High Quality and Purified DNA Extraction Protocol from Transplastomic Potato Lines by Cetyltrimethylammonium Bromide (CTAB)-Based Method
DOI:
https://doi.org/10.14719/tcb.3114Keywords:
CTAB, high quality DNA, non-toxic chemicals, cost effectiveAbstract
For the advanced molecular techniques high quality and pure DNA is important requirement where a quick and cost-effective extraction method is a crucial factor. Commonly, prolong incubation period, multiple precipitations, and highly expensive commercial kits are remaining basic barrier to introduce swift and easiest method of DNA extraction from transgenic plants. Non-cellulose components present in the leaf and elevated level of starch content as well as protein content also makes this extraction procedure challenging and difficult. Present study was conducted to establish a unique DNA isolation method with some modification of existing CTAB method to ensure high-quality and purified genomic DNA from the potato plants. Through the implementation of solution based and selective DNA precipitation method, 100 mg of potato leaves from every transplastomic potato lines was applied to extract genomic DNA. Ethanol (70%) was used as elution buffer where maximum DNA yield was 3415.500 ng/µl and the ranges of DNA purity (A260/A280 nm) was recorded as 1.954-2.048, respectively. Compared to existing methods, this modified CTAB mediated procedure is swift (at least one hour can be saved ) and proficient enough for high quality DNA yield, free from the selective precipitation, regents and laboratory equipment’s are cost-effective and non-toxic to human health.
Downloads
References
Doyle JJ and Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. DOI: 10.4236/ijoc.2019.92009
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X and Yu QB (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 135(3): 1198-1205. DOI: 10.1104/pp.103.038463
Feng D, Xia G, Zhao S and Chen F (2004) Two quality associated HMW glutenin subunits in a somatic hybrid line between Triticum aestivum and Agropyron elongatum. Theor. Appl. Genet. 110(1): 136-144. Doi: 10.1007/s00122-004-1810-x
Brandfass C & Karlovsky P (2006) Simultaneous detection of Fusarium culmorum and F. graminearum in plant material by duplex PCR with melting curve analysis. BMC Microbiol. 6. DOI: 10.1186/1471-2180-6-4
Foti N, Onori R, Donnarumma E, De Santis B and Miraglia M (2006) Real-time PCR multiplex method for the quantification of Roundup Ready soybean in raw material and processed food. Eur. Food Res. Technol. 222(1): 209-216. DOI: 10.1007/s00217-005-0107-x
Xu Q, Gao W, Ding SY, Kenig R, Shoham Y, Bayer, EA and Lamed R (2003) The cellulosome system of Acetivibrio cellulolyticus includes a novel type of adaptor protein and a cell surface anchoring protein. J. Bacteriol. Res. 185(15): 4548-4557. https://doi.org/10.1128/JB.185.15.4548-4557.2003
Thuan NTN, Bigirimana J, Roumen E, Van Der Straeten D and Höfte M (2006) Molecular and pathotype analysis of the rice blast fungus in North Vietnam. Eur. J. Plant Pathol. 114(4): 381-396. DOI 10.1007/s10658-006-0002-8
Appelbee AJ, Frederick LM, Heitman TL and Olson ME (2003) Prevalence and genotyping of Giardia duodenalis from beef calves in Alberta, Canada. Vet. Parasitol. 112(4): 289-294. Doi: 10.1016/s0304-4017(02)00422-3
Chiang YC, Hung KH, SCHAAL BA, Ge XJ, Hsu TW and Chiang TY (2006) Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex. Mol. Ecol. 15(3): 765-779. Doi: 10.1111/j.1365-294X.2005.02833.x.
Alonso JM and Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat. Rev. Genet. 7(7): 524-536. DOI:10.1038/nrg1893
He G Luo, X Tian, F Li, K Zhu, Z Su W, Qian X, Fu Y, Wang X, Sun C and Yang J (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res. 16(5) : 618-626. DOI: 10.1101/gr.4814006
Ye J, Ji A, Parra EJ, Zheng X, Jiang C, Zhao X, Hu L and Tu Z (2004) A simple and efficient method for extracting DNA from old and burned bone. J. Forensic Sci. 49(4): 1-6.
Sika KC, Kefela T, Adoukonou-Sagbadja H, Ahoton L, Saidou A, Baba-Moussa L, Baptiste LJ, Kotconi SO and Gachomo EW (2015) A simple and efficient genomic DNA extraction protocol for large scale genetic analyses of plant biological systems. Plant Gene. 1: 43-45. Doi.org/10.1016/j.plgene.2015.03.001
Hossain MJ, Aksoy E, Gökçe ZNÖ, Joiya FA, Khan MS and Bakhsh A (2021) Rapid and efficient in vitro regeneration of transplastomic potato (Solanum tuberosum L.) plants after particle bombardment. Turk J Agric For. 45(3) : 313-323. Doi:10.3906/tar-2010-103
Wilson K and Walker J (2010) Principles and techniques of biochemistry and molecular biology. Cambridge university press. https://doi.org/10.1017/CBO9780511841477
Black JA and Foarde KK (2007) Comparison of four different methods for extraction of Stachybotrys chartarum spore DNA and verification by real-time PCR. J. Microbiol. Methods, 70(1) : 75-81. Doi: 10.1016/j.mimet.2007.03.017
Peterson DG, Boehm KS and Stack SM (1997) Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), a plant containing high levels of polyphenolic compounds. Plant Mol. Biol. Rep. 15(2):148-153. DOI: 10.1007/BF02812265
Sahu SK, Thangaraj M and Kathiresan K (2012) DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. Int Sch Res Notices. Doi:10.5402/2012/205049
Moreira PA and Oliveira DA (2011) Leaf age affects the quality of DNA extracted from Dimorphandra mollis (Fabaceae), a tropical tree species from the Cerrado region of Brazil. Genet Mol Res. 10(1): 353-358. Doi: 10.4238/vol10-1gmr1030.
Khanuja SP, Shasany AK, Darokar MP and Kumar S (1999) Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Mol. Biol. Rep. 17(1) : 74-74. DOI:10.1023/A:1007528101452
Clark MS (2013) Plant molecular biology—a laboratory manual. Springer Science & Business Media.
Aljanabi SM, Forget L and Dookun A (1999) An improved and rapid protocol for the isolation of polysaccharide-and polyphenol-free sugarcane DNA. Plant Mol. Biol. Rep 17(3): 281-282. DOI:10.1023/A:1007692929505
Muhammad I, Zhang T, Wang Y, Zhang C, Qing M, Zhang L and Lin F (2013) Modification of CTAB protocol for maize. Res J Biotech. 8: 41-5.
Abdel-Latif A and Osman G (2017) Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13(1): 1-9. DOI 10.1186/s13007-016-0152-4
Sambrook J and David Russell (2001). Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, N.Y.
Saghai-Maroof MA, Soliman KM, Jorgensen RA and Allard RWL (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. PNAS. 81(24): 8014-8018. Doi: 10.1073/pnas.81.24.8014
Couch JA and Fritz PJ (1990) Isolation of DNA from plants high in polyphenolics. Plant Mol. Biol. Rep 8(1):8-12.
Chaudhry A Yasmeen T Husnain and S Riazuddin (1999) Mini-scale genomic DNA extraction from cotton. Plant Mol. Biol. Rep 17: 1–7.
Zhang J and Stewart JM (2000). Economical and rapid method for extracting cotton genomic DNA. J Cotton Sci. 4(3) 193-201.
Maliyakal JE (1992) An efficient method for isolation of RNA and DNA from plants. Nucleic Acids Res. Spec. Publ. 20: (9) : 2381https://doi.org/10.1093/nar/20.9.2381
Psifidi A, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G and Banos G (2015) Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PloS one, 10(1): 0115960. Doi: 10.1371/journal.pone.0115960.
Dauphin LA, Walker RE, Petersen JM and Bowen MD (2011) Comparative evaluation of automated and manual commercial DNA extraction methods for detection of Francisella tularensis DNA from suspensions and spiked swabs by real-time polymerase chain reaction. Diagn. Microbiol. Infect. Dis.70 (3): 299-306.
Wilson IG (1997) Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63(10): 3741-3751. Doi: 10.1128/aem.63.10.3741-3751.1997.
Salonen A, Nikkilä J, Jalanka-Tuovinen J, Immonen O, Rajili?-Stojanovi? M, Kekkonen R.A, Palva A and de Vos WM (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J. Microbiol. Methods. 81(2): 127-134. DOI: https://doi.org/10.1016/j.mimet.2010.02.007
Pervaiz ZH, Turi NA, Khaliq I, Rabbani MA and Malik SA (2011) Methodology: a modified method for high-quality DNA extraction for molecular analysis in cereal plants. Genet Mol Res. 10(3):1669-1673. Doi: 10.4238/vol10-3gmr1346
Osman, G., Munshi, A., Altf, F. and Mutawie, H., (2013). Genetic variation and relationships of Zea mays and Sorghum species using RAPD-PCR and. Afr. j. Biotechnol. 12(27). DOI: 10.5897/AJB12.2644
Weising K, Nybom H, Pfenninger M, Wolff K and Kahl G (2005) DNA fingerprinting in plants: principles, methods, and applications. CRC press. Doi: 10.1093/aob/mcj057
Porebski S, Bailey LG and Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol. Biol. Rep. 15(1): 8-15.
Weising K, Nybom H, Pfenninger M, Wolff K and Meyer W (1994) DNA fingerprinting in plants and fungi. CRC press.
Ribeiro RA and Lovato M.B (2007) Comparative analysis of different DNA extraction protocols in fresh and herbarium specimens of the genus Dalbergia. Genet. Mol. Res 6(1): 173-187.
Khan S, Qureshi MI, Alam T and Abdin MZ (2007) Protocol for isolation of genomic DNA from dry and fresh roots of medicinal plants suitable for RAPD and restriction digestion. Afr. j. Biotechnol. 6(3): 175-178. DOI:10.5897/AJB06.612
Vinod KK 2004. Total genomic DNA extraction, quality check and quantitation. Tamil Nadu Agricultural University, Coimbatore 1:109-121.
Heikrujam J, Kishor R. and Mazumder PB 2020. The Chemistry behind Plant DNA Isolation Protocols. Biochemical Analysis Tools: Methods for Bio-Molecules Studies 19:131-42
Hamblin MT 2009. Plant Genotyping II: SNP Technology.
Henry RJ 2008. Plant genotyping II: SNP technology. CABI.
Downloads
Published
Issue
Section
License
Copyright (c) 2024 Dr. Md. Jakir Hossain, Allah Bakhsh, Faiz Ahmad Joiya, Emre Aksoy, Neslihan Zahide Özturk Gökçe, Muhammad Sarwar Khan
This work is licensed under a Creative Commons Attribution 4.0 International License.
