Advertisement

Ancient DNA pp 71-79 | Cite as

Ancient DNA Extraction from Plants

  • Logan KistlerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 840)

Abstract

A variety of protocols for DNA extraction from archaeological and paleobotanical plant specimens have been proposed. This is not surprising given the range of taxa and tissue types that may be preserved and the variety of conditions in which that preservation may take place. Commercially available DNA extraction kits can be used to recover ancient plant DNA, but modifications to standard approaches are often necessary to improve yield. In this chapter, I describe two protocols for extracting DNA from small amounts of ancient plant tissue. The CTAB protocol, which I recommend for use with single seeds, utilizes an incubation period in extraction buffer and subsequent chloroform extraction followed by DNA purification and suspension. The PTB protocol, which I recommend for use with gourd rind and similar tissues, utilizes an overnight incubation of pulverized tissue in extraction buffer, removal of the tissue by centrifugation, and DNA extraction from the buffer using commercial plant DNA extraction kits.

Key words

Ancient DNA Plant DNA DNA extraction CTAB extraction PTB extraction 

References

  1. 1.
    Schlumbaum A, Tensen M, Jaenicke-Despres V (2008) Ancient plant DNA in archaeobotany. Veg Hist Archaeobot 17(2):233–244CrossRefGoogle Scholar
  2. 2.
    Gugerli F, Parducci L, Petit RJ (2005) Ancient plant DNA: review and prospects. New Phytol 166:409–418PubMedCrossRefGoogle Scholar
  3. 3.
    Jaenicke-Deprés V et al (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302:1206–1208CrossRefGoogle Scholar
  4. 4.
    Erickson DL et al (2005) An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proc Natl Acad Sci USA 102(51):18315–18320PubMedCrossRefGoogle Scholar
  5. 5.
    Parducci L et al (2005) Ancient DNA from pollen: a genetic record of population history in Scots pine. Mol Ecol 14:2873–2882PubMedCrossRefGoogle Scholar
  6. 6.
    Gould BA et al (2010) Evidence of a high-Andean, mid-Holocene plant community: an ancient DNA analysis of glacially preserved remains. Am J Bot 97(9):1579–1584PubMedCrossRefGoogle Scholar
  7. 7.
    Pollmann B, Jacomet S, Schlumbaum A (2005) Morphological and genetic studies of waterlogged Prunus species from the Roman vicus Tasgetium (Eschenz, Switzerland). J Archaeol Sci 32:1471–1480CrossRefGoogle Scholar
  8. 8.
    Schlumbaum A, Neuhaus JM, Jacomet S (1998) Coexistence of tetraploid and hexaploid naked wheat in a Neolithic lake dwelling of Central Europe. Evidence from morphology and ancient DNA. J Archaeol Sci 25:1111–1118CrossRefGoogle Scholar
  9. 9.
    Brown TA et al (1994) DNA in wheat seeds from European archaeological sites. Cell Mol Life Sci 50(6):571–575CrossRefGoogle Scholar
  10. 10.
    Cappelini E et al (2010) A multidisciplinary study of archaeological grape seeds. Naturwissenschaften 97:205–217CrossRefGoogle Scholar
  11. 11.
    Manen JF et al (2003) Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. J Archaeol Sci 30:721–729CrossRefGoogle Scholar
  12. 12.
    Li C et al (2011) Ancient DNA analysis of desiccated wheat grains excavated from a Bronze Age cemetery in Xinjiang. J Archaeol Sci 38:115–119CrossRefGoogle Scholar
  13. 13.
    Szabó Z et al (2005) Genetic variation of melon (C. melo) compared to an extinct landrace from the Middle Ages (Hungary). I. rDNA, SSR and SNP analysis of 47 cultivars. Euphytica 146:87–94CrossRefGoogle Scholar
  14. 14.
    Kistler L, Shapiro B (2011) Ancient DNA confirms a local origin of domesticated chenopod in Eastern North America. J Archaeol Sci 38(12):3549–3554CrossRefGoogle Scholar
  15. 15.
    Smith BD, Yarnell RA (2009) Initial formation of an indigenous crop complex in eastern North America at 3800 B.P. Proc Natl Acad Sci USA 106:6561–6566PubMedCrossRefGoogle Scholar
  16. 16.
    Dumolin-Lapegue S (1999) Amplification of oak DNA from ancient and modern wood. Mol Ecol 8:2137–2140PubMedCrossRefGoogle Scholar
  17. 17.
    Deguilloux MF et al (2006) Genetic analysis of archaeological wood remains: first results and prospects. J Archaeol Sci 33:1216–1227CrossRefGoogle Scholar
  18. 18.
    Liepelt S et al (2006) Authenticated DNA from ancient wood remains. Ann Bot 98:1107–1111PubMedCrossRefGoogle Scholar
  19. 19.
    Suyama Y, Gunnarsson U, Parducci L (2008) Analysis of short DNA fragments from Holocene peatmoss samples. Holocene 18:1003–1006CrossRefGoogle Scholar
  20. 20.
    Raniello R, Procaccini G (2002) Ancient DNA in the seagrass Posidonia oceanica. Mar Ecol Prog Ser 227:269–273CrossRefGoogle Scholar
  21. 21.
    Bennett KD, Parducci L (2006) DNA from pollen: principles and potential. Holocene 16:1031–1034CrossRefGoogle Scholar
  22. 22.
    Hansson MC, Foley BP (2008) Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck. J Archaeol Sci 35:1169–1176CrossRefGoogle Scholar
  23. 23.
    Elbaum R et al (2009) New methods to isolate organic materials from silicified phytoliths reveal fragmented glycoproteins but no DNA. Quat Int 193:11–19CrossRefGoogle Scholar
  24. 24.
    Elbaum R et al (2006) Ancient olive DNA in pits: preservation, amplification and sequence analysis. J Archaeol Sci 33:77–88CrossRefGoogle Scholar
  25. 25.
    Russo EB et al (2008) Phytochemical and genetic analyses of ancient cannabis from Central Asia. J Exp Bot 59(15):4171–4182PubMedCrossRefGoogle Scholar
  26. 26.
    Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  27. 27.
    Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5:69–76CrossRefGoogle Scholar
  28. 28.
    Kalisz (2008) CTAB DNA Extraction Protocol. Univ. Pitt. http://www.pitt.edu/∼kalisz/Protocols.html. Accessed 29 November 2010.
  29. 29.
    Poinar HN et al (1998) Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281(402):402–406PubMedCrossRefGoogle Scholar
  30. 30.
    Rohland N, Hofreiter M (2007) Ancient DNA extraction from bones and teeth. Nat Protoc 2(7):1756–1762PubMedCrossRefGoogle Scholar
  31. 31.
    Poinar HN (2002) The genetic secrets some fossils hold. Acc Chem Res 35(8):676–684PubMedCrossRefGoogle Scholar
  32. 32.
    Asif MJ, Cannon CH (2005) DNA extraction from processed wood: a case study for the identification of an endangered timber species (Gonystylus bancanus). Plant Mol Biol Rep 23:185–192CrossRefGoogle Scholar
  33. 33.
    Rachmayanti Y et al (2006) Extraction, amplification and characterization of wood DNA from Dipterocarpaceae. Plant Mol Biol Rep 24:45–55CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkUSA

Personalised recommendations