RAPD (RANDOM AMPLIFIED POLYMORPHIC DNA) MARKERS AND PLANT SYSTEMATICS

Year 2004, Issue: 006, 113 - 130, 15.10.2004

S. Öz Aydın

Abstract

RAPD (Randomly Amplified Polimorphic DNA)is a PCR

based method to detect genetic polymorphism. The major advantages

of RAPD include: no need for prior knowledge of genom sequence in

polymophism studies, large amount of DNA of high purity, Southern

blot or radioactive chemicals. Furthermore, the technique is speed and

low cost. RAPD technique is being succesfully used widely for the

estimation of genetic variability in various plant species.

Keywords

RAPD-PCR, Plant Systematics

RAPD (RASTGELE ARTTIRILMIŞ POLİMOFİK DNA) BELİRLEYİCİLERİ VE BİTKİ SİSTEMATİĞİ

Abstract

RAPD (Rastgele Arttırılmış Polimofik DNA) genetik polimorfizmi

belirleyen PCR temelli bir tekniktir. Tekniğin en büyük avantajları genom

dizisi hakkında ön bilgiye, yüksek saflıktaki DNA’dan çok miktarlara,

Southern blot veya radyoaktiv kimyasallara ihtiyaç duymamasıdır. Ayrıca

hızlı ve düşük maliyetlidir. RAPD tekniği pek çok alanda olduğu gibi değişik

bitki türlerinin genetik değişkenliğinin belirlenmesinde yaygın bir şekilde

başarıyla uygulanmaktadır.

Keywords

RAPD-PCR, Bitki Sistematiği

References

• [1] Hillis, D. M., Moritz, C., Molecular Systematics, Sinauer Associates, İnc. Publishers, USA (1990)
• [2] Işık K., Karakter Kavramı ve Karakterlerin Genetik Temeli, Taksonomi Yaz Okulu Ders Notları, Ed. Dr. Çıplak B., Antalya, 7-13 Eylül, 74 (1997).
• [3] Quıcke, D., L.J., Principles and Techniques of Contemporary Taxonomy, Blackıe Academic &Professıonal, Glasgow, (1993).
• [4] Başıbüyük, H. H., Bardakçı, F., Belshaw, R., Quicke, D. L. J., Phylogenetic Systematics, Önder Matbaa, Sivas, (2000).
• [5] Gottlieb, O.,R., Micromolecular Evolution, Systematics and Ecology, Springer-Verlag, Berlin, NewYork (1982).
• [6] Crawford D.J., Plant Molecular Systematics, John , Willey&Sons, New York, (1990).
• [7] Buth, D. G., "The Applıcatıon of Electrophoretıc Data In Systematıc Studıes", Ann. Rev. Ecol. Syst. 15, 501-22 (1984).
• [8] Crawford, D. J., "Plant Macromolecular Systematics İn The Past 50 Years: One View", Taxon, 49, 81-103 (2000).
• [9] Doyle, J.J. and Doyle J.L., DNA And hıgher plant systematıcs: Princıples And Results: Molecular technics in taxonomy, ed.Hewitt et all., Springer-Verlag Berlin Heidelberg (1991).
• [10] Mullis, K., Faloona F., Scharf, S., Saiki R., Horn, G. and Erlich H., Specific Enzymatic Amplification of DNA İn Vitro: The Polymerase Chain Reaction., Cold Spring Harbour Symp Quant Biol 51: 263-273 (1986).
• [11] Williams, J.G.K.,Kubelik, A.R.,Livak, K.J.,Rafalski, J.A., Tingey, S.V., "DNA Polimorphism Amplified By Arbitrary Primers Are Useful As Genetic Markers", Nucleic Acids Research,Vol 18, 6531-6535 (1990).
• [12] Welsh, J., McClelland, M., "Fingerprinting Genomes Using PCR With Arbitrary Primers", Nucleic Acids Research,Vol 18, 7213-7218 (1990).
• [13] Caetano-Anolles, G., Bassam, B.J., Gresshoff, P.M., "High Resolution DNA Amplification Fingerprinting Using Very Short Arbtrary Oligonucleotide Primers", Biotechnology 9: 553- 557 (1991).
• [14] http:avery.nutgers.edu.WSSP Students senoiars project arenives onions napa.html
• [15] Öz Aydın S. Bazı Satureja Türlerinin Morfolojik, Moleküler ve Sistematik Yönden Değerlendirilmesi, Doktora Tezi, Balıkesir Üniversitesi, Fen Bilimleri Enstitüsü, Biyoloji Eğitimi Anabilim Dalı, Balıkesir, (2004).
• [16] Rafalskı, A., Tingey, S.V., Williams, J.G.K., " (RAPD) markers", Plant Molecular Biology Mannual, 114, (1994) 1-8.
• [17] Welsh, J., Petersen, C. And "Polimorphisms Genereted By Arbitrarily Primed PCR İn The Mouse: Application To Strain İdentification And Genetic Mapping", Nucleic Acids Research,Vol 19, 303-306 (1991).
• [18] Mathieu-Daudé, F., Ralph D. and McClelland M., "Arbitrarily Primed PCR Fingerprints: Laboratory Methods for the Detectıon of Mutations and Polymorphisms in DNA", ed. Taylor, G. R., CRS Press, Boca Raton, (1997).
• [19] Halldén, C., Nilsson, N-O, Rading, IM and Sall T, "Evaluation of RFLP and RAPD Markers İn A Comparison Of Brassica Napus Breding Lines", Theor Appl Genet 88: 123-128 (1994).
• [20] Tingey, S.V., Del Tufa, J.P.,"Genetic Analysis With Random Amplified Polimorphic DNA Markers", Plant Physiol.101, 349- 352 (1993).
• [21] Halldén, C., Characterization and Use of a Multiplex PCRbased System: Random Amplified Polymorphic DNA, Ph.D. Thesis, Department of Genetics Lund University, Lund, (1998).
• [22] Atienzar,F.,Evenden,A.,Jha,A.,Savva,D.and Depledge M., "Optimized RAPD Analysis Generates High-Quality Genomic DNA Profiles at High Annealing Temperature" BioTechniques 28:52-54 (2000).
• [23] Demeke,T.and Adams R.,P., "The Effects of Pllant Polysaccharides and Buffer Additives on PCR" BioFeedback Vol. 12,No.3(1992).
• [24] Khandka, D.K., Tuna, M., Tal, M., Nejidat, A., Goldhirsh, A.G., "Variability İn The Pattern Of Random Amplified Polymorphic DNA", Electrophoresis, 18, 2852-2856 (1997).
• [25] Doulıs, A.G., Harfouche, A.L., Aravanopoulos, F.A, "Rapid, High Quality DNA Isolation from Cypress (Cupressus sempervirens L.)Needles and Optimization of the RAPD Marker Technique " Plant Molecular Biology Reporter 17, 1- 14(2000).
• [26] Boiteux, L.S., Fonseca, M.E.N., Simon, " Effects of Plant Tissue and P.W., DNA Purification Method on Randomly Amlified Polymorphic DNA-Based Genetic Fingerprinting Analysis in Carrot", J. Amer. Soc. Hort. Scı., 124:1, 32-38 (1999).
• [27] Aljanabi, S.M., Forget,L., Dookun, A., "An İmproved and Rapid Protocol for the Isolation of Polisaccaride and Polyphenol-Free Sugarcane ", Plant Molecular biology Reporter, 17, 1-8 (1999).
• [28] Kohel, R.,J.; Park,Y., "Effect Of Concentration Of MgCl2 On Random Amplified DNA" BioTechniques, 16:652-656
• [29] Halldén, C. And Sall, T., "Primer mixtures in RAPD analysis".Submitted to Genomics (In Press).
• [30] Halldén, C., Hansen, M., Nilsson, N-O, Hjerdin, A. and Sall T., "Competition as a of Errors in RAPD analysis", Theor Appl Genet 92: 1185-1192 (1996).
• [31] Weeden N.F., Timmerman G.M., Hermmat M., Hneen B.E. and Lodhi M.A., Inheritance and Reliability of RAPD markers, Proceedings of the symposium: Applications of RAPD Techology to Plant Breeding, pp:12-17, Minneapolis (1992).
• [32] Gallego, F. J. and Martínez, I., "Method to Improve Reliabilityof Random-Amplified Polymorphic DNA Markers", BioTechniques, 23:663-664 (1997).
• [33] Hansen, M., Halldén, C., Sall T., "Error rates and Polymorphism Frequencies For Three RAPD Protocols", Plant Molecular Biology Reporter 16: 139-146 (1998).
• [34] Doyle J.J.and Doyle J.L. "A Rapid DNA İsolation Procedure From Small Quantities Of Fresh Leaf Tissue" Phytochem Bull19:11-15(1987).
• [35] Dellaporta, S. L., Wood, J., Hicks, J.B., “A Plant DNA Mini Preparation Version II”, Plant Molecular Biology Reporter, Voll 1, pp:19 (1983).
• [36] Saghai-Maroof, M.,A., Soliman, K.,M., Jorgensen, R.,A., And Allard, R., W., "Ribosomal DNA Spacer-Length Polymorphisms İn Barley: Mendelian İnheritance, Chromosomal Location and Population Dynamics", Population Biology, 81, 8014-8018 (1984).
• [37] Krishna, T.G.and Jawali, N.,"DNA Isolation from Single or Half Seeds Suitable for Random Amplifıed Polymorphic DNA", Analyses Analytıcal Bıochemıstry, 250, 125-127 (1997).
• [38] Stewart C.N., Via l.e., " A rapid CTAB DNA İsolation Technique Useful For RAPD Fingerprinting And Other PCR Aplications", BioTechniques 14:4, 748-749 (1993).
• [39] Pich, U. And Schubert, I., Minipep Method For İsolation Of DNA From Plants With A High Contentof Polyfenols ",Nüc. Acid. Res.,21, 3328 (1993).
• [40] Khanuja, S.P.S.,Shasany, A.K., Darokar, M.P., Kumar, S., "Rapid Isolation of DNA from Dry and Fresh Samples of plants Producing Large Amount of Secondary Metabolites and Essantial oils", Plant Molecular biology Reporter, Protocols-17 (1999).
• [41] Do N. and Adams R.P. “A Simple Technique For Removing Plant Polysaccharide Contaminants From DNA” BioTechniques 10: 163–166(1991).
• [42] Weishing,K., Nybom H.,Wolff ,K. and Meyer ,W., "DNA İsolation And Purification. In: DNA Fingerprinting İn Plants And Fungi", pp 44-59. CRC Press, Boca Raton, Florida (1995).
• [43] Loomis MD, "Overcoming Problems Of Fhenolics And Quinones İn İsolation Of Plant Enzymes And Organelles", Methods Enzymol 31: 528-544 (1974).
• [44] Porebski S., Bailey L.G. and Baum B.R., "Modification of a CTAB DNA Extraction Protokol For Plants Containing High Polysaccharide And Polyphenol Components", Plant Mol. Biol. Reptr. 15:8-15(1997).
• [45] Williams, J.G.K., Rafalski, J.A. and Tingey, S.V., "Genetic Analysis Using RAPD Markers", Methods Enzymol, 218:704- 740(1993).
• [46] Southern, E.M., "Detection Of Specific Sequences Among DNA Fragments Separeted By Gej Electrophoresis", J.Mol.Biol.98:503-517(1975)
• [47] Zabeau M. And Vos, P., Selective Restriction Fragment Amplification: A General Method For DNA Fingerprinting European Patent Application EP 534858A1 (1993).
• [48] Vos, P., Hogers R., Bleeker M., Reijans M., Van De Lee T., Homes M.,Frijeters A., Pot J., Kulper M., Zabeau M., "AFLP: A new technique for DNA fingerprinting", Nucl. Acids Res.23: 4407-4414(1995).
• [49] Payne S.J., Microsatellite Analysis: Laboratory Methods for the Detectıon of Mutations and Polymorphisms in DNA, ed. Taylor, G. R., CRS Press, Boca Raton, (1997).
• [50] Zietkiewicz E, Rafalski A and Labuda D., "Genome Fingerprinting By Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification" Genomics 20,176- 183 (1994).
• [51] Orita, M., Ivahana, H., Kazanawa,H., Hayashi, K. And Sekiya, T., Proc.Natl.Acad.Sci., USA 86, 2766-2770 (1989).
• [52] Myers, R.M., Sheffied, V.C., Cox, D.R., "Mutation Detection By PCR, GC-Clamps and Denaturing Gradient Gel Electrophoresis, in PCR Tecnology Prenciples And Applications for DNA Amplification", Academic Press İnc., USA(1987).
• [53] Konieczyn A., Ausubel F.A., "A Procedure For Mapping Arabidopsis Mutation Using Co-Dominant Acotype-Specific PCR-based markers", Plant J., 4:403-410 (1993).
• [54] Paran, I., Michelmora, R.W., "Devolopment of Reliable PCRBased Markers Linked To Downy Mildew Resistance Genes İn Lettuce", Theor Appl Genet 85: 985-993 (1993).
• [55] Glick B.R.,Pasternak J.J., Molecular Biotechnology (Principles and Applications of Recombinant DNA), ASM Press., Washıngton, D.C., (1998).
• [56] Khanuja, S.P.S., Shasany, A.K., Srivastava, A., Kumar, S., "Assessment of Genetic Relationships İn Mentha Species" Euphytica, 111, 121,125 (2000).
• [57] Hosokawa, K., Minami, Kawahara, K., Nakamura, I., Shibata, T., "Discrimination Among Three Species of Medicinal Scutellaria Plants Using RAPD Markers", Planta Medica, 66, 270-272 (2000).
• [58] M, Sun, "Cleistogamy in Scutellaria indica (Labiatae): Effective Mating System and Population Genetic Structure", Molecular Ecology, 8(8), 1285-95 (1999).
• [59] Gauer, L., Cavalli-Molina, S.,"Genetic Variation İn Natural Populations Of Mate (İlex paraguariensis A.St.-Hil., Aquifoliaceae) Using RAPD Marker", Heredity, 84, 647-656 (2000).
• [60] Cullis, C. A., Swami, S., and Song, Y., "RAPD Polymorphisms Detected Among The Flax Genotrophs", Plant Molecular Biology, 41, 795-800 (1999).
• [61] Kennington, W. J.,Waycott, M., and James, S. H., "DNA Fingerprinting Supports Notions Of Clonality İn A Rare Mallee, Eucalyptus argutifolia", Molecular Ecology, 5, (1996) 693-696.
• [62] Skepner, Adam, P., K., Krane, Dan.E., "RAPD Reveals Genetic Similarity Of Acer saccharum and Acer nigrum", Heredity, 80(4), 422-428 (1998).
• [63] Fıscher, M., Husı, R., Prati, D., Peintinger, M., Kleunen, M. and Schmıd, B., "RAPD Variation Among And Wıthın Small And Large Populatıons Of The Rare Clonal Plant Ranunculus reptans (Ranunculaceae) ", American Journal of Botany 87(8), 1128-1137 (2000).
• [64] Drouzas, A.D., Aravanopoulos, F.A., Panetsos, K.P., " RAPD Variation Of A Natural Hibrid Population Among Pinus brutia Ten. And P.halepensis Mill." Mytılene Pine and Cedars, 77 (2000).
• [65] Ağaoğlu, Y.S.,Ergül, A., "Identification of some Turkish Table Grape Cultivars (Vitis vinifera L.)by Random Amplified Polimorphic DNA (RAPD) ", Plants of the Balkan Peninsula:into the next Millennium, Volume-II, 147-154 (2001).
• [66] Martin, J., P.,Bermejo, H., Esteban, J.,"Genetic Variation İn The Endemic and Endangered Rosmarinus tomentosus Huber- Morath & Maire (Labiatae) Using RAPD Markers", Heredity, 85(5), 434-443 (2000).
• [67] Harfouche, A.L., Aravanopoulos, F.A, Doulıs, A.G., Xenopoulos, S.," Identıfıcatıon of RAPD Markers Assocıated Wıth Crown Form In Cupressus sempervirens By Bulked Segregant Analysıs ", Forest Genetics 7(3), 171-178 (2000).
• [68] Nocelli, E., Giovannini, T., Bioni, M., and Alicchio, R., "RFLP- and RAPD- Based Genetic Relationships Of Seven Diploid Species Of Avena With The A Genome", Genome 42, 950-959 (1999).
• [69] Saliba-Colombani, V., Causse, M., Gervais, L., and Philouze, J., "Efficiency of RFLP, RAPD, and AFLP Markers For The Construction Of An İntraspecific Map Of The Tomato Genome", Genome 43, 29-40 (2000).
• [70] Dalbo, M. A., Ye, G. N., Weeden, N. F., Steinkellner, H., Sefc, K. M., and Reisch, B. I., "A Gene Controlling Sex İn Grapevines Placed On A Molecular Marker-Based Genetic Map", Genome 43, 333-340 (2000).
• [71] Laroche, A., Demeke, T., Gaudet, D. A., Puchalski, B., Frick, M., and McKenzie,R., "Development of a PCR Marker For Rapid İdentification Of The Bt-10 Gene For Common Bunt Resistance İn Wheat", Genome 43, 217-223 (2000).
• [72] Persson, H.A., Gustavsson, B.A., "The Extent Of Clonality And Genetic Diversity İn Lingonberry (Vaccinium vitis-ideae L.) Revealed By RAPDs And Leaf–Shape Analysis " Molecular Ecology 10,1385-1397 (2001).
• [73] Gourmet, C., Rayburn, A.Lane, "Identification of RAPD Markers Associated With The Presence Of B Chromosomes İn Maize", Heredity, 77(3), 240-244 (1996).
• [74] Kohjyouma, M.,Nakajıma,S.,Namer, A., Shımızu, R., Mızukamı, H. And Kohda, H., "Random Amplified Polymorphic DNA Analysis and Variation of Essential Oil Components of Atractylodes Plant", Biol. Pharm. Bull.20(5), 502-506 (1997).
• [75] D’Ennequin, M.L.T., Panaud, O.,Robert, T., Rıcroch, A., "Assesment of genetic relationships among sexual and asexsual forms of Allium cepa using morphological traits and RAPD markers", Heredity, 78(4), 403-409 (1997).
• [76] Esselman, E., J., Crawford, D., J., Brauner, S., Stuessy, T., F., Anderson, G., J., and O., M., S., "RAPD Marker Diversity Winhin And Divergence Among Species Of Dendroseris (Asteraceae: Lactuceae) ", Botanical Society of America, 87, 591-596 (2000).
• [77] Klug, W. S., Cummings, M. R., Çev. Öner, C., Genetik, Palme Yayıncılık, Ankara (2002).
• [78] Mayr, E. And Ashlock, P.D. Princeples of Systematic Zoology. McGraw-Hill, İnc.,Newyork, London, 475, (1991).
• [79] Özkan, M. Taksonominin Prensipleri, Atatürk Üniv. Fen–Ed. Fak. Yayın no:45, Erzurum 137 (1988).
• [80] Svafford, D.L., Phylogenetic Analysis Using Parsimony (PAUP), Version 3.0. İllinois Natural History Survey, Urbana,178 (1990).
• [81] Sokal, R.R., Michener, “A Statistical Method For Evaluating Systematic Relationships” University of Kansas Science Bulletin, 38:1409-1438(1958).
• [82] Panchen A L, Classification Evolution and the Nature of Biology ,Cambridge University Press, USA(1992).
• [83] Wen-Hsiung Li, Molecular Evolution, Sinauer Associates, Inc, Canada (1997).
• [84] Saitou, N.and M. Nei, “The neighbor-joining method: A new method for reconstructing phylogenetic trees”, Mol. Biol. Evol. 4:406-425 (1987).
• [85] Hartl D.L. and Clark A.G., Principles of Population Genetics, Sinauer Associates, Inc.,Canada (1997).