Skip to main content
Log in

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

  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Ali S, Muller CR, Epplen JT (1986) DNA fingerprinting by oligonuc-leotide probes specific for simple repeats. Hum Genet 74:239–248

    Google Scholar 

  • 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 84:345–354

    Google Scholar 

  • 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 83:691–694

    Google Scholar 

  • Buitkamp J, Kuhn C, Zischler H, Epplen JT, Geldermann H (1991) DNA fingerprinting in cattle using oligonucleotide probes. Anim Genet 12:169–174

    Google Scholar 

  • Dallas JF (1988) Detection of DNA “fingerprints” of cultivated rice by hybridization with a human minisatellite probe. Proc Natl Acad Sci USA 85:8631–6835

    Google Scholar 

  • 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 23:1–9

    Google Scholar 

  • Epplen JT (1988) On simple repetitive GATA/GACA sequences: a critical reappraisal. J Hered 79:409–417

    Google Scholar 

  • George M, Lequarre AS, Catelli M, Hanset R, Vassart G (1988) DNA fingerprinting in domestic animals using four different minisatellite probes. Cytogenet Cell Genet 47:127–131

    Google Scholar 

  • Goldshalk EB, Lee M, Lamkey KR (1990) Relationship of restriction fragment length polymorphisms to single cross hybrid performance of maize. Theor Appl Genet 80:273–280

    Google Scholar 

  • 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 22:299–305

    Google Scholar 

  • 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 124:783–789

    Google Scholar 

  • Jeffreys AJ, Wilson V, Thein SL (1985a) Hypervariable “minisatellite” regions in human DNA. Nature 314:67–73

    Google Scholar 

  • Jeffreys AJ, Wilson V, Thein SL (1985a) Individual specific “fingerprints” of human DNA. Nature 316:76–79

    CAS  PubMed  Google Scholar 

  • Jena KK, Khush GS (1990) Introgression of genes from Oryza officinalis Well Ex. Watt to cultivated rice, O. sativa L. Theor Appl Genet 80:737–745

    Google Scholar 

  • 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 18:1129–1132

    Google Scholar 

  • 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 82:57–64

    Google Scholar 

  • 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 29:1067–1071

    Google Scholar 

  • Nybom H, Hall HK (1991) Minisatellite DNA “fingerprints” can distinguish Rubus cultivars and estimate their degree of relatedness. Euphytica 53:107–114

    Google Scholar 

  • 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 79:153–156

    Google Scholar 

  • 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, Dordrecht

    Google Scholar 

  • Rogstad SH, Patton JC, Schaal BA (1988) M13 repeat probe detects DNA minisatellite like sequences in gymnosperms and angiosperms. Proc Natl Acad USA 85:9176–9178

    Google Scholar 

  • 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 233:388–392

    Google Scholar 

  • Schafer R, Zischler H, Birsner U, Becker A, Epplen JT (1988) Optimized oligonucleotide probes for DNA fingerprinting. Electrophoresis 9:369–374

    Google Scholar 

  • Tanskley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding — new tools for an old science. Bio/technology 7:257–264

    Google Scholar 

  • Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471

    CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Tsao SGS, Brunk CF, Pearlman RE (1983) Anal Biochem 131:365–372

    Google Scholar 

  • 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 89:10643–10647

    Google Scholar 

  • Vosman B, Avens P, Rus-Kortekaas W, Smulders MJM (1992) Identification of highly polymorphic DNA regions in tomato. Theor Appl Genet 85:239–244

    Google Scholar 

  • 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 12:159–169

    Google Scholar 

  • 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 35:436–442

    Google Scholar 

  • Wetton JH, Carter RE, Parkin DT, Walters D (1987) Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 327:147–149

    Article  CAS  PubMed  Google Scholar 

  • 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 83:903–911

    Google Scholar 

  • 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 82:227–233

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Additional information

Communicated by P. M. A. Tigerstedt

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ramakishana, W., Lagu, M.D., Gupta, V.S. et al. DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences. Theoret. Appl. Genetics 88, 402–406 (1994). https://doi.org/10.1007/BF00223651

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00223651

Key words

Navigation