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Theoretical and Applied Genetics

, Volume 88, Issue 3–4, pp 402–406 | Cite as

DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences

  • W. Ramakishana
  • M. D. Lagu
  • V. S. Gupta
  • P. K. Ranjekar
Article

Abstract

In this report we describe the use of five oligonucleotide probes, namely (GATA)4, (GACA)4, (GGAT)4, (GAA)6 and (CAC)5, to reveal highly polymorphic DNA regions in rice. With each of the oligonucleotide probes, the level of polymorphism was high enough to distinguish several rice genotypes. Moreover, individual plants of one cultivar showed the same cultivar-specific DNA fingerprint. The multilocus fingerprint patterns were somatically stable. Our study demonstrates that microsatellite-derived DNA fingerprints are ideally suited for the identification of rice genotypes. As the majority of the probes detected a high level of polymorphism, they can be very useful in monitoring and aiding gene introgression from wild rice into cultivars.

Key words

DNA fingerprinting Genotype identification Oligo probes Rice 

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References

  1. Ali S, Muller CR, Epplen JT (1986) DNA fingerprinting by oligonuc-leotide probes specific for simple repeats. Hum Genet 74:239–248Google Scholar
  2. Amante-Bordeos A, Sitch LA, Nelson R, Dalmacio RD, Oliva NP, Aswidinnoor H, Leung H (1992) Transfer of bacterial blight and blast resistance from Oryza minuta to cultivated rice, Oryza sativa. Theor Appl Genet 84:345–354Google Scholar
  3. Beyermann B, Nurnberg P, Weihe A, Meixner M, Epplen JT, Borner T (1992) Fingerprinting plant genomes with oligonucleotide probes specific for simple repetitive DNA sequences. Theor Appl Genet 83:691–694Google Scholar
  4. Buitkamp J, Kuhn C, Zischler H, Epplen JT, Geldermann H (1991) DNA fingerprinting in cattle using oligonucleotide probes. Anim Genet 12:169–174Google Scholar
  5. Dallas JF (1988) Detection of DNA “fingerprints” of cultivated rice by hybridization with a human minisatellite probe. Proc Natl Acad Sci USA 85:8631–6835Google Scholar
  6. Ellegren H, Andersson L, Johansson M, Sandberg K (1992) DNA fingerprinting using a simple (TG)n probe and its application to population comparisons. Anim Genet 23:1–9Google Scholar
  7. Epplen JT (1988) On simple repetitive GATA/GACA sequences: a critical reappraisal. J Hered 79:409–417Google Scholar
  8. George M, Lequarre AS, Catelli M, Hanset R, Vassart G (1988) DNA fingerprinting in domestic animals using four different minisatellite probes. Cytogenet Cell Genet 47:127–131Google Scholar
  9. Goldshalk EB, Lee M, Lamkey KR (1990) Relationship of restriction fragment length polymorphisms to single cross hybrid performance of maize. Theor Appl Genet 80:273–280Google Scholar
  10. Haberfeld A, Cahaner A, Yoffe O, Plotsky Y, Hillel J (1991) DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes. Anim Genet 22:299–305Google Scholar
  11. Hillel J, Schaap T, Haberfeld A, Jeffreys AJ, Plotzky Y, Cahaner A, Lavi U (1990) DNA fingerprints applied to gene introgression in breeding programs. Genetics 124:783–789Google Scholar
  12. Jeffreys AJ, Wilson V, Thein SL (1985a) Hypervariable “minisatellite” regions in human DNA. Nature 314:67–73Google Scholar
  13. Jeffreys AJ, Wilson V, Thein SL (1985a) Individual specific “fingerprints” of human DNA. Nature 316:76–79PubMedGoogle Scholar
  14. Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Well Ex. Watt to cultivated rice, O. sativa L. Theor Appl Genet 80:737–745Google Scholar
  15. Kashi Y, Tikochinsky Y, Genislav E, Traqi F, Nave A, Beckmann JS, Gruenbaum Y, Soller M (1990) Large restriction fragments containing poly-TG are highly polymorphic in a variety of vertebrates. Nucleic Acids Res 18:1129–1132Google Scholar
  16. Kochko AD, Keifer MC, Cordesse F, Reddy AS, Delseny M (1991) Distribution and organization of a 352-bp tandem repeat in Oryzae family. Theor Appl Genet 82:57–64Google Scholar
  17. Lee M, Godshalk EB, Lamkey KR, Woodman WW (1989) Association of restriction fragment length polymorphisms among maize inbreds with agronomic performance of their crosses. Crop Sci 29:1067–1071Google Scholar
  18. Nybom H, Hall HK (1991) Minisatellite DNA “fingerprints” can distinguish Rubus cultivars and estimate their degree of relatedness. Euphytica 53:107–114Google Scholar
  19. Nybom H, Rogstad SH, Schaal BA (1990) Genetic variation detected by use of M13 “DNA fingerprint” probe in Malus, Prunus, and Rubus (Rosaceae). Theor Appl Genet 79:153–156Google Scholar
  20. Rogers SO, Bendich AJ (1988) Extraction of DNA from plant tissues. In: Gelvin SB, Schilperoort RA (eds) Plant molecular biology manual A6:1. Kluwer Academic Publishers, DordrechtGoogle Scholar
  21. Rogstad SH, Patton JC, Schaal BA (1988) M13 repeat probe detects DNA minisatellite like sequences in gymnosperms and angiosperms. Proc Natl Acad USA 85:9176–9178Google Scholar
  22. Ryskov AP, Jincharadze AG, Prosnayak MT, Tvanov PL, Limborska SA (1988) M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants and microorganisms. FEBS Lett 233:388–392Google Scholar
  23. Schafer R, Zischler H, Birsner U, Becker A, Epplen JT (1988) Optimized oligonucleotide probes for DNA fingerprinting. Electrophoresis 9:369–374Google Scholar
  24. Tanskley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding — new tools for an old science. Bio/technology 7:257–264Google Scholar
  25. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedGoogle Scholar
  26. Tautz D, Trick M, Dover GA (1986) Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652–656Google Scholar
  27. Tsao SGS, Brunk CF, Pearlman RE (1983) Anal Biochem 131:365–372Google Scholar
  28. Turner BC, Elder JF, Laughlin TF, Davis WP, Taylor DS (1992) Extreme clonal diversity and divergence in populations of a selfing hermaphroditic fish. Proc Natl Acad Sci USA 89:10643–10647Google Scholar
  29. Vosman B, Avens P, Rus-Kortekaas W, Smulders MJM (1992) Identification of highly polymorphic DNA regions in tomato. Theor Appl Genet 85:239–244Google Scholar
  30. Weising K, Beyermann B, Ramser J, Kahl G (1991) Plant DNA fingerprinting with radioactive and digoxy geneted oligonucleotide probes complementary to simple repectitive DNA sequences. Electrophoresis 12:159–169Google Scholar
  31. Weising K, Kaemmer D, Weigand F, Epplen JT, Kahl G (1992) Oligonucleotide fingerprinting reveals various probe dependent levels of informativeness in chick pea (Cicer arietinum). Genome 35:436–442Google Scholar
  32. Wetton JH, Carter RE, Parkin DT, Walters D (1987) Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 327:147–149CrossRefPubMedGoogle Scholar
  33. Zehr BE, Dudley JW, Chojecki J, Saghai Maroof MA, Mowers RP (1992) Use of RFLP markers to search for alleles in a maize population for improvement of an elite hybrid. Theor Appl Genet 83:903–911Google Scholar
  34. Zischler H, Nanda T, Schafer R, Schmid M, Epplen JT (1989) Digoxygenated oligonucleotide probes specific for simple repeats in DNA fingerprinting and hybridization in situ. Hum Genet 82:227–233Google Scholar

Copyright information

© Springer-Verlag 1994

Authors and Affiliations

  • W. Ramakishana
    • 1
  • M. D. Lagu
    • 1
  • V. S. Gupta
    • 1
  • P. K. Ranjekar
    • 1
  1. 1.Plant Molecular Biology Unit, Division of Biochemical SciencesNational Chemical LaboratoryPuneIndia

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