Advertisement

Russian Journal of Genetics

, Volume 54, Issue 5, pp 576–586 | Cite as

Comparison of Some Plant DNA Extraction Methods

  • V. A. Scobeyeva
  • D. O. Omelchenko
  • L. M. Dyakov
  • A. S. Konovalov
  • A. S. Speranskaya
  • A. A. Krinitsina
Methods

Abstract

DNA isolation is a routine procedure when performed in laboratory environment, yet in the field it may still remain problematic. This is especially true of some crop species bred for useful metabolites that may also hinder DNA extraction. Here we compare the efficiency of DNA extraction protocols and commercial DNA isolation kits when used on samples from Helianthus and Allium. Since extraction of DNA is known to be compromised by co-extraction of PCR-inhibiting metabolites, the isolation of DNA was followed by PCR as a testing procedure for the isolation step. The MagnoPrime Fact and MagnoPrime Uni DNA isolation kits were better suited for field work due to faster processing times and smaller required amount of starting material (20 mg fresh/0.5 mg dry). In all cases the subsequent PCR managed to amplify the DNA fragments of interest well enough to be useful in further research.

Keywords

DNA isolation PCR Helianthus annuus Allium field conditions 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Quick, J., Loman, N.J., Duraffour, S., et al., Realtime, portable genome sequencing for Ebola surveillance, Nature, 2016, vol. 530, no. 7589, pp. 228–232. doi 10.1038/nature16996CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Johnson, S.S., Zaikova, E., Goerlitz, D.S., et al., Realtime DNA sequencing in the Antarctic dry valleys using the Oxford Nanopore Sequencer, J. Biomol. Tech., 2017, vol. 28, no. 1, pp. 2–7. doi 10.7171/jbt.17-2801-009PubMedPubMedCentralGoogle Scholar
  3. 3.
    Brown, B.L., Watson, M., Minot, S.S., et al., MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach, Gigascience, 2017, vol. 6, no. 1, pp. 1–10. doi 10.1093/gigascience/gix007CrossRefGoogle Scholar
  4. 4.
    Parker, J., Helmstetter, A.J., Devey, D., et al., Fieldbased species identification of closely related plants using real-time nanopore sequencing, Sci. Rep., 2017, vol. 7, p. 8345.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Wilson, I.G., Inhibition and facilitation of nucleic acid amplification, Appl. Environ. Microbiol., 1997, vol. 63, no. 10, pp. 3741–3751.PubMedPubMedCentralGoogle Scholar
  6. 6.
    Demeke, T. and Jenkins, G.R., Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnologyderived traits, Anal. Bioanal. Chem., 2010, vol. 396, pp. 1977–1990. doi 10.1007/s00216-009-3150-9PubMedGoogle Scholar
  7. 7.
    Perez-Vich, B., Fernandez-Martinez, J.M., Grondona, M., et al., Stearoyl-ACP and oleoyl-PC desaturase genes cosegregate with quantitative trait loci underlying high stearic and high oleic acid mutant phenotypes in sunflower, Theor. Appl. Genet., 2002, vol. 104, nos. 2-3, pp. 338–349.CrossRefPubMedGoogle Scholar
  8. 8.
    Al-Chaarani, R.G., Gentzbittel, L., Huang, X.Q., and Sarrafi, A., Genotypic variation and identification of QTLs for agronomic traits, using AFLP and SSR markers in RILs of sunflower (Helianthus annuus L.), Theor. Appl. Genet., 2004, vol. 109, no. 7, pp. 1353–1360.CrossRefPubMedGoogle Scholar
  9. 9.
    Burke, J.M., Knapp, S.J., and Rieseberg, L.H., Genetic consequences of selection during the evolution of cultivated sunflower, Genetics, 2005, vol. 171, pp. 1933–1940.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Ebrahimi, A., Maury, P., Berger, M., et al., QTL mapping of seed-quality traits in sunflower recombinant inbred lines under different water regimes, Genome, 2008, vol. 51, no. 8, pp. 599–615.CrossRefPubMedGoogle Scholar
  11. 11.
    Premnath, A., Narayana, M., Ramakrishnan, C., et al., Mapping quantitative trait loci controlling oil content, oleic acid and linoleic acid content in sunflower (Helianthus annuus L.), Mol. Breed., 2016, vol. 36, p. 106. https://doi.org/. doi 10.1007/s11032-016-0527-2.CrossRefGoogle Scholar
  12. 12.
    Horne, E.C., Kumpatla, S.P., Patterson, K.A., et al., Improved high throughput sunflower and cotton genomic DNA extraction and PCR fidelity, Plant Mol. Biol. Rep., 2004, vol. 22, no. 1, pp. 83–84.CrossRefGoogle Scholar
  13. 13.
    Brewster, J.L., Onion and Other Cultivated Alliums, CAB International, 2008.CrossRefGoogle Scholar
  14. 14.
    Ranjan, S., Kishore, G., Jadon, V.S., et al., Standardization of extraction of genomic DNA and PCR-RFLP conditions of Allium stracheyi: a high altitude plant, Acad. Arena, 2010, vol. 2, no. 7, pp. 11–14.Google Scholar
  15. 15.
    Li, J., Yang, J., Chen, D., et al., An optimized minipreparation method to obtain high quality genomic DNA from mature leaves of sunflower, Genet. Mol. Res., 2007, vol. 6, no. 4, pp. 1064–1071.PubMedGoogle Scholar
  16. 16.
    Zeinalzadehtabrizi, H., Hosseinpour, A., Aydin, M., and Haliloglu, K., A modified genomic DNA extraction method from leaves of sunflower for PCR based analyzes, J. Biodiv. Environ. Sci., 2015, vol. 7, no. 6, pp. 222–225.Google Scholar
  17. 17.
    Guetat, A, Boulila, N, Messaoud, C., et al., A simple, rapid and efficient method for the extraction of genomic DNA from Allium roseum L. (Alliaceae), Afr. J. Biotechnol., 2009, vol. 8, no. 17, pp. 4020–4024.Google Scholar
  18. 18.
    Doyle, J.J. and Doyle, J.L., A rapid DNA isolation procedure for small quantities of fresh leaf tissue, Phytochem. Bull., 1987, vol. 19, pp. 11–15.Google Scholar
  19. 19.
    Liu, Q., Li, J., Liu, H., et al., Rapid, cost-effective DNA quantification via a visually-detectable aggregation of superparamagnetic silica-magnetite nanoparticles, Nano Res., 2014, vol. 7, no. 5, pp. 755–764.CrossRefGoogle Scholar
  20. 20.
    Psifidi, A., Dovas, C.I., Bramis, G., et al., Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and longterm DNA banking using blood samples, PLoS One, 2015, vol. 10, no. 1. e0115960. doi 10.1371/journal. pone.0115960CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    White, T.J., Bruns, T., Lee, S., and Taylor, J., Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, in PCR Protocols: A Guide to Methods and Applications, San Diego: Academic Press, 1990, pp. 315–322.Google Scholar
  22. 22.
    Li, Y., Gao, L.-M., Poudel, R.C., et al., High universality of matK primers for barcoding gymnosperms, J. Syst. Evol., 2011, vol. 49, no. 3, pp. 169–175.CrossRefGoogle Scholar
  23. 23.
    Fulton, T.M., Chunzoongse, J., and Tanksley, S.D., Microprep protocol for extraction of DNA from tomato and other herbaceous plants, Plant Mol. Biol. Rep., 1995, vol. 13, no. 3, pp. 207–209.CrossRefGoogle Scholar
  24. 24.
    Narzary, D., Verma, S., Mahar, K.S., and Rana, T.S., A rapid and effective method for isolation of genomic DNA from small amount of silica-dried leaf tissues, Natl. Acad. Sci. Lett., 2015, vol. 38, no. 5, pp. 441–444.CrossRefGoogle Scholar
  25. 25.
    Deragon, J.M. and Landry, B.S., RAPD and other PCR-based analyses of plant genomes using DNA extracted from small leaf disks, Genome Res., 1992, vol. 1, pp. 175–180.CrossRefGoogle Scholar
  26. 26.
    Cheung, W.Y., Hubert, N., and Landry, B.S., A simple and rapid DNA microextraction method for plant, animal, and insect suitable for RAPD and other PCR analyses, Genome Res., 1993, vol. 3, pp. 69–70.CrossRefGoogle Scholar
  27. 27.
    Khanuja, S.P.S., Shasany, A.K., Darokar, M.P., and Kumar, S., Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils, Plant Mol. Biol. Rep., 1999, vol. 17, pp. 1–7.CrossRefGoogle Scholar
  28. 28.
    Mukherjee, A., Sikdar, B., Ghosh, B., et al., RAPD and ISSR analysis of some economically important species, varieties, and cultivars of the genus Allium (Alliaceae), Turk. J. Bot., 2013, vol. 37, pp. 605–618.Google Scholar
  29. 29.
    Li, H., Li, J., Cong, X.H., et al., A high-throughput, high-quality plant genomic DNA extraction protocol, Genet. Mol. Res., 2013, vol. 12, no. 4, pp. 4526–4539.CrossRefPubMedGoogle Scholar
  30. 30.
    Schmiderer, C., Lukas, B., and Novak, J., Effect of different DNA extraction methods and DNA dilutions on the amplification success in the PCR of different medicinal and aromatic plants, J. Med. Spice Plants, 2013, vol. 18, no. 2, pp. 65–72.Google Scholar

Copyright information

© Pleiades Publishing, Inc. 2018

Authors and Affiliations

  • V. A. Scobeyeva
    • 1
  • D. O. Omelchenko
    • 2
  • L. M. Dyakov
    • 2
  • A. S. Konovalov
    • 3
  • A. S. Speranskaya
    • 1
  • A. A. Krinitsina
    • 1
  1. 1.Department of Biological Evolution, Department of Higher PlantsMoscow State UniversityMoscowRussia
  2. 2.Medical Institute, Center for Biotechnological and Bioinformatics Studies in MedicinePeople’s Friendship University of RussiaMoscowRussia
  3. 3.NextBio Ltd.MoscowRussia

Personalised recommendations