Standardization of DNA Extraction Method from Mature Dried Leaves and ISSR-PCR Conditions for <i>Melia dubia</i> Cav. —A Fast Growing Multipurpose Tree Species — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Standardization of DNA Extraction Method from Mature Dried Leaves and ISSR-PCR Conditions for <i>Melia dubia</i> Cav. —A Fast Growing Multipurpose Tree Species
Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
,
Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
,
Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
,
Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
,
Department of Crop Physiology, University of Agricultural Sciences GKVK, Bengaluru, India
1 Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
2 Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
3 Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
4 Tree Improvement and Genetics Division, Institute of Wood Science and Technology, Bengaluru, India
5 Department of Crop Physiology, University of Agricultural Sciences GKVK, Bengaluru, India
Melia dubia Cav. of family Meliaceae is a fast growing, high value tree species native to India. Isolating DNA from matured dried leaves of M. dubia was difficult due to accumulation of secondary metabolites, majorly polyphenolics, which resulted in dark brown to black colour of the pellet. In this study, a modified STE-(Sucrose, Tris-HCl and Ethylene Diamine Tetra Acetic Acid) CTAB (hexadecyltrimethylammonium bromide) method was standardized for removal of polyphenolics. The protocol developed yielded 200 - 1000 ng/μl of quality DNA without any impurities as evident by A260/280 ratio ranging from 1.75 - 2.0. It was also suitable for extracting quality DNA from other members of Meliaceae like Azadirachta indica and Melia azedarach . In downstream applications, the extracted DNA was used for PCR amplification by using ISSR and SSR markers. ISSR PCR conditions were optimized in a reaction volume of 25 μl, consisting of 30 ng of template DNA, 1.5 mM MgCl 2 , 200 μM of each of dNTPs and 2 U of Taq polymerase. The best amplification was observed and the same was applicable for SSR markers.
Anon (1966) The Wealth of India. Raw Materials, Vol. VI. L-M, CSIR, Delhi.
Parthiban, K.T., Bharathi, A.K., Seenivasan, R., Kamala, K. and Rao, M.G. (2009) Integrating Melia dubia in Agroforestry Farms as an Alternate Pulpwood Species. Asia Pacific Agroforestry Newsletter, 34, 3-4.
Vijayan, P., Raghu, C., Ashok, G., Dhanaraj, S.A. and Suresh, B. (2004) Antiviral Activity of Medicinal Plants of Nilgiris. Indian Journal of Medical Research, 120, 24-29.
Nagalakshmi, M.A.H., Thangadurai, D. and Pullaiah, T. (2003) In Vitro Antimicrobial Efficacy of Leaf Essential Oils of Chukrasia tabularis Adr. Juss. and Melia dubia Cav. (Meliaceae). Phytotherapy Research, 17, 414-416. http://dx.doi.org/10.1002/ptr.1147
Koul, O., Singh, G., Singh, R., Singh, J., Daniewski, W.M. and Berlozecki, S. (2004) Bioefficacy and Mode-of-Action of Some Limonoids of Salannin Group from Azadirachta indica A. Juss and Their Role in a Multicomponent System against Lepidopteran Larvae. American Journal of Bioscience, 29, 409-416. http://dx.doi.org/10.1007/BF02712112
Kiritkar, K.R. and Basu, B.D (1999) Indian Medicinal Plants, Vol. 1. International Book Distributors, Dehradun.
Susheela, T., Balaravi, P., Theophilus, J., Reddy, N.T. and Reddy, P.U.M. (2008) Evaluation of Hypoglycaemic and Antidiabetic Effect of Melia dubia Cav. Fruits in Mice. Current Science, 94, 1191-1195.
Tan, S.C. and Yiap, B.C. (2009) DNA, RNA, and Protein Extraction: The Past and the Present. Journal of Biomedicine and Biotechnology, 2009, Article ID: 574398.
Sangwan, N.S., Sangwan, R.S. and Kumar, S. (1998) Isolation of Genomic DNA from the Antimalarial Plant Artemisia annua. Plant Molecular Biology Reporter, 16, 365. http://dx.doi.org/10.1023/A:1007545102889
Weising, K., Nybom, H., Wolff, K. and Meyer, W. (1995) DNA Isolation and Purification. In: Editor’s name, Ed., DNA Fingerprinting in Plants and Fungi, CRC Press, Boca Raton, 44-59.
Do, N. and Adams, R.P. (1991) A Simple Technique for Removing Polysaccharide Contaminants from DNA. BioTechniques, 10, 162-166.
Fang, G., Hammar, S. and Grumet, R. (1992) A Quick and Inexpensive Method for Removing Polysaccharides from Plant Genome DNA. BioTechniques, 13, 52-56.
Pandey, R.N., Adams, R.P. and Flournoy, L.E. (1996) Inhibition of Random Amplified Polymorphic DNAs (RAPDs) by Plant Polysaccharides. Plant Molecular Biology Reporter, 14, 17-22. http://dx.doi.org/10.1007/BF02671898
Katterman, F.R.H. and Shattuck, V.I. (1983) An Effective Method of DNA Isolation from Mature Leaves of Gossypium Species That Contain Large Amounts of Phenolic Terpinoids and Tannins. Preparative Biochemistry, 13, 347-359. http://dx.doi.org/10.1080/00327488308068177
Porebski, S., Bailey, L.G. and Baum, B.R. (1997) Modification of a CTAB DNA Extraction Protocol for Plants Containing High Polysaccharides and Polyphenol Component. Plant Molecular Biology Reporter, 15, 8-15. http://dx.doi.org/10.1007/BF02772108
Lefort, F. and Douglas, G.C. (1999) An Efficient Micro-Method of DNA Isolation from Mature Leaves of Four Hardwood Tree Species Acer, Fraxinus, Prunus, and Quercus. Annals of Forest Science, 56, 259-263. http://dx.doi.org/10.1051/forest:19990308
Fernandez, J.F., Sork, V.L., Gallego, G., Lopez, J., Bohorques, A. and Tomhe, J. (2000) Cross-Amplification of Microsatellite Loci in a Neotropical Quercus Species and Standardization of DNA Extraction from Mature Leaves Dried in Silica Gel. Plant Molecular Biology Reporter, 18, 397. http://dx.doi.org/10.1007/BF02825070
Sahu, S.K., 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. ISRN Molecular Biology, 2012, Article ID: 205049. http://dx.doi.org/10.5402/2012/205049
Das, S.S., Das, S. and Ghosh, P. (2013) Optimization of DNA Isolation and RAPD-PCR Protocol of Acanthus volubilis wall., Arare Mangrove Plant from Indian Sundarban, for Conservation Concern. European Journal of Experimental Biology, 3, 33-38.
Bhandari, A., Lamichhane, N., Lamichhane, S. and Shakya, P. (2014) An Efficient Method for Isolation of Genomic DNA from Silica Gel Dried Leaves of Taxus sps. International Journal of Biosciences, 5, 147-152. http://dx.doi.org/10.12692/ijb/5.5.147-152
Pandey, A. and Tamta, S. (2015) High-Molecular-Weight DNA Extraction from Six Quercus Species of Himalaya, India. International Journal of Advanced Research, 3, 30-34.
Khanuja, S.P.S., Shasany, A.K., Darokar, M.P. and Kumar, S. (1999) Rapid Isolation of DNA from Dry and Fresh Samples of Plants Producing Large Amounts of Secondary Metabolites and Essential Oil. Plant Molecular Biology Reporter, 17, 74. http://dx.doi.org/10.1023/A:1007528101452
Doyle, J.J. and Doyle, J.L. (1987) A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue. Phytochemical Bulletin, 19, 11-15.
Ahmed, S.M., Ganaie, M.M., Qazi, P.H., Vijeshwar, V., Basir, S.F. and Qazi, G.N. (2004) Rapid DNA Isolation Protocol for Angiospermic Plants. Bulgarian Journal of Plant Physiology, 30, 25-33.
Sambrook, J., Maccallum, P. and Russell, D. (2001) Molecular Cloning: A Laboratory Manual. 3rd Edition, Cold Spring Harbor Press, Cold Spring Harbor, 2344 p.
Coley, P.D. and Barone, J.A. (1996) Herbivory and Plant Defences in Tropical Forests. Annual Review of Ecology and Systematics, 27, 305-335. http://dx.doi.org/10.1146/annurev.ecolsys.27.1.305
Lodhi, M.A., Ye, G.N., Weeden, N.F. and Reisch, B.I. (1994) A Simple and Efficient Method of DNA Extraction from Grapevine Cultivars and Vitis Species and Ampelopsis. Plant Molecular Biology Reporter, 12, 6-13. http://dx.doi.org/10.1007/BF02668658
Ginwal, H.S. and Maurya, S.S. (2010) Evaluation and Optimization of DNA Extraction Method for Dalbergia sissoo Leaf. Indian Journal of Biotechnology, 9, 69-73.
Moreira, P.A. and Oliveira, D.A. (2011) Leaf Age Affects the Quality of DNA Extracted from Dimorphandra mollis (Fabaceae), a Tropical Tree Species from the Cerrado Region of Brazil. Genetics and Molecular Research, 10, 353-358. http://dx.doi.org/10.4238/vol10-1gmr1030
Maliyakal, E.J. (1992) An Efficient Method for Isolation of RNA and DNA from Plants Containing Polyphenolics. Nucleic Acids Research, 20, 2381. http://dx.doi.org/10.1093/nar/20.9.2381
Suman, P.S.K., Ajit, K.S., Darokar, M.P. and Sushil, K. (1999) Rapid Isolation of DNA from Dry and Fresh Samples of Plants Producing Large Amounts of Secondary Metabolites and Essential Oils. Plant Molecular Biology Reporter, 17, 1-5. http://dx.doi.org/10.1023/A:1017213630972
Pan, H., Yang, C.-P., Wei, Z.-G. and Jiang, J. (2006) DNA Extraction of Birch Leaves by Improved CTAB Method and Optimization of Its ISSR System. Journal of Forestry Research, 17, 298-300. http://dx.doi.org/10.1007/s11676-006-0068-3
Huang, J.C. and Sun, M. (2000) Genetic Diversity and Relationship of Sweet Potato and Its Wild Relatives in Pomoea Series Batatas as Revealed by Inter-Simple Sequence Repeat (ISSR) and Restriction Analysis of Chloroplast. Theoretical and Applied Genetics, 10, 1050-1060. http://dx.doi.org/10.1007/s001220051386
Zhang, H.Q., An, L.J. and Zu, Y.G. (1999) Effect on the Experimental Results of the Content of Compositions in RAPD Experiment of Pinus koraiensis. Bulletin of Botanical Research, 19, 183-186.
Padmalatha, K. and Prasad, M.N.V. (2006) Optimization of DNA Isolation and PCR Protocol for RAPD Analysis of Selected Medicinal and Aromatic Plants of Conservation Concern from Peninsular India. African Journal of Biotechnology, 5, 230-234.
Harini, S.S., Leelambika, M., Shiva Kameshwari, M.N. and Sathyanarayana, N. (2008) Optimization of DNA Isolation and PCR-RAPD Methods for Molecular Analysis of Urginea indica Kunth. International Journal of Integrative Biology, 2, 138-144.