Vitis vinifera L.; DNA extraction; RAPD; Optimisation
Abstract :
[en] Various problems are encountered during DNA extraction from Vitis species, harbouring high levels of secondary metabolites and polysaccharides. A simple and highly efficient protocol for
isolating large quantities (0.5±0.3 mg.g-1 of leaf tissue) of high-quality DNA, from dry young Vitis
vinifera leaves, is described in the present study. Thus, three different DNA extraction protocols were examined. The isolated DNA is essentially free of polysaccharides, polyphenols, and other major contaminants as judged by viscosity, clear color, A260/280 ratio, and RAPD suitability. Moreover, the RAPD profiling from the isolated DNA was optimized to produce scorable and clear amplicons in all studied cultivars.
Disciplines :
Agriculture & agronomy
Author, co-author :
Ghaffari, Sana; Arid Land Institute, Km 22.5, 4119, El Fjè- Medenine, Tunisia > Dry Land Farming and Oasis Cropping Laboratory
K. ARUMUGANATHAN, E.D. EARLE, Estimation of nuclear DNA content of plants by flow cytometry. Plant Mol. Bio. Rep., 9, 229-233 (1991).
K.D. SCOTT, J. PLAYFORD, DNA extraction technique for PCR in rain forest plant species. Biotechniques, 20, 974-948 (1996).
D.J. MERLO, J.D. KEMP, Effect of polysaccharides on kinetics of DNA. Plant Physiol., 58, 1522-1526 (1976).
N. DO, R.P. ADAMS, A simple technique of removing plant polysaccharides contaminants from DNA. Biotechniques, 10, 162-166 (1991).
A.D. SHARMA, P.K. GILL, P. SINGH, DNA isolation from dry and fresh samples of polysaccharide-rich plants. Plant Mol. Biol. Rep., 20, 415a-f (2002).
S.E. WILKIE, P.G. ISSAC, R.J. SLATER, Random amplification polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theor. Appl. Genet., 86, 497-504 (1993).
C.R. DAWSON, R.J. MAGEE, Plant tyrosinase (polyphenol oxidase), S.P. COLOWICK, N.O. KAPLAN, eds., Academic Press, New York, 1995, pp. 817-827.
M.S. CLARK, Plant Molecular Biology - A Laboratory Manual, Springer-Verlog Berlin Heidelberg, New York, 1997, pp. 305-328.
M.A. REZAIAN, L.R. KRAKE, Nucleic acid extraction and virus detection in grapevine. J. Virol. Meth., 17, 277-285 (1987).
S.L. DELLAPORTA, J. WOOD, J.B. HICKS, A plant DNA minipreparation: Version II. Plant Mol. Biol. Rep., 1, 19-21 (1983).
J.E. BOWERS, E.B. BANDMANN, C.P. MEREDITH, DNA fingerprinting characterization of some wine grape cultivars. Am. J. Enol. Viticult., 44, 266-274 (1993).
P. THIS, C. CUISSET, J.M. BOURSIQUOT, Development of stable RAPD markers for the identification of grapevine rootstocks and the analysis of genetic relationships. Am. J. Enol. Viticult., 48(4), 492-501 (1997).
F. LEFORT, G.C. DOUGLAS, An efficient micro-method of DNA isolation from mature leaves of four hardwood tree species Acer, Fraxinus, Prunus and Quercus. Ann. For. Sci., 56, 259-263, 1999.
G.G. COLLINS, R.H. SYMONS, Extraction of nuclear DNA from grape vine leaves by modified procedure. Plant Mol. Biol. Rep., 10, 233-235 (1992).
S.O ROGERS, Phylogenetic and Taxonomic Information from Herbarium and Mummified DNA. In: Conservation of Plant Genes II: Utilization of Ancient and Modern DNA, R.P. ADAMS, J.S. MILLER, E.M. GOLDENBERG, J.E. ADAMS, eds., Missouri Botanical Garden, St. Louis, MO, 1994, pp. 47-67.
N.R. NAZHAD, M. SOLOUKI, Separation of DNA for molecular markers analysis from leaves of the Vitis vinifera. Pak. J. Biol. Sci., 11(11), 1436-1442 (2008).
G. DI GASPERO, G. CIPRIANI, A.F. ADAM-BLONDON, R. RESTOLIN, Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R-gene candidates. Theor. Appl. Genet., 114, 1249-1263 (2007).
M.A. LODHI, G.N. YE, N.F. WEEDEN, B.I. REISCH, A simple and efficient method for DNA extraction from grapevine cultivars, Vitis species and Ampelopsis. Plant Mol. Biol. Rep., 12(1), 6-13 (1994).
S.O. ROGERS, A.J. BENDICH, Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. Rep., 5, 69-76 (1985).
J.J. DOYLE, J.L. DOYLE, A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem. Bull., 19, 11-15 (1987).
D.E. HOWLAND, R.P. OLIVER, A.J. DAVY. A method of extraction of DNA from birch. Plant Mol. Biol. Rep., 9, 340-344 (1991).
U. HANANIA, M. VELCHEVA, N. SAHAR, A. PERL, An Improved Method for Isolating High-Quality DNA From Vitis vinifera Nuclei. Plant Mol. Biol. Rep., 22, 173-177 (2004).
M. ALAEY, R. NADERI, A. VEZVAEI, A. KHALICHI, A. SALAMI, Comparing study between four different methods of genomic DNA extraction from Cyclamen persicum Mill. Int. J. Agric. Biol. Rep., 9, 208-218 (2005).
E.J. MALIYAKAL, An efficient method for isolation of RNA and DNA from plants containing polyphenolics. Nucleic Acids Res, 20(9), 2381 (1992).
M.G. MURRAY, W.F. THOMPSON, Rapid isolation of high molecular weight DNA. Nucleic Acids Res., 8, 4321-4325 (1980).
A.H. PATERSON, C.L. BRUBAKER, J.F. WENDEL, A rapid method for extraction of Cotton (Gossypium spp) genomic DNA suitable for RFLP or PCR analysis. Plant Mol. Biol. Rep., 11, 122-127 (1993).
P.S.K. SUMAN, K.S. AJIT, M.P. DAROKAR, S. KUMAR, 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, 1-7 (1999).
S.M. ALJANABI, L. FORGET, A. DOOKUN, An improved rapid protocol for the isolation of polysaccharide and polyphenol-free sugarcane DNA. Plant Mol. Biol. Rep., 17, 1-8 (1999).
D. THOMPSON, R.J. HENRY, Single step protocol for preparation of plant tissue for analysis by PCR. Biotechniques, 19, 394-397 (1995).
G. FANG, S. HAMMAR, R. REBECCA, A quick and inexpensive method for removing polysaccharides from plant genomic DNA. BioTechniques, 13, 52-56 (1992).
J.J. ZHANG, Y.J. WANG, X.P. WANG, K.Q. YANG, J.X. YANG, An improved method for rapidly extracting total RNA from Vitis. J. Fruit Sci., 20, 178-189 (2003).
J.A. Couch, P. Fritz, Isolation of DNA from plants high in polyphenolics. Plant Mol. Biol. Rep., 8, 8-12 (1990).
CHAUDHRY, B., A. YASMEEN, T. HUSNAIN AND S. RIAZUDDIN. Mini-scale genomic DNA extraction from cotton. Plant Mol. Biol. Rep., 17, 1-7 (1999).
C.N. STEWART, L.E. VIA, A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques, 14, 748-758 (1993).
S. POREBSKI, G.L. BAILEY, B.R. BAUM, Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol. Biol. Rep., 15, 8-15 (1997).
J. ZHANG, J. STEWART, Economical and rapid method for extracting cotton genomic DNA. J. Cotton Sci., 4, 193-201 (2000).
J.R. VIDAL, S. MORENO, Y. GOGORCENA, A. MASA, J.M. ORTIZ, On the genetic relationships and origins of six grape cultivars of Galicia (Spain) using RAPD markers. Am. J. Enol. Viticult., 50(1), 69-75 (1999).
J.G.K. WILLIAMS, A.R. KUBELIK, K.J. LIVAK, J.A. RAFALSKI, S.V. TINGEY, DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res., 18, 6531-6535 (1990).
S. CASTIGLIONE, W. WANG, P. BAO, W. LI, E. GIORDANI, E. DESTANCHINA, G. DAMIANI, C. BANDI, S. BISOFFI, F. SALA, RAPDs for the assessment of DNA plasticity and genetic diversity. Current Topics in Mol. Genet. (Life Sci. Adv.), 2, 219-243 (1994).
K. WEISING, H. NYBON, K. WOLFF, W. MEYER, DNA fingerprinting in plants and fungi. CRC Press Inc., London, 1995, 322 pp.
M. MUNTHALI, B.V. FORD-LLOYD, H.J. NEWBURY, The random amplification of genomic DNA for fingerprinting plants. PCR Methods Appl., 1, 274-276 (1992).
I. VROH BI, P. DU JARDIN, G. MERGEAI, J.P. BAUDOIN, Optimisation et application de la RAPD dans un programmme de selection recurrente chez le cotonnier (Gossypium spp.). Biotechnol. Agron. Soc. Environ., 1, 142-150 (1997).
M.A. INNIS, D.H. GELFAND, J.J. SNINSKY, T.J. WHITE, PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990, 482 pp.
