Skip to main content
SpringerLink
Log in

Randomly Amplified Polymorphic DNA (RAPD)

A Useful Tool for Genomic Characterization of Different Organisms

  • Protocol
Molecular Biomethods Handbook

Part of the book series: Springer Protocols Handbooks ((SPH))

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Williams JG, Kubelik AR, Livak KJ, Rafalsky JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful genetic markers. Nucleic Acids Res 18:6531–6535

    Article  PubMed  CAS  Google Scholar 

  2. Caetano-Anolles G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 9: 553–557

    Article  PubMed  CAS  Google Scholar 

  3. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218

    Article  PubMed  CAS  Google Scholar 

  4. Rafalski JA, Tingey SV, William JGK (1991) RAPD markers – a new technology for genetic mapping and plant breeding. AgBiotech News Inform 3:645–648

    Google Scholar 

  5. Steindel M, Dias-Neto E, Menezes CLP, Romanha AJ, Simpson AJG (1993) Random amplified polymorphic DNA analysis of Trypanosoma cruzi strains. Mol Biochem Parasitol 60:71–80

    Article  PubMed  CAS  Google Scholar 

  6. Zingales B, Pereira MES, Almeida KA, Umezawa ES, Nehme NS, Oliveira RP, Macedo A, Souto RP (1997) Biological parameters and molecular markers of clone CL Brener – the reference organism of the Trypanosoma cruzi genome project. Mem Inst Oswaldo Cruz 92:811–814

    Article  PubMed  CAS  Google Scholar 

  7. Riedy MF, Hamilton III WJ, Aquadro CF (1992) Excess of non-parental bands in offspring from known primate pedigrees assayed using RAPD PCR. Nucleic Acids Res 20:918

    Article  PubMed  CAS  Google Scholar 

  8. Ellsworth DL, Rittenhouse KD, Honeycut RL (1993) Artifactual variation in randomly amplified polymorphic DNA banding patterns. BioTechniques 14: 214–217

    PubMed  CAS  Google Scholar 

  9. Parar I, Kesseli R, Michelmore R (1991) Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near-isogeniclines. Genome 34: 1021–1027

    Google Scholar 

  10. Macedo AM, Melo MN, Gomes R, Pena SDJ (1992) DNA fingerprints: a tool for identification and determination of the relationships between species and strains of Leishmania. Mol Biochem Parasitol 53:63–70

    Article  PubMed  CAS  Google Scholar 

  11. Theodorakis CW, Bickham JW (2004) Molecular characterization of contaminantindicativ e RAPE markers. Ecotoxicology 13:303–309

    Article  PubMed  CAS  Google Scholar 

  12. Black WC 4TH (1993) PCR with arbitrary primers: approach with care. Insect Mol Biol 2:1–6

    Article  PubMed  CAS  Google Scholar 

  13. Tibayrenc M, Neubauer K, Barnabé C, Guerrini F, Skarecky D, Ayala FJ (1993) Genetic characterization of six parasitic protozoa: parity between random-primer DNA typing and multilocus enzyme electrophoresis. Proc Natl Acad Sci USA 90: 1335–1339

    Article  PubMed  CAS  Google Scholar 

  14. Singh B (1997) Molecular methods for diagnosis and epidemiological studies of parasitic infections. Int J Parasitol 27:1135–1145

    Article  PubMed  CAS  Google Scholar 

  15. Jaramilo C, Montana MF, Castro LR, Vallejo GA, Guhl F (2001) Differentiation and genetic analysis of Rhodnius prolixus and Rhodnius colombiensis by rDNA and RAPD amplification. Mem Inst Oswaldo Cruz 96:1043–1048

    Article  Google Scholar 

  16. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

    Google Scholar 

  17. Macedo AM, Martins MS, Chiari E, Pena SDJ (1992) DNA fingerprinting of Trypanosoma cruzi: a new tool for characterization of strains and clones. Mol Biochem Parasitol 55:147–154

    Article  PubMed  CAS  Google Scholar 

  18. Araújo WL, Angelis DA, Azevedo JL (2004) Direct RAPD evaluation of bacteria without conventional DNA extraction. Braz Arch Biol Technol 47:375–380

    Article  Google Scholar 

  19. Dias-Neto E, Steindel M, Passos LK, Souza CP, Rollinson D, Katz N, Romanha AJ, Pena SD, Simpson AJ (1993) The usse of RAPDs for the study of the genetic diversity of Schistosoma mansoni and Trypanosoma cruzi. EXS 67:339–345

    PubMed  CAS  Google Scholar 

  20. Bosseno MF, Barnabé C, Magallón-Gastélum E, Kasten FL, Ramsey J, Espinoza B, Brenière SF (2002) Predominance of Trypanosoma cruzi lineage I in Mexico. J Clin Microbiol 40:627–632

    Article  PubMed  Google Scholar 

  21. Meunier JR, Grimont PAD (1993) Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. Res Microbiol 144:373–379

    Article  PubMed  CAS  Google Scholar 

  22. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669

    PubMed  CAS  Google Scholar 

  23. Lodhi MA, Weeden NF, Reisch BI (1997) Characterization of RAPD markers in Vitis. Vitis 36:133–140

    Google Scholar 

  24. Masumi Y, Hiromi A, Michiharu N, Akira N (2002) PCR-based molecular markers in Asiatic hybrid lily. Sci Horticult 1831:1–10

    Google Scholar 

  25. Welsh J, McClelland M (1991) Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Res 19: 5275–5279

    Article  PubMed  CAS  Google Scholar 

  26. Muralidharan K, Wakeland EK (1993) Concentration of primer and template qualitatively affects products in random-amplified polymorphic DNA PCR. BioTechniques 14:362–364

    PubMed  CAS  Google Scholar 

  27. Schierwater B, Ender A (1993) Different thermostable DNA polymerases may amplify different RAPD products. Nucleic Acids Res 21:4647–4648

    Article  PubMed  CAS  Google Scholar 

  28. Oury B, Jamonneau V, Tibayrenc M, Truc P (2004) Characterization of Trypanosoma brucei gambiense isolated from humans by RAPD fingerprinting in Côte d'Ivoire: another evidence for multiple infections. J Biotechnol 3:94–98

    CAS  Google Scholar 

  29. Paran I, Kesseli R, Michelmore R (1991) Identification of restriction-fragment-length-polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near isogenic lines. Genome 34: 1021–1027

    PubMed  CAS  Google Scholar 

  30. Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaudoise Sci Nat 44:223–270

    Google Scholar 

  31. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  32. Barnabe C, Brisse S, Tibayrenc M (2003) Phylogenetic diversity of bat trypanosomes of subgenus Schizotrypanum based on multilocus enzyme eletrophoresis, random amplified polymorphic DNA, and cytochrome b nucleotide sequence analyses. Infect Genet Evol 2:201–208

    Article  PubMed  CAS  Google Scholar 

  33. Felsenstein J (1993) Phylogeny interference package (PHYLIP). 3.5c. Seattle: distributed by the author. Department of Genetics, University of Washington

    Google Scholar 

  34. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357,358

    PubMed  CAS  Google Scholar 

  35. Felsenstein J (1985) Confidence limitson phylogenies: an approach utilizing the bootstrap. Evolution 39: 783–791

    Article  Google Scholar 

  36. Bardakci F. (2001) Random amplified polymorphic DNA (RAPD) markers. Turk J Biol 25: 185–196

    CAS  Google Scholar 

  37. Williams JG, Hanafey MK, Rafalski JA, Tingey SV (1993) Genetic analysis using random amplified polymorphic DNA markers. Methods Enzymol 218: 704–740

    Article  PubMed  CAS  Google Scholar 

  38. Paran I, Michelmore RW (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet 85:985–993

    Article  CAS  Google Scholar 

  39. Baird E, Cooper-Bland S, Waugh R, DeMaine M, Powell W (1992) Molecular characterization of inter- and intra-specific somatic hybrids of potato using randomly amplified polymorphic DNA (RAPD) markers. Mol Gen Genet 233: 469–475

    Article  PubMed  CAS  Google Scholar 

  40. Martin GB, Williams JGK, Tanksley SD (1991) Rapid identification of markers linked to a Pseudomonas resistance gene in tomato by using random primers and near-isogenic lines. Proc Natl Acad Sci USA 88:2336–2340

    Article  PubMed  CAS  Google Scholar 

  41. Hadrys H, Balick M, Schierwater B (1992) Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Mol Ecol 1:55–63

    Article  PubMed  CAS  Google Scholar 

  42. Gaunt MW, Yeo M, Frame IA, Stothard JR, Carrasco HJ, Taylor MC, Mena SS, Veazey P, Miles GAJ, Acosta N, Arias AR, Miles MA (2003) Mechanism of genetic exchange in American trypanosomes. Nature 421:936–939

    Article  PubMed  CAS  Google Scholar 

  43. Maravilla P, Souza V, Valera A, Romerp-Valdovinos M, Lopex-Vidal Y, Dominguez-Alpizar JL, Ambrosio J, Kawa S, Flisser A (2003) Detection of genetic variation in Taenia solium. J Parasitol 89:1250–1254

    Article  PubMed  CAS  Google Scholar 

  44. Campbell G, Garcia HH, Nakao M, Ito A, Craig PS (2006) Genetic variation in Taenia solium. Parasitol Int 55:S121–S126

    Article  PubMed  CAS  Google Scholar 

  45. Snipes LJ, Gamard PM, Narcisi EM, Beard CB, Lehmann T, Secor WE (2000) Molecular epidemiology of metronidazole resistance in a population of Trichomonas vaginalis clinical isolates. J Clin Microbiol 38:3004–3009

    PubMed  CAS  Google Scholar 

  46. Hampl J, Vanacova S, Kulda J, Flegr J (2001) Concordance between genetic relatedness and phenotypic similarities of Trichomonas vaginalis. BMC Evol Biol 48: 1–11

    Google Scholar 

  47. Rojas L, Fraga J, Sariego I (2004) Genetic variability between Trichomonas vaginalis isolates and correlation with clinical presentation. Infect Genet Evol 4: 53–58

    Article  PubMed  CAS  Google Scholar 

  48. Steindel M, Dias-Neto E, Pinto CJ, Grisard E, Menezes CLP, Murta SMF, Simpson AJG, Romanha AJ (1994) Random amplified polymorphic DNA (RAPD) and isoenzyme analysis of Trypanosoma rangeli strains. J Euk Microbiol 41:261–267

    Article  PubMed  CAS  Google Scholar 

  49. Souto RP, Fernandes O, Macedo AM, Campbell D, Zingales B (1996) DNA markers define two major phylogenetic lineages of Trypanosoma cruzi. Mol Biochem Parasitol 83:141–152

    Article  PubMed  CAS  Google Scholar 

  50. Fernandes CD, Murta SMF, Ceràvolo IP, Krug LP, Vidigal PG, Steindel M, Nardi N, Romanha AJ (1997) Characterization of Trypanosoma cruzi isolated from chronic chagasic patients, triatomines and opossums naturally infected from state of Rio Grande do Sul, Brazil. Mem Inst Oswaldo Cruz 92:343–351

    Article  PubMed  CAS  Google Scholar 

  51. Brisse S, Barnabé C, Tibayrenc M (2000) Identification of six Trypanosoma cruzi phylogenetic lineages by random amplified polymorphic DNA and multilocus enzyme electrophoresis. Int J Parasitol 30:35–44

    Article  PubMed  CAS  Google Scholar 

  52. Murta SMF, Gazzinelli RT, Brener Z, Romanha AJ (1998) Molecular characterization of susceptible and naturally resistant strains of Trypanosoma cruzi to benznidazole and nifurtimox. Mol Biochem Parasitol 93:203–214

    Article  PubMed  CAS  Google Scholar 

  53. Tibayrenc M (1995) Population genetics of parasitic protozoa and other microorganisms. Adv Parasitol 36:48–115

    Google Scholar 

  54. D'Ávila DA, Gontijo ED, Lages-Silva E, Meira WSF, Chiari E, Galvão LMC (2006) Random amplified polymorphic DNA profiles of Trypanosoma cruzi isolates from chagasic patients with different clinical forms. Parasitol Res 98: 455–461

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Departamento de Parasitologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil

    Lúcia Maria da Cunha Galvão

  2. Departamento de Ciências Biológicas, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil

    Eliane Lages-Silva

Authors
  1. Lúcia Maria da Cunha Galvão
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eliane Lages-Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. School of Life Sciences, University of Hertfordshire, Hatfield, Hertfordshire, UK

    John M. Walker (Professor Emeritus) & Ralph Rapley (Professor Emeritus) & 

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Humana Press, a part of Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Galvão, L.M.C., Lages-Silva, E. (2008). Randomly Amplified Polymorphic DNA (RAPD). In: Walker, J.M., Rapley, R. (eds) Molecular Biomethods Handbook. Springer Protocols Handbooks. Humana Press. https://doi.org/10.1007/978-1-60327-375-6_10

Download citation

  • DOI: https://doi.org/10.1007/978-1-60327-375-6_10

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-370-1

  • Online ISBN: 978-1-60327-375-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation