Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD)

Summary

A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (“RAPD mapping”). We have now adapted the RAPD assay to tomato. Using a set of 11 oligonucleotide decamer primers, each primer directed the amplification of a genome-specific “fingerprint” of DNA fragments. The potential of the original RAPD assay to generate polymorphic DNA markers with a given set of primers was further increased by combining two primers in a single PCR. By comparing “fingerprints” of L. esculentum, L. pennellii, and the L. esculentum chromosome 6 substitution line LA1641, which carries chromosome 6 from L. pennellii, three chromosome 6-specific RAPD markers could be directly identified among the set of amplified DNA fragments. Their chromosomal position on the classical genetic map of tomato was subsequently established by restriction fragment length polymorphism (RFLP) linkage analysis. One of the RAPD markers was found to be tightly linked to the nematode resistance gene Mi.

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

References

  1. Beckmann JS, Soller M (1986) Restriction fragment length polymorphism in plant genetic improvement. In: Miflin BJ (ed) Oxford survey of plant molecular biology, vol 3. Oxford Press, Oxford, pp 196–250

  2. Beckmann JS, Soller M (1990) Toward a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellite sites. Biotechnology 8:930–932

  3. Bonierbale MW, Paisted RL, Tanksley SD (1988) RFLP maps based on a common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120:1095–1103

  4. Coe EH, Hoisington DA, Neuffer MG (1990) Linkage map of corn (maize) (Zea mays L.). In: O'Brien SJ (ed) Genetic maps, 5th edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/NY

  5. D'Ovido R, Tanzarella OA, Porceddu E (1990) Rapid and efficient detection of genetic polymorphism in wheat through amplification by polymerase chain reaction. Plant Mol Biol 15:169–171

  6. Feinberg AP, Vogelstein B (1984) A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 137:266–267

  7. Gebhardt C, Ritter E, Debener T, Schachtschabel U, Walkemeier B, Uhrig H, Salamini F (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor Appl Genet 78:65–75

  8. Hoelzel R (1990) The trouble with “PCR” machines. Trends Genet 6:237–238

  9. Innis MA, Gelfand DH, Sninsky JJ, White TJ (1990) PCR protocols. Academic Press, San Diego, pp 134–135

  10. Klein-Lankhorst RM, Rietveld P, Machiels B, Verkerk R, Weide R, Gebhardt C, Koornneef M, Zabel P (1991) RFLP markers linked to the root knot nematode resistance gene Mi in tomato. Theor Appl Genet 81:661–667

  11. Koornneef M, Zabel P (1990) A new look at old linkage data of chromosome 6. TGC Rep 40:17–19

  12. Landry BS, Kesseli RV, Farrara B, Michelmore RW (1987) A genetic map of lettuce (Lactuca sativa L.) with restriction fragment length polymorphism, isozyme, disease resistance and morphological markers. Genetics 116:331–337

  13. Love JM, Knight AM, McAleer MA, Todd JA (1990) Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellites. Nucleic Acids Res 18:4123–4130

  14. Maniatis T, Fritsch E, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/NY

  15. McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76:815–829

  16. Miller JC, Tanksley SD (1990) RFLP analysis of phylogenic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448

  17. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8:4321–4325

  18. Rick CM (1969) Controlled introgression of chromosomes of Solanum pennellii into Lycopersicon esculentum: segregation and recombination. Genetics 62:753–768

  19. Rick CM (1979) Biosystematic studies in Lycopersicon and closely related species of Solanum. In: Hawkes JC, Lester RN, Skelding AD (eds) The biology of the Solanaceae. Academic Press, New York, pp 1–27

  20. Slocum MK, Figdore SS, Kennard WC, Suzuki YJ, Osborn TC (1990) Linkage arrangement of restriction fragment length polymorphism loci in Brassica oleracea. Theor Appl Genet 80:57–64

  21. Tanksley SD, Mutschler MA, (1990) Linkage map of tomato (Lycopersicon esculentum). In: O'Brien SJ (ed) Genetic maps, 5th edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/NY

  22. Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Biotechnology 7:257–264

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

  24. Warnock SJ (1988) A review of taxonomy and phylogeny of the genus Lycopersicon. HortScience 23:669–673

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

  26. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic acids Res 18:6531–6535

Download references

Author information

Additional information

Communicated by J Beckmann

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Klein-Lankhorst, R.M., Vermunt, A., Weide, R. et al. Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD). Theoret. Appl. Genetics 83, 108–114 (1991). https://doi.org/10.1007/BF00229232

Download citation

Key words

  • Tomato
  • Genome fingerprinting
  • Polymerase chain reaction (PCR)
  • RFLP markers
  • Root knot nematode resistance