Hostname: page-component-78c5997874-g7gxr Total loading time: 0 Render date: 2024-11-12T06:28:40.989Z Has data issue: false hasContentIssue false
  • English
  • Français

The utility of aged seeds in DNA banks

Published online by Cambridge University Press:  22 February 2007

Christina Walters ,
Ann A. Reilley ,
Patrick A. Reeves ,
Jennifer Baszczak  and
Christopher M. Richards
Christina Walters*
Affiliation:
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO 80521, USA
Ann A. Reilley
Affiliation:
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO 80521, USA
Patrick A. Reeves
Affiliation:
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO 80521, USA
Jennifer Baszczak
Affiliation:
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO 80521, USA
Christopher M. Richards
Affiliation:
USDA-ARS National Center for Genetic Resources Preservation, Fort Collins, CO 80521, USA
*
*Correspondence: Fax: +1 970 221 1427, Email: Christina.Walters@ars.usda.gov
Get access Rights & Permissions [Opens in a new window]

Abstract

The long-term utility of DNA banks is predicated on the stability of DNA during storage. The quality and yield of DNA extracted from seeds from four garden species, which varied in age from 1 to 135 years old, was used to examine the early stages of DNA degradation. Seeds that were 70 years old yielded high molecular weight DNA, which permitted amplification of a 650 bp segment of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and a 487 bp segment of the plastid-encoded large subunit of rubisco (rbcL). DNA extracted from seeds estimated to be about 135 years old was degraded, but still permitted amplification when routine extraction procedures were used. The rbcL sequences obtained from c. 135-year-old cucurbit seed DNA were consistent with species identifications based on seed morphological features; however, ITS sequences from the same samples were determined to be of fungal origin. A comparison of our results with studies of DNA stability in leaf specimens suggested that DNA degraded within both tissues, but perhaps more slowly within seeds. Evidence that high-quality DNA can be extracted from old, non-viable seeds expands the utility of seed banks in preserving genetic resources.

Keywords

DNA banksgenetic resourcesITS sequencesribosomal DNArubiscoseed ageingseed DNA stability
Type
Research Article
Information
Seed Science Research , Volume 16 , Issue 3 , September 2006 , pp. 169 - 178
Copyright
Copyright © Cambridge University Press 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Allaby, R.G., Jones, M.K. and Brown, T.A. (1994) DNA in charred wheat grains from the Iron Age hillfort at Danebury, England. Antiquity 68, 126–132.CrossRefGoogle Scholar
Allaby, R.G., O'Donoghue, K., Sallares, R., Jones, M.K. and Brown, T.A. (1997) Evidence for the survival of ancient DNA in charred wheat seeds from European archaeological sites. Ancient Biomolecules 1, 119–129.Google Scholar
AOSA (Association of Official Seed Analysts) (2003) Rules for testing seeds. Sacramento, Association of Official Seed Analysts.Google Scholar
Austin, M.A., Ordovas, J.M., Eckfeldt, J.H., Tracy, R., Boerwinkle, E., Lalouel, J.M. and Printz, M. (1996) Guidelines of the National Heart, Lung, and Blood Institute Working Group on blood drawing, processing, and storage for genetic studies. American Journal of Epidemiology 144, 437–441.CrossRefGoogle Scholar
Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S. and Donoghue, M.J. (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82, 247–277.CrossRefGoogle Scholar
Blatter, R.H.E., Jacomet, S. and Schlumbaum, A. (2002) Spelt-specific alleles in HMW glutenin genes from modern and historical European spelt (Triticum spelta L.). Theoretical and Applied Genetics 104, 329–337.CrossRefGoogle ScholarPubMed
Britt, A.B. (1996) DNA damage and repair in plants. Annual Review of Plant Physiology and Plant Molecular Biology 47, 75–100.CrossRefGoogle ScholarPubMed
Brown, T.A. (1999) How ancient DNA may help in understanding the origin and spread of agriculture. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 354, 89–97.CrossRefGoogle Scholar
Cheah, K.S.E. and Osborne, D.J. (1978) DNA lesions occur with loss of viability in embryos of aging rye seed. Nature 272, 593–599.CrossRefGoogle ScholarPubMed
Cooper, A. and Poinar, H.N. (2000) Ancient DNA: Do it right or not at all. Science 289, 1139CrossRefGoogle ScholarPubMed
Dandoy, E., Schyns, R., Deltour, R. and Verly, W.G. (1987) Appearance and repair of apurinic/apyrimidinic sites in DNA during early germination of Zea mays. Mutation Research 181, 57–60.CrossRefGoogle Scholar
Deakin, W.J., Rowley-Conwy, P. and Shaw, C.H. (1998) Amplification and sequencing of DNA from preserved sorghum of up to 2800 years antiquity found at Qasr Ibrim. Ancient Biomolecules 1, 27–41.Google Scholar
De Castro, O. and Menale, B. (2004) PCR amplification of Michele Tenore's historical specimens and facility to utilize an alternative approach to resolve taxonomic problems. Taxon 53, 147–151.CrossRefGoogle Scholar
Drábková, L., Kirschner, J. and Vlcek, C. (2002) Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Molecular Biology Reporter 20, 161–175.CrossRefGoogle Scholar
Dumolin-Lapègue, S., Pemonge, M-H., Gielly, L., Taberlet, P. and Petit, R.J. (1999) Amplification of oak DNA from ancient and modern wood. Molecular Ecology 8, 2137–2140.CrossRefGoogle ScholarPubMed
Freitas, F.O., Bendel, G., Allaby, R.G. and Brown, T.A. (2003) DNA from primitive maize landraces and archaeological remains: implications for the domestication of maize and its expansion into South America. Journal of Archaeological Science 30, 901–908.CrossRefGoogle Scholar
Goloubinoff, P., Páábo, S. and Wilson, A.C. (1993) Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proceedings of the National Academy of Sciences, USA 90, 1997–2001.CrossRefGoogle ScholarPubMed
Gugerli, F., Parducci, L. and Petit, R.J. (2005) Ancient plant DNA: review and prospects. New Phytologist 166, 409–418.CrossRefGoogle ScholarPubMed
Halliwell, B. and Gutteridge, J.C. (1999) Free radicals in biology and medicine. New York, Oxford University Press.Google Scholar
Höss, M., Jaruga, P., Zastawny, T.H., Dizdaroglu, M. and Páábo, S. (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Research 24, 1304–1307.CrossRefGoogle ScholarPubMed
Jaenicke-Després, V., Buckler, E.S., Smith, B.D., Gilbert, M.T.P., Cooper, A., Doebley, J. and Páábo, S. (2003) Early allelic selection in maize as revealed by ancient DNA. Science 302, 1206–1208.CrossRefGoogle ScholarPubMed
Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709–715.CrossRefGoogle ScholarPubMed
Madisen, L., Hoar, D.I., Holroyd, C.D., Crisp, M. and Hodes, M.E. (1987) DNA banking: The effects of storage of blood and isolated DNA on the integrity of DNA. American Journal of Medical Genetics 27, 379–390.CrossRefGoogle ScholarPubMed
Manen, J.-F., Bouby, L., Dalnoki, O., Marinval, P., Turgay, M. and Schlumbaum, A. (2003) Microsatellites from archaeological Vitis vinifera seeds allow a tentative assignment of the geographical origin of ancient cultivars. Journal of Archaeological Science 30, 721–729.CrossRefGoogle Scholar
Maunder, M., Culham, A., Bordeu, A., Allainguillaume, J. and Wilkinson, M. (1999) Genetic diversity and pedigree for Sophora toromiro (Leguminosae): A tree extinct in the wild. Molecular Ecology 8, 725–738.CrossRefGoogle Scholar
Murata, M., Roos, E. and Tsuchiya, T. (1980) Mitotic delay in root tips of peas induced by artificial seed aging. Botanical Gazette 141, 19–23.CrossRefGoogle Scholar
O'Donoghue, K., Clapham, A., Evershed, R.P. and Brown, T.A. (1996) Remarkable preservation of biomolecules in ancient radish seeds. Proceedings of the Royal Society of London, Series B, Biological Sciences 263, 541–547.Google ScholarPubMed
Osborne, D.J., Boubriak, I. and Leprince, O. (2002) Rehydration of dried systems: Membranes and the nuclear genome. pp. 343–364. in Black, M.;, Pritchard, H.W. (Eds) Desiccation and survival in plants: Drying without dying. Wallingford, CABI Publishing.CrossRefGoogle Scholar
Páábo, S., Higuchi, R.G. and Wilson, A.C. (1989) Ancient DNA and the polymerase chain reaction. Journal of Biological Chemistry 264, 9709–9712.CrossRefGoogle ScholarPubMed
Páábo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L. and Hofreiter, M. (2004) Genetic analyses from ancient DNA. Annual Review of Genetics 38, 645–679.CrossRefGoogle ScholarPubMed
Peters, J. (2000) Tetrazolium testing handbook. Lincoln, Nebraska, Association of Official Seed Analysts.Google Scholar
Phillips, J.R., Oliver, M.J. and Bartels, D. (2002) Molecular genetics of desiccation and tolerant systems. pp. 319–342. in Black, M.;, Pritchard, H.W. (Eds) Desiccation and survival in plants: Drying without dying. Wallingford, CABI Publishing.CrossRefGoogle Scholar
Poinar, H.N., Hofreiter, M., Spaulding, W.G., Martin, P.S., Stakiewicz, B.A., Bland, H., Evershed, R.P., Possnert, G. and Páábo, S. (1998) Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281, 402–406.CrossRefGoogle ScholarPubMed
Pyle, M.M. and Adams, R.P. (1989) In situ preservation of DNA in plant specimens. Taxon 38, 576–581.CrossRefGoogle Scholar
Ristaino, J.B., Groves, C.T. and Parra, G.R. (2001) PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411, 695–697.CrossRefGoogle ScholarPubMed
Roberts, E.H. (1978) Mutations during seed storage. Acta Horticulturae 83, 279–282.CrossRefGoogle Scholar
Roberts, E.H. (1988) Seed aging: The genome and its expression. pp. 456–498. in Nooden, L.D.;, Leopold, A.C. (Eds) Senescence and aging in plants. New York, Academic Press.Google Scholar
Rogers, S.O. and Bendich, A.J. (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Molecular Biology 5, 69–76.CrossRefGoogle ScholarPubMed
Rollo, F., Venanzi, R.M. and Amici, A. (1991) Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize. Genetical Research 58, 193–201.CrossRefGoogle ScholarPubMed
Saltonstall, K. (2002) Cryptic invasion by a non-native genotype of the common reed, Phragmites australis into North America. Proceedings of the National Academy of Sciences, USA 99, 2445–2449.CrossRefGoogle ScholarPubMed
Savolainen, V. and Reeves, G. (2004) A plea for DNA banking. Science 304, 1445CrossRefGoogle ScholarPubMed
Savolainen, V., Cuénoud, P., Spichiger, R., Martinez, M.D.P., Crévecoeur, M. and Manen, J.F. (1995) The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Systematics and Evolution 197, 87–89.CrossRefGoogle Scholar
Shearer, L. (2001) Sowing the seeds of history. Athens Daily News 37, 85 1Google Scholar
Shirkey, B., McMaster, N.J., Smith, S.C., Wright, D.J., Rodiguez, H., Jaruga, P., Birincioglu, M., Helm, R.F. and Potts, M. (2003) Genomic DNA of Nostoc commune (Cyanobacteria) becomes covalently modified during long-term (decades) desiccation but is protected from oxidative damage and degradation. Nucleic Acids Research 31, 2995–3005.CrossRefGoogle ScholarPubMed
Taylor, J.W. and Swann, E.C. (1994) DNA from herbarium specimens. pp. 166–181. in Herrmann, B.;, Hummell, S. (Eds) Ancient DNA. New York, Springer-Verlag.CrossRefGoogle Scholar
Threadgold, J. and Brown, T.A. (2003) Degradation of DNA in artificially charred wheat seeds. Journal of Archaeological Science 30, 1067–1076.CrossRefGoogle Scholar
Vasan, S., Zhand, X., Zhang, X., Kapurniotu, A., Bernhagen, J., Teichberg, S., Basgen, J., Wagle, D., Shih, D., Terlecky, I., Bucala, R., Cerami, A., Egan, J. and Ulrich, P. (1996) An agent cleaving glucose-derived protein crosslinks in vitro and in vivo. Nature 382, 275–278.CrossRefGoogle ScholarPubMed
Walters, C., Wheeler, L.M. and Grotenhuis, J.M. (2005) Longevity of seeds stored in a genebank: species characteristics. Seed Science Research 15, 1–20.CrossRefGoogle Scholar
Whittle, C.A., Beardmore, T. and Johnston, M.O. (2001) Is G1 arrest in plant seeds induced by a p53-related pathway?. Trends in Plant Science 6, 248–251.CrossRefGoogle ScholarPubMed