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Plant Molecular Biology Reporter

, Volume 24, Issue 1, pp 45–55 | Cite as

Extraction, amplification and characterization of wood DNA from dipterocarpaceae

  • Yanti Rachmayanti
  • Ludger Leinemann
  • Oliver Gailing
  • Reiner Finkeldey
Commentary

Abstract

A successful DNA extraction from wood yielding appropriate DNA quality for PCR amplification allows molecular genetic investigations of wood tissue. Genotypes, the origin of sampled material, and species can be identified based on an investigation of wood if suitable information on genetic variation patterns within and among species is available. Potential applications are in forensics and in the control of the timber and wood trade. We extracted DNA from wood of Dipterocarpaceae, a family that dominates rainforests and comprises many important timber species in Southeast Asia. Several different DNA isolation techniques were compared and optimized for wood samples from natural populations and from wood processing enterprises. The quality of the DNA was tested by spectrophotometry, PCR amplification, and PCR inhibitor tests. An average DNA yield of 2.2 μg was obtained per 50–100 mg of dried wood sample. Chloroplast DNA (cpDNA) regions of different length were amenable to PCR amplification from the extracted DNA. Modification of DNA isolation techniques by the addition of polyvinylpyrrolidone (PVP) addition up to 3.1% into lysis buffer reduced PCR inhibition effectively. In order to evaluate the extraction method, we analyzed leaves and wood from the same tree by PCR amplification, genotyping and sequencing of chloroplast microsatellites.

Key words

chloroplast microsatellites Dipterocarpaceae DNA extraction genotyping PCR amplification PCR inhibitor PVP sequencing wood 

Abbreviations

ccmp

consensus chloroplast microsatelline primer

cpDNA

chloroplast DNA

cpSSR

chloroplast simple sequence repeat

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References

  1. Appanah S and Turnbull JM (1998) A review of dipterocarps, taxonomy, ecology and silviculture. CIFOR, Bogor, Indonesia.Google Scholar
  2. Bär W, Kratzer A, Mächler M, and Schmid W (1988) Postmortem instability of DNA. Forensic Sci Int 39: 59–70.PubMedCrossRefGoogle Scholar
  3. Cao CP (2006) Genetic variation of the genusShorea (Dipterocarpaceae) in Indonesia. http://webdoc.sub.gwdg.de/diss/2006/cao/cao.pdf. Electronic Dissertations of the Georg-August university of Goettingen. Goettingen.Google Scholar
  4. Deguilloux MF, Pemonge MH, and Petit RJ (2002) Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proc R Soc London 269: 1039–1046.CrossRefGoogle Scholar
  5. Dumolin-Lapègue S, Pemonge MH, Gielly L, Taberlet P, and Petit RJ (1999) Amplification of aok DNA from ancient and modern wood. Mol Ecol 8: 2137–2140.PubMedCrossRefGoogle Scholar
  6. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95–98.Google Scholar
  7. Hummel S (2003) Ancient DNA typing. Methods, strategies and applications, pp 104–105. Springer, Heidelberg.Google Scholar
  8. Indrioko S (2005) Chloroplast DNA variation in Indonesian Dipterocarpaceae-phylogenetic, taxonomic and population genetic aspects, pp 31–35. Cuvilier Verlag, Göttingen.Google Scholar
  9. Ito T, Akao Y, Yi H, Ohguchi K, Matsumoto K, Tanaka T, Iinuma M, and Nozawa Y (2003) Antitumor effect of resveratrol oligomers against human cancer cell lines and the molecular mechanism of apoptosis induced by vaticanol C. Carcinogenesis 24: 1489–1497.PubMedCrossRefGoogle Scholar
  10. Kamiya K, Harada K, Tachida H, and Ashton PS (2005) Phylogeny ofpigC gene inShorea and its closely related genera (Dipterocarpaceae), the dominant trees in southeast Asian tropical rain forests. Am J Bot 92: 33–46.CrossRefGoogle Scholar
  11. Khanuja SPS, Shasany AK, Darokar MP, and Kumar S (1999) Rapid isolation of DNA from dry and fresh samples of plants producing large amount of secondary metabolites and essential oils. Plant Mol Biol Rep 17: 1–7.CrossRefGoogle Scholar
  12. Lamprecht H (1986) Waldbau in den Tropen. Parey, Hamburg, Berlin.Google Scholar
  13. Latruffe N, Delmas D, Jannin B, Malki MC, Passilly-Degrace P, and Berlot JP (2002) Molecular analysis on the chemopreventive properties of resveratrol, a plant polyphenol microcomponent. Int J Mol Med 10: 755–760.PubMedGoogle Scholar
  14. Lee AB and Cooper TA (1995) Improved direct PCR screen for bacterial colonies: wooden toothpicks inhibit PCR amplification. Biotechniques 18: 225–226.PubMedGoogle Scholar
  15. Lindhal T (1993) Instability and decay of the primary structure of DNA. Nature 362: 709–715.CrossRefGoogle Scholar
  16. Sambrook J, Fritsch EF, and Maniatis T (1989) Molecular cloning. A laboratory manual. 2nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.Google Scholar
  17. Sun NJ, Woo SH, Cassady JM, and Snapka RM (1998) DNA polymerase and topoisomerase II inhibitors fromPsorelea corylifolia. J Nat Prod 61: 362–366.PubMedCrossRefGoogle Scholar
  18. Taberlet P, Gielly L, Pautou G, and Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105–1109.PubMedCrossRefGoogle Scholar
  19. Tanaka T, Ito T, Ido Y, Nakaya K, Iinuma M, and Chelladurai V (2001) Hopeafuran and a C-glucosyl resveratrol isolated from stem wood ofHopea utilis. Chem Pharm Bull 49: 785–787.PubMedCrossRefGoogle Scholar
  20. Thompson JD, Higgins DG, and Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucleic Acids Res 33: 4673–4680.CrossRefGoogle Scholar
  21. Weising K, Nybom H, Wolff K, and Meyer W (1995) DNA isolation and purification. In: DNA fingerprinting in plants and fungi, pp. 44–59. CRC Press, Boca Raton, Florida.Google Scholar
  22. Weising K and Gardner RC (1999) A set of conserved primers for the analysis of simple sequence repeat polymorphisms in chloroplast genomes of dicotyledonous angiosperms. Genome 42: 9–19.PubMedCrossRefGoogle Scholar
  23. Whitmore TC (1975) Tropical rain forest of the far east. Clarendon Press, Oxford.Google Scholar
  24. Wood Density Database, World Agroforestry Centre http://www.worldagroforestry.org/sea/products/afdbases/wd/index.htm.Google Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Yanti Rachmayanti
    • 1
  • Ludger Leinemann
    • 1
  • Oliver Gailing
    • 1
  • Reiner Finkeldey
    • 1
  1. 1.Institute of Forest Genetics and Forest Tree BreedingGeorg-August-Universität GöttingenGöttingenGermany

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