Forthcoming

Comparison of DNA extraction methods from Halocnemum strabilaceum (Amaranthaceae)

Authors

  • Abolfazl Tahmasebi Department of Range and Watershed Management, Faculty of Agriculture and Natural Resources, Gonbad Kavous University, Gonbad, Iran
  • Fatemeh Nasrollahi Department of Biology, Faculty of Sciences, University of Qom, Qom, Iran

DOI:

https://doi.org/10.5281/zenodo.6498963

Keywords:

Agarose Gel Electrophoresis, CTAB, PCR, Nano-Drop, plant tissue

Abstract

Molecular techniques such as DNA extraction and DNA sequencing are playing an important role in studying the genetic makeup of the plant and identifying the evolutionary relationship using DNA barcoding. Extraction of DNA from plant tissue is often problematic, as many plants contain high levels of secondary metabolites that can interfere with downstream applications, such as PCR. Removal of these secondary metabolites usually requires further purification of the DNA using organic solvents or other toxic substances. In this study, we have focused on the DNA isolation process using three isolation techniques: the cetyl trimethyl ammonium bromide (CTAB) method that uses the ionic detergent hexadecyltrimethyl ammonium bromide and chloroformisoamyl alcohol, BioFACT, and GeneAll methods on desert/rangeland plant including Halocnemum. Quantity and quality of extracted genomic DNAs were compared by employing the spectrophotometer, Nano-Drop, agarose gel electrophoresis, polymerase chain reaction (PCR) methods, and molecular markers such as ISSR. Our results showed that the modified method of CTAB provided the best results than the BioFACT and GeneAll methods for extracting DNA from tissues of Halocnemum. We present a safe and cost-efficient DNA purification procedure and recommend using this CTAB method to extract DNA from plant tissues and to use the young leaf for the highest DNA yields.

References

Abdel-Latif, A. & Osman, G. (2017). Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods, 23(1), 13-19

Allen, G.C., Flores-Vergara, M.A., Krasynanski, S., Kumar, S., & Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Protocol, 21(3),1-19

Assadi, M. (2001). Chenopodiaceae. – Pp. 27-65 in: Assadi, M., Maassoumi, A. A. & Khatamsaz, M. (ed.), Flora of Iran 38. – Tehran.

Brondmann, P. (2008). DNA extraction from different matrices. Molecular Biology Methods for Traceability Purposes, BfR Berlin, Germany, pp. 18–19.

Chen, S.L., Yao, H., Han, J.P., Liu, C., Song, J.Y., Shi, L.C., Zhu, Y.J., Ma, X.Y., Gao, T., Pang, X.H., Luo, K., Li, Y., Li, X.W., Jia, X. C., Lin, Y.L. & Leon, C. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLos One, 76(2), 8-13.

Cheng, T., Xu, C., Lei, L., Li, C., Zhang, Y. & Zhou, S. (2016). Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity. Molecular Ecology Resources, 16(3), 138–49.

Cullings, K.W. (1992). Design and testing of a plant-specific PCR primer for ecological and evolutionary studies. Molecular Ecology, 1(3), 233-240.

Dabo, S.M., Mitchell, E.D. & Melcher, U. (1993). A method for the isolation of nuclear DNA from Cotton (Gossypium) leaves. Analytical Biochemistry, 210(1), 34–38.

Doyle, J.J. & Doyle, J.L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin,19(2), 11–15.

Doyle, J.J. & Dickson, E.E. (1987). Preservation of plant samples for DNA restriction endonuclease analysis. Taxon, 36(1),715–722.

Gaudeul, M. & Rouhan, G. (2013). A plea for modern botanical collections to include DNA-friendly material. Trends in Plant Science, 18 (1), 184–185.

Hosseini, S.A. & Shahmoradi, A.A. (2011). Autecology of Halocnemum strobilaceum (Pall.) M. Bieb. in Saline and Alkaline Rangelands of Golestan Province. Journal on Plant Science Researches, 22 (6), 18-30.

Lade, B.D., Patil, A.S. & Paikrao, H.M. (2014). Efficient genomic DNA extraction method from medicinal rich passiflora foetida containing a high level of polysaccharide and polyphenol. SpringerPlus, 3(1), 1–7.

Lagisz, M., Port, G. & Wolff, K. (2010). A cost-effective, simple and high-throughput method for DNA extraction from insects. Insect Science, 17(2), 465–470.

Loomis, W.D. (1974). Overcoming problems of phenolics and quinones in the isolation of plant enzymes and organelles. Methods in Enzymology, 31(3), 528-545.

Murray, M. G. & Thompson, W. F. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8 (1), 4321–4325.

Moritz, C. & Cicero, C. (2004). DNA Barcoding: Promise and Pitfalls. PLOS Biology, 10(2), 35-45.

Moyo, M., Amoo, S.O., Bairu, M.W., Finnie, J.F. & Van Staden, J. (2008). Optimising DNA isolation for medicinal plants. South African Journal of Botany, 74(4), 771–775.

Nasrollahi, F., Kazempour-Osaloo, Sh., Saadati, N., Mozaffarian, V. & Zare-Maivan, H. (2019). Molecular phylogeny and divergence times of Onosma (Boraginaceae s.s.) based on nrDNA ITS and plastid rpl32-trnL(UAG) and trnH–psbA sequences. Nordic Journal Of Botany, 37 (1), 1-12.

Saghai-Maroof, M. A., Soliman, K. M., Jorgensen, R. A. & Allard, R. W. (1984): Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81: 8014–8018.

Sahu, S.K., Thangaraj, M. & Kathiresan, K. (2012). DNA Extraction Protocol for Plants with High Levels of Secondary Metabolites and Polysaccharides without Using Liquid Nitrogen and Phenol. International Scholarly Research Network molecular biology, 11(2), 1–6.

Shaw, J., Lickey, E.B., Schilling, E.E. & Small, R.L. (2007). Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany, 94(2), 275–288.

Shokatyari, S., Faghir, M.B., Kazempour Osaloo, Sh. & Sohani, M.M. (2020). Optimized DNA extraction and purification method from Alchemilla species using polyethylene glycol. Rostaniha, 21(2), 218–230.

Tahmasebi, A. & Nasrollahi, F. (2021). Morphologic and genetic study of Halocnemum strobilaceum in rangeland ecosystems of Golestan province (north of Iran). Rostaniha, 22(1), 134- 146.

Talebi-Baddaf, M., Sharifi-Neia, B. & Bahar, M. (2003). Analysis of genetic diversity in pomegranate cultivars of Iran, using random amplified polymorphic DNA (RAPD) markers. Proceeds., Third National Congress of Biotechnology, Iran, pp. 343–345.

Tamari, F., Hinkley, C.S &, Ramprashad, N. (2010). A Comparison of DNA Extraction Methods using Petunia hybrida Tissues. Journal of Biomolecular Techniques, 24(1),113-118.

Toranjzar, H. & Fathi, A. (2006). Study of the Morphometric Characteristics of Halocnemum strobilaceum Nebkhas Type in Mighan Playa (Arak). The Desert Ecosystem Engineering Journa. 4 (9), 35-42.

Weishing, K., Nybom, H., Wolff, K. & Meyer, W. (1995). DNA Isolation and Purification. Pp. 44–59. In: DNA Fingerprinting in Plants and Fungi. CRC Press, Boca Raton, Florida, USA.

White, T.J., Bruns, T., Les, S. & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. – In: Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J. (eds): PCR protocols: a guide to methods and application. Academic Press, San Diego, pp. 315–322.

Wilmington, D.E. (2008). NanoDrop 1000 Spectrophotometer V3.7 User’s Manual. Thermo Fisher Scientific Inc. :105 pp.

Downloads

Published

2022-04-01

How to Cite

Tahmasebi, A. ., & Nasrollahi, F. . (2022). Comparison of DNA extraction methods from Halocnemum strabilaceum (Amaranthaceae). Journal of Wildlife and Biodiversity, 6(X). https://doi.org/10.5281/zenodo.6498963

Issue

Section

Original Article