Abstract
Preparation of large quantity and high-quality DNA is a major bottleneck for most genetic studies. Although a number of high-throughput methods are available, but degradation of genomic DNA is still one of the major constraints in many plant species. The present study is designed to evaluate the low-cost, high-throughput genomic DNA extraction method that yields high-quality DNA, which has consistency for SSRs amplification. Five different DNA isolation procedures from three different tissue sources were employed for efficient and easy recovery of high-purity DNA. It was evident that procedures 2 and 3 was more suitable to yield amplifiable DNA from any of the three tissue sources. Analysis of variance revealed that DNA extraction procedures have significant impact on DNA yield and DNA quality while tissue source was not found to impose any significant impact on both DNA yield and DNA quality. Effect of DNA quality on the efficiency of Taq polymerase and SSRs amplification revealed that procedures 2 and 3 was more suitable to yield amplifiable DNA from any of the three tissue sources. It is concluded that during PCR analysis, excessive magnesium amount results in accumulation of nonspecific PCR products, whereas insufficient magnesium results in reduced yield of the desired PCR product. However, template concentration had negligible effects on amplification while annealing temperatures had significant effects on PCR amplification as stringent annealing temperature, especially during the first several cycles, is necessary for proper amplification.
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References
Tautz, D.: Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17, 6463–6471 (1989)
Ellsworth, D.L.; Rittenhouse, D.; Honeycutt, R.L.: Artifactual variation in randomly amplified polymorphic DNA banding patterns. BioTech. 14, 214–217 (1993)
Pandey, R.N.; Adams, R.P.; Flournoy, L.E.: Inhibition of random amplified polymorphic DNAs (RAPDs) by plant polysaccharides. Plant Mol. Biol Rep. 14, 17–22 (1996)
Memon, A.A.; Memon, N.; Luthria, L.D.L.; Bhanger, M.L.; Pitafi, A.A.: Phenolic acids profiling and antioxidant potential of mulberry (Morus laeviagata., Morus nigra L., Morus alba L.) leaves and fruits grown in Pakistan. PJFNS 60(1), 25–32 (2010).
Xin, Z.; Chen, J.: A high throughput DNA extraction method with high yield and quality. Plant Method 8, 26 (2012)
Warude, D.; Preeti, C.; Joshi, K.; Patwardhan, B.: DNA isolation from fresh and dry plant samples with highly acidic tissue extracts. Plant Mol. Biol. Rep. 21, 467–467 (2003)
Dellaporta, S.L.; Wood, J.; Hicks, J.B.: A plant DNA minipreparation: version II. Plant Mol. Biol. Rep. 1(4), 19–21 (1983)
Moore, D.; Dowhan, D.: Preparation and analysis of DNA. In: Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A., Struhl, K. (eds.) Current Protocols in Molecular Biology, pp. 2.1.1–2.1.10. Wiley, New York (2002)
Kang, T.J.; Yang, M.S.: Rapid and reliable extraction of genomic DNA from various wild—type and transgenic plants. BMC Biotechnol. 4(20), 1–12 (2004)
Saghai-Maroof, M.A.; Soliman, K.M.; Jorgensen, R.A.; Allard, R.W.: Ribosomal DNA spacer-length polymorphism in barley: mendelian inheritance, chromosomal locations and population dynamics. P Natl. Acad. Sci. USA 81, 8014–8018 (1984)
Doyle, J.J.; Doyle, J.L.: Isolation of plant DNA from fresh tissue. Focus 12, 13–15 (1990)
Liu, W.; Biyashev, R.M.; Saghai-Maroof, M.A.: Development of simple sequence repeat DNA markers and their integration in to a barley linkage map. Theor. Appl. Genet. 93, 869–876 (1996)
Ramsay, L.; Macaulay, M.; Ivanissevich, S.D.; Maclean, K.; Cardle, L.; Fuller, J.; Edwards, K.J.; Tuvesson, S.; Morgante, M.; Massari, A.; Maestri, E.; Marmiroli, N.; Sjakste, T.; Ganal, M.; Powell, W.; Waugh, R.: A simple sequence repeat-based linkage map of barley. Genet 156, 1997–2005 (2000)
Macaulay, M.; Ramsay, L.; Powell, W.; Waugh, R.: A representative, highly informative’genotyping set’of barley SSRs. Theor. Appl. Genet. 102, 801–809 (2001)
Sharma, A.D.; Gill, P.K.; Singh, P.: DNA isolation from dry and fresh samples of polysaccharide-rich plants. Plant Mol. Biol. Rep. 20, 415–415 (2002)
Khanuja, S.P.S.; Shasany, A.K.; Darokar, M.P.; Kumar, S.: Rapid isolation of DNA for dry and fresh samples of plants producing large amounts of secondary metabolites and secondary essential oils. Plant Mol. Biol. Rep. 17, 1–7 (1999)
Innis, M.A.; Gelfand, D.H.: Optimization of PCR’s. In: Innis, M.A., Gelfend, D.H., Sninsky, J.J., White, T.J. (eds.) PCR Protocols: A Guide to Methods and Applications, pp. 3–12. Academic Press, New York (1990)
Rahman, M.H.; Jaquish, B.; Khasa, P.D.: Optimization of PCR protocol in microsatellite analysis with silver and SYBR® stains. Mol. Biol. Report. 18, 339–348 (2000)
Gelfand, D.H.: Taq DNA polymerase. In: Erlich, H.A. (ed.) PCR Technology: Principles and Applications for DNA Amplification, pp. 17–22. Stockton Press, New York (1989)
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Naeem, R., Mirza, B. High-Throughput DNA Extraction and Optimization of PCR Efficiency for Barley SSRs Genotyping. Arab J Sci Eng 43, 143–154 (2018). https://doi.org/10.1007/s13369-017-2749-y
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DOI: https://doi.org/10.1007/s13369-017-2749-y