Theoretical and Applied Genetics

, Volume 92, Issue 3–4, pp 326–333 | Cite as

Abundance and length polymorphism of microsatellite repeats in Beta vulgaris L.

  • M. Mörchen
  • J. Cuguen
  • G. Michaelis
  • C. Hänni
  • P. Saumitou-Laprade
Article

Abstract

Simple sequence repeats (SSRs) are known to exhibit high degrees of variability even among closely related individuals. Their usage as nuclear genetic markers requires their conversion into sequence-tagged sites (STSs). In this paper we present the development of simple sequences as STSs for Beta vulgaris. This species comprises wild, cultivated, and weedy forms; the latter are thought to originate from accidental hybridisation between the other two. Two partial genomic libraries were screened with simple sequence motifs (AT, CA, CT, ATT, GTG, and CA, CT, respectively). Clones of 22 CA, nine CT, eight ATT, and one GTG sequence were obtained. AT micro satellites were present in compound motifs, not recognised by the probe. Sequence comparisons revealed that 20 CA clones containing short motifs (<16 bp) were variants of a previously described approximately 320-bp satellite DNA (Schmidt et al. 1991), and hence did not correspond to unique loci. Polymorphism of one (ATT)15 and three (CT)n, with n=15, 17 and 26, was detected by PCR on a sample of 64 plants from the different forms of B. vulgaris. 13 (ATT), 13 (CT), nine (CT) alleles and one (CT) allele were detected. One of the ATT alleles was much larger than the others (>800 bp). Genetic variability was high among wild beets, lower among cultivated beets, and intermediate among weed beets. One allele of each locus was found at high frequencies in cultivated beets and, to a lower extent, in weed beets. The combination of three polymorphic loci allowed the individual identification of 17/17 wild and 15/15 weed beets, and 21/32, mostly homozygous, cultivated beets.

Key words

Beet VNTR Simple sequence length polymorphism Microsatellite Sequence-tagged sites 

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References

  1. Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1139PubMedGoogle Scholar
  2. Ali S, Müller CR, Epplen JT (1986) DNA finger printing by oligonucleotide probes specific for simple repeats. Hum Genet 74:239–243Google Scholar
  3. Allefs JJHM, Salentijn EMJ, Krenz FA, Rouwendal GJA (1990) Optimization of non-radioactive Southern-blot hybridization, single-copy detection and reuse of blots. Nucleic Acids Res 18:3099–3100Google Scholar
  4. Barzen E, Mechelke W, Ritter E, Seitzer JF, Salamini F (1992) RFLP markers for sugar beet breeding — chromosomal linkage maps and location of major genes for Rhizomania resistance, monogermy and hypocotyl color. The Plant Jour 2:601–611Google Scholar
  5. Barzen E, Mechelke W, Ritter E, Schultekappert E, Salamini F (1995) An extended map of the sugar beet genome containing RFLP and RAPD loci. Theor Appl Genet 90:189–193Google Scholar
  6. Beckmann JS, Weber JL (1992) Survey of human and rat microsatellites. Genomics 12:627–631PubMedGoogle Scholar
  7. Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144Google Scholar
  8. Boudry P, Mörchen M, Saumitou-Laprade P, Vernet P, Van Dijk H (1993) The origin and evolution of weed beets: consequences for the breeding and release of herbicide-resistant transgenic sugar beets. Theor Appl Genet 87:471–478Google Scholar
  9. Boudry P, Broomberg K, Saumitou-Laprade P, Mörchen M, Cuguen J, van Dijk H (1995) Gene escape in transgenic sugar beet: what can be learned from molecular studies of weed beet populations? In: Jones DD (ed) Proc 3rd Int Symp on the Biosafety Results of Field Tests of Genetically Modified Plants and Microorganisms. Montery, California (in press)Google Scholar
  10. Caskey C, Pizzuti A, Fu Y-H, Fenwick RG, Nelson DL (1992) Triplet repeat mutations in human disease. Science 256:784–789Google Scholar
  11. Condit R, Hubbell SP (1991) Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66–71Google Scholar
  12. Daly MJ, Lincoln SE, Lander ES (1991) PRIMER, Ver. 0.5. Whitehead Institute, MIT Center for Genome Research, Cambridge, MassachusettsGoogle Scholar
  13. Dellaporta SL, Wood VP, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21Google Scholar
  14. Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) “Touchdown” PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008Google Scholar
  15. Jeffreys AJ, Wilson V, Thein SL (1985) Hypervariable “minisatellite” regions in human DNA. Nature 314:67–73Google Scholar
  16. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res 21:1111–1115Google Scholar
  17. Levinson G, Gutman GA (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221PubMedGoogle Scholar
  18. Litt M, Luty JA (1989) A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet 44:397–401Google Scholar
  19. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. The Plant Jour 3:175–182Google Scholar
  20. Nakamura Y, Leppert M, O'Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, White R (1987) Variable number of tandem repeat (VNTR) markers for human genome mapping. Science 235:1616–1622Google Scholar
  21. Olson M, Hood L, Cantor D, Botstein D (1989) A common language for physical mapping of the human genome. Science 245:1434–1435Google Scholar
  22. Pillen K, Steinrücken G, Wricke G, Herrmann RG, Jung C (1992) A linkage map of sugar beet (Beta vulgaris). Theor Appl Genet 84:129–135Google Scholar
  23. Rohlf JF (1992) BIOM, a package of statistical programs to accompany the text Biometry. Applied Biostatistics Inc., Setauket, New YorkGoogle Scholar
  24. Rongwen J, Akkaya MS, Bhagwat AA, Lavi U, Cregan PB (1995) The use of microsatellite DNA markers for soybean genotype identification. Theor Appl Genet 90:43–48Google Scholar
  25. Saghai Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91:5466–5470PubMedGoogle Scholar
  26. Santoni S, Bervillé A (1992) Two different satellite DNAs in Beta vulgaris L.: evolution, quantification and distribution in the genus. Theor Appl Genet 84:1009–1016Google Scholar
  27. Schlötterer C, Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20:211–215Google Scholar
  28. Schmidt T, Jung C, Metzlaff M (1991) Distribution and evolution of two satellite DNAs in the genus Beta. Theor Appl Genet 82:793–799Google Scholar
  29. Schmidt T, Blobenz K, Metzlaff M, Kaemmer D, Weising K, Kahl G (1993) DNA fingerprinting in sugar beet (Beta vulgaris) — identification of double-haploid breeding lines. Theor Appl Genet 85:653–657Google Scholar
  30. Serikawa T, Kuramoto T, Hilbert P, Mori M, Yamada J, Dubay CJ, Lindpainter K, Ganten D, Guénet J-L, Lathrop GM, Beckmann J (1992) Rat gene mapping using PCR-analyzed microsatellites. Genetics 131:701–721Google Scholar
  31. Smith DN, Devey ME (1994) Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37:977–983Google Scholar
  32. Sokal RR, Rohlf J (1981) Biometry (2nd edn.). Freeman and Co, San FranciscoGoogle Scholar
  33. Tautz D (1989) Hypervariability of simple sequences as a source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedGoogle Scholar
  34. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138Google Scholar
  35. Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–990Google Scholar
  36. Wang Z, Weber JL, Zhong G, Tanksley SD (1994) Survey of plant short tandem DNA repeats. Theor Appl Genet 88:1–6Google Scholar
  37. Weber JL (1990) Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 7:524–530PubMedGoogle Scholar
  38. Weber JL, May PE (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet 44:388–396PubMedGoogle Scholar
  39. Weising K, Ramser J, Kaemmer D, Kahl G, Epplen JT (1991) Oligonucleotide fingerprinting in plants and fungi. In: Burke T, Dolf G, Jeffreys AJ, Wolff R (eds) DNA fingerprinting: approaches and applications. Birkhäuser Verlag, Basel, pp 312–328Google Scholar
  40. Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M (1992) A second-generation linkage map of the human genome. Nature 359:794–801Google Scholar
  41. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235PubMedGoogle Scholar
  42. Yang GP, Saghai Maroof GP, Xu CG, Zhang Q, Biyashev RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet 245:187–194PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1996

Authors and Affiliations

  • M. Mörchen
    • 1
  • J. Cuguen
    • 1
    • 2
  • G. Michaelis
    • 3
  • C. Hänni
    • 4
  • P. Saumitou-Laprade
    • 1
  1. 1.Laboratoire de Génétique et Evolution des Populations Végétales, URA-CNRS 1185, Bât. SN2Université de Lille 1Villeneuve d'Ascq CedexFrance
  2. 2.Institut Agricole et Alimentaire de LilleUniversité de Lille 1Villeneuve d'Ascq CedexFrance
  3. 3.Botanisches Institut der Heinrich-Heine Universität DüsseldorfUniversitätsstrasse 1DüsseldorfFederal Republic of Germany
  4. 4.Unité d'Oncologie Moléculaire, URA-CNRS 1160, Institut Pasteur de LilleLille CedexFrance

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