tandem DNA repeats. Theor Appl Genet 88: 1–6 (1994).Google Scholar
  46. 46.
    Weber JL, May PE: Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44: 388–396 (1989).PubMedGoogle Scholar
  47. 47.
    Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M: A secondgeneration linkage map of the human genome. Nature 359: 794–801 (1992).CrossRefPubMedGoogle Scholar
  48. 48.
    vanWettstein-Knowles P: Barley (Hordeum vulgare) 2N=14. In: O'Brien SJ (ed) Genetic Maps, pp. 6.110–6.129. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (1993).Google Scholar
  49. 49.
    Whittier RF, Dean DA, Rogers JC: Unpublished. Data from EMBL, accession number X05167 (1987).Google Scholar
  50. 50.
    Wu K-S, Tanksley S: Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241: 225–235 (1993).CrossRefPubMedGoogle Scholar
  51. 51.
    Yu YG, Saghai Maroof MA, Buss GR, Maughan PJ, Tolin SA: RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance. Phytopathology 84: 60–64 (1994).Google Scholar
  52. 52.
    Zhao X, Kochert G: Characterization and genetic mapping of a short, highly repeated interspersed DNA sequence from rice (Oryza sativa L.). Mol Gen Genet 231: 353–359 (1992).CrossRefPubMedGoogle Scholar
  53. 53.
    Zhao X, Kochert G: Phylogenetic distribution and genetic mapping of a (GGC) n microsatellite from rice (Oryza sativa L.) Plant Mol Biol 21: 607–614 (1993).PubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 1995

Authors and Affiliations

  • J. Becker
    • 1
  • M. Heun
    • 1
  1. 1.Max-Planck-Institut für ZüchtungsforschungKölnGermany

Personalised recommendations