Random Amplified Polymorphic DNA (RAPD)

Stock Identification Methods

Volumn , Issue , 2005, Pages 371-387

  Smith, P J ^a  

^a NATIONAL INSTITUTE OF WATER AND ATMOSPHERIC RESEARCH   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77958164206     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012154351-8/50019-8     Document Type: Chapter

References (97)

1. Allegrucci G., Fortunato C., Catudella S., Sbordoni V. Acclimation to freshwater of the sea bass: evidence of selective mortality and allozyme genotypes. Genetics and Evolution of Marine Organisms 1994, 486-502. Chapman & Hall, London, UK. A. Beaumont (Ed.).
2. Allegrucci G., Caccone A., Catudella S., Powell J.R. Acclimation of the European sea bass to freshwater: monitoring genetic changes by RAPD polymerase chain reaction to detect DNA polymorphisms. Marine Biology 1995, 121:591-599.
3. Allegrucci G., Fortunato C., Sbordoni V. Genetic structure and allozyme variation in sea bass ({biDicentrarchus labrax} and {biD. punctatus}) in the Mediterranean Sea. Marine Biology 1997, 128:347-358.
4. Andre C., Lindegarth M., Jonsson P.R., Sundberg P. Species identification of bivalve larvae using random amplified polymorphic DNA (RAPD) differentiation between {biCerastoderm edule} and {biC. lamarcki}. Journal of the Marine Biological Association of the UK 1999, 79:563-565.
5. Appleyard A.S., Mather B.P. Investigation into the mode of inheritance of allozyme and random amplified polymorphic DNA markers in tilapia {biOreochromis mossambicus} (Peters). Aquaculture Research 2000, 31:435-445.
6. Aubert H., Lightner D.V. Identification of genetic populations of the pacific blue shrimp {biPenaeus stylirostris} of the Gulf of California, Mexico. Marien Biology 2000, 137:875-885.
7. Ayliffe M.A., Lawrence G.J., Ellis J.G., Pryor A.J. Heteroduplex molecules formed between allelic sequences cause nonparental RAPD bands. Nucleic Acids Research 1994, 2:1632-1636.
8. Bakar T.A., Azizah M.N.S. Fingerprinting of two species of the grouper, {biEpinephelus} off the coast of Pulau Pinang. Asia Pacific Journal of Molecular Biology and Biotechnology 2000, 8:177-179.
9. Bardakci F., Skibinski D.O.F. Application of the RAPD technique in tilapia fish: species and subspecies identification. Heredity 1994, 73:117-123.
10. Bell D.A., DeMarini D.M. Excessive cycling converts PCR products to random length higher molecular weight fragments. Nucleic Acids Research 1991, 19:5079.
11. Bentzen P., Taggart C.T., Ruzzante D.E., Cook D. Microsatellite polymorphism and the population structure of Atlantic cod ({biGadus morhua}) in the northwest Atlantic Canadian. Journal of Fisheries and Aquatic Science 1996, 53:2706-2721.
12. Bielawski J.P., Pumo D.E. Randomly amplified polymorphic DNA (RAPD) analysis of Atlantic coast striped bass. Heredity 1997, 78:32-40.
13. Black W.C., DuTeau N.M., Puterka G.J., Nechols J.R., Pettorini J.M. Use of the random amplified DNA polymerase chain reaction (RAPD-PCR) to detect DNA polymorphisms in aphids (Homoptera: Aphididae). Bulletin Entomological Research 1992, 82:151-159.
14. Caccone A., Allegrucci G., Fortunato C., Sbordoni V. Genetic differentiation within the European sea bass ({biD. labrax}) as revealed by RAPD-PCR assays. Journal of Heredity 1997, 88:316-324.
15. Caetano-Anolles G., Bassam G.J., Gresshof P.M. High resolution DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology 1991, 9:553-556.
16. Cagigas M.E., Vazquez E., Blanco G., Sanchez J.A. Combined assessment of genetic variability in populations of brown trout ({biSalmo trutta} L.) based on allozymes, microsatellites and RAPD markers. Marine Biotechnology 1999, 1:286-296.
17. Callejas C., Ochando M.D. Molecular identification (RAPD) of the eight species of the genus {biBarbus} (Cyprinidae) in the Iberian Peninsula. Journal of Fish Biology 2001, 59:1589-1599.
18. Chen C., Shi T., Sun S., Yu H., Sun Z., Kong J. Identification and phylogenetic relationships among four species of pufferiish in Fugu as determined by RAPD markers. Marine Fisheries Research 2001, 22:32-36.
19. Chow S., Takeyama H. Intron length variation observed in the creatine kinase and ribosomal protein genes of the swordfish {biXiphias gladius}. Fisheries Science 1998, 64:397-402.
20. Cifarelli R.A., Gallitelli M., Cellini F. Random amplified hybridisation microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones. Nucleic Acids research 1995, 23:3802-3803.
21. Clark A.G., Lanigan C.M.S. Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution 1993, 10:1096-1111.
22. Cafforth M.A., Milawka J.M. Identification of marine invertebrate larvae by means of PCR-RAPD species-specific markers. Limnology and Oceanography 1995, 40:181-189.
23. Comincini S., Lanfredi M., Rossi R., Fontana F. Use of RAPD markers to determine the genetic relationships among sturgeons (Acipenseridae, Pisces). Fisheries Science 1998, 64:35-38.
24. Dahle G., Rahman M., Eriksen A.G. RAPD fingerprinting used for discriminating among three populations of Hilsa shad ({biTenualosa ilisha}). Fisheries Research 1997, 32:263-269.
25. D'Amoto E., Corach D. Genetic diversity of populations of the freshwater shrimp {biMacrobrachium borelli} (Caridea: palaemonidae) evaluated by RAPD analysis. Journal of Crustacean Biology 1996, 16:650-655.
26. Degani G., Jackson K., Goldberg D., Yehuda Y. Application of RAPD in study of genetic variations in Cichlidae in Israel. Journal of Aquaculture in the Tropics 2000, 15:219-227.
27. Devos K.M., Gale M.D. The use of random amplified DNA markers in wheat. Theoretical Applied Genetics 1992, 84:567-572.
28. Dinesh K.R., Lim T.M., Chua K.L., Chan W.K., Phang V.P.E. RAPD analysis; an efficient method of DNA fingerprinting in fishes. Zoological Science 1993, 10:849-854.
29. Ellsworth D.L., Rittenhouse K.D., Honeycutt R.L. Artifactual variation in randomly amplified polymorphic DNA (RAPD) banding patterns. Bio Techniques 1993, 14:214-217.
30. Elo K., Ivanoff S., Vuorinen J.A., Piironen J. Inheritance of RAPD markers and detection of interspecific hybridization with brown trout and Atlantic salmon. Aquaculture 1997, 152:55-65.
31. Foo C.L., Dinesh K.R., Lim T.M., Cahn W.K., Phang V.P.E. Inheritance of RAPD markers in the guppy fish {biPoecilia reticulata}. Zoological Science 1995, 12:535-541.
32. Fuchs H., Gross R., Stein H., Rottmann O. Application of molecular genetic markers for the differentiation of bream ({biAbramis brama} L.) populations from the rivers Main and Danube. Journal of Applied Ichthyology 1998, 14:49-55.
33. Garcia D.K., Benzie J.A.H. RAPD markers of potential use in penaeid prawn ({biPenaeus monodon}) breeding programs. Aquaculture 1995, 130:137-144.
34. Garcia D.K., Dhar A.K., Aicivar-Warren A. Molecular analysis of a RAPD marker (B20) reveals two microsatellites and differential mRNA expression in {biPenaeus vannamei}. Molecular Marine Biology and Biotechnology 1996, 5:71-83.
35. Gasper B.R., Koppelman J.B., Schwery S.P., Eckdahl T.T. Genetic variation among {biCottus} species in Missouri revealed by RAPD analysis. American Midland Naturalist 2001, 146:264-270.
36. Gilbert D.A., Lehman N., O'Brien S.J., Wayne R.K. Genetic fingerprinting reflects population differentiation in the California Channel Island fox. Nature 1990, 344:764-766.
37. Gomes C., Dales R.B.G., Oxenford H.A. The application of RAPD markers in stock discrimination of the four-wing flying fish, {biHirundichthys affinis}, in the central western Atlantic. Molecular Ecology 1998, 7:1029-1039.
38. Gomes C., Oxenford H.A., Dales R.B.G. Mitochondrial DNA d-loop variation and implications for stock structure of the four-wing flying fish, {biHirundichthys affinis}, in the central western Atlantic. Bulletin of Marine Science 1999, 64:485-500.
39. Hadrys H., Balick M., Schierwater B. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Molecular Ecology 1992, 1:55-63.
40. Harding G.C., Kenchington E.L., Bird C.J., Pezzack D.S., Landry D.C. Genetic relationships among subpopulations of the American lobster ({biHomarus americanus}) as revealed by random amplified polymorphic DNA. Canadian Journal of Fisheries and Aquatic Sciences 1997, 54:1762-1771.
41. Heipel D.A., Bishop J.D., Brand A.R., Thorpe J.P. Population genetic differentiation of the great scallop {biPecten maximus} in western Britain investigated by random amplified polymorphic DNA. Marine Ecology Progress Series 1998, 162:163-171.
42. Hillis D.M., Moritz C. Molecular Systematics 1990, Sinauer Associates, Sunderland, MA.
43. Hu J., Quiros C.F. Identification of broccoli and cauliflower cultivars with RAPD markers. Plant Cell Reports 1991, 10:505-511.
44. Huang B.X., Peakall R., Hanna P.J. Analysis of genetic structure of blacklip abalone ({biHaliotis rubra}) populations using RAPD, minisatellite and microsatellite markers. Marine Biology 2000, 136:207-216.
45. Hunt G.J., Page R.E. Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee. Theoretical and Applied Genetics 1992, 85:15-20.
46. Iyengar A., Piyapattanakorn S., Stone D.M., Howell D.A., Baynes S.M., Maclean N. Identification of microsatellite repeats in turbot ({biScophthalmus maximus}) and Dover sole ({biSolea solea}) using RAPD based technique: characterization of microsatellite markers in Dover sole. Marine Biotechnology 2000, 2:49-56.
47. Jackson K., Goldberg D., Yehuda Y., Degani G. Molecular variation in koi ({biCyprinus carpio}) of various color patterns. Israeli Journal of Aquaculture 2000, 52:151-158.
48. Jayasankar P., Dharmalingam K. Analysis of RAPD polymorphisms in {biRastrelliger kanagurta} off India. Naga, the ICLARM Quarterly: July-Dec. 1997, 1997:52-56.
49. Jeffreys A.J., Morton D.B. DNA fingerprinting of dogs and cats. Animal Genetics 1987, 18:1-15.
50. Kessing B., Croom H., Martin A., McIntosh C., McMillan W.O., Palumbi S. The Simple Fool's Guide to PCR 1990, University of Hawaii, Honolulu.
51. Klinburga S., Boonyapakdee A., Pratoomchat B. Development of species-specific markers of the tropical oyster {biCrassostrea belcheri} in Thailand. Marine Biotechnology 2000, 2:476-484.
52. Klinburga S., Boonyapakdee A., Pratoomchat B. Genetic diversity and species diagnostic markers of mud crabs (genus {biScylla}) in Eastern Thailand determined by RAPD analysis. Marine Biotechnology 2000, 2:180-187.
53. Klinburga S., Siludjai D., Wudthijinda W., Tassanakajon A., Jaraybhand P., Menasveta P. Genetic heterogeneity of the giant tiger shrimp ({biPenaeus monodon}) in Thailand revealed by RAPD and mitochondrial DNA RFLP analysis. Marine Biotechnology 2001, 3:428-438.
54. Lehmann D., Hettwer H., Taraschewski H. RAPD-PCR investigations of systematic relationships among four species of eels (Teleostei: Anguillidae), particularly {biAnguilla anguilla} and {biA. rostrata}. Marine Biology 2000, 137:195-204.
55. Liu Z., Li P., Argue B.J., Dunham R.A. Inheritance of RAPD markers in channel catfish ({biIctalurus punctatus}), blue catfish ({biI. furcatus}), and their F1, F2 and backross hybrids. Animal Genetics 1998, 29:58-62.
56. Lu R., Shi T., Liu X., Chen C., Kong J. Identification of three populations (Chinese {biFugu rubripes}, Japanese {biFugu rubripes} and {biFugu pseudommus}) using RAPD markers. Transactions of Oceanology and Limnology 1999, 4:38-42. (in Chinese with English abstract).
57. Lu R., Qiu T., Xiang C., Xie H., Zhang J. RAPD and AFLP techniques for the analysis of genetic relationships in two genera of Decapoda. Crustaceana 2000, 73:1027-1036.
58. Lynch M. The similarity index and DNA fingerprinting. Molecular Biology and Evolution 1990, 7:478-484.
59. Lynch M., Milligan B.G. Analysis of population genetic structure with RAPD markers. Molecular Ecology 1994, 3:91-99.
60. Macaranas J.M., Mather P.B., Hoeben P., Capra M.F. Assessment of genetic variation in wild populations of the redclaw crayfish ({biCherax quadricarinatus}, von Martens 1868) by means of allozyme and RAPD-PCR markers. Marine and Freshwater Research 1995, 46:1217-1218.
61. Mamuris Z., Apostolidis A.P., Theodororou A.J., Triantaphyllidis C. Application of random amplified polymorphic DNA (RAPD) markers to evaluate intraspecifc genetic variation in red mullet ({biMullus barbatus}). Marine Biology 1998, 132:171-178.
62. Mamuris Z., Apostolidis A.P., Triantaphyllidis C. Genetic protein variation in red mullet ({biMullus barbatus}) and striped red mullet ({biM. surmultus}) populations from the Mediterranean Sea. Marine Biology 1998, 130:353-360.
63. Mamuris Z., Stamatis C., Bani M., Triantaphyllidis C. Taxonomic relationships between four species of the Mullidae family revealed by three genetic methods: allozymes, random amplified polymorphic DNA and mitochondrial DNA. Journal of Fish Biology 1999, 55:572-587.
64. Meruane J., Takagi M., Taniguchi N. Species identification and polymorphisms using RAPD-PCR in penaeid prawns {biPenaeus japonicus} and {biMetanephrops ensis}. Fisheries Science 1997, 63:149-151.
65. Nadeau J.H., Bedigian H.G., Bouchard G., Denial T., Kosowsky M., Norberg R., Pugh S., Sargent E., Turner R., Paigen B. Multilocus markers for mouse genome analysis: PCR amplification based on single primers of arbitrary sequence. Mammalian Genome 1992, 3:55-64.
66. Naish K.A., Warren M., Bardakci F., Skibinski D.O.F., Carvalho G.R., Mair G.C. Multilocus DNA fingerprinting and RAPD reveal similar genetic relationships between strains of {biOreochromis niloticus} (Pisces: Cichlidae). Molecular Ecology 1995, 4:271-274.
67. Nei M. Molecular Evolutionary Genetics 1987, 512 pp., Columbia University Press, New York.
68. Nesbo C.L., Magnhagen C., Jakobsen K.S. Genetic differentiation among stationary and anadromous perch ({biPerca fluviatilis}) in the Baltic Sea. Hereditas 1998, 129:241-249.
69. Nilsson J., Schmitz M. Random amplified polymorphic DNA (RAPD) in Arctic char. Nordic Journal of Freshwater Research 1995, 71:372-377.
70. Parker R.W., Paige K.N., DeVries A.L. Genetic variation among populations of the Antarctic toothfish: evolutionary insights and implications for conservation. Polar Biology 2002, 25:256-261.
71. Patwary M.U., Mackay R.M., van der Meer J.P. Revealing genetic markers in {biGelidium vagum} (Rhodophyta) through the random amplified polymorphic DNA (RAPD) technique. Journal Phycology 1993, 29:216-222.
72. Patwary M.U., Kenchington E.L., Bird C.J., Zouros E. The use of random amplified polymorphic DNA markers in genetic studies of the sea scallop {biPlacopecten magellanicus} (Gmelin, 1791). Journal of Shellfish Research 1994, 13:547-553.
73. Penner G.A., Bush A., Wise R., Kim W., Domier L., Kasha K., Laroche A., Scoles G., Molnar S.J., Fedak G. Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. PCR Methods and Applications 1993, 2:341-345.
74. Pierce J.C., Tan G., Gaffney P.M. Delaware Bay ands Chesapeake Bay populations of the horseshoe crab {biLimulus polyphemus} are genetically distinct. Estuaries 2000, 23:690-698.
75. Rabouam C., Comes A.M., Bretagnolle V., Humbert J.-F., Periquets G., Bigots Y. Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) analysis. Molecular Ecology 1999, 8:493-503.
76. Riedy M.F., Hamilton W.J., Aquadro C.F. Excess of non-parental bands in offspring from known primate pedigrees assayed using RAPD PCR. Nucleic Acids Research 1992, 20:918.
77. Royo L.J., Cristobal C., Canon J., Dunner S. Analysis of genetic variation of brown trout ({biSalmo trutta fario}) populations using RAPD markers in pools of DNA. Animal Genetics 1996, 27:17-42.
78. Saitoh K. Genetic variation and local differentiation in the Pacific cod {biGadus macrocephalus} around Japan revealed by mtDNA and RAPD markers. Fisheries Science 1998, 64:673-679.
79. Schneider M., Mandorf T.H., Rubach K. Species identification of fishes with the DNA analysis and RAPD technique. Deutsche Lebensmittel-Rundscahu 1997, 93:137-140.
80. Smith J.J., Scott-Craig J.S., Leadbetter J.R., Bush G.L., Roberts D.L., Fulbright D.W. Characterization of random amplified polymorphic DNA (RAPD) products from {biXanthomas campestris} and some comments on the use of RAPD products in phylogenetic analysis. Molecular Phylogenetics and Evolution 1994, 3:135-145.
81. Smith P.J., Roberts C.D., McVeagh S.M., Benson P.G. Genetic evidence for two species of tarakihi (Teleostei: Cheilodactylidae {biNemadactylus}) in New Zealand waters. New Zealand Journal of Marine and Freshwater Research 1996, 30:209-220.
82. Smith P.J., Benson P.G., McVeagh S.M. A comparison of three genetic methods for stock discrimination of orange roughy, {biHoplostethus atlanticus}: allozymes, PCR amplified mitochondrial DNA and random amplified polymorphic DNA. Fishery Bulletin 1997, 94:800-811.
83. Song L., Xiang J., Zhou L., Zhang S., Liu R. Studies of random amplified polymorphic DNA (RAPD) markers on genomic DNA polymorphism in six species of marine shrimp. Oceanologia et Limnologia Snicia 1999, 30:62-67.
84. Song L., Liu B., Xiang J., Qian P.-Y. Molecular phylogeny and species identification of pufferfish of the genus {biTakifugu} (Tetraodontiformes, Tetraodontiade). Marine Biotechnology 2001, 3:398-406.
85. Song L., Liu B., Wang Z., Li H., Xiang J., Qian P.-Y. Phylogenetic relationships among pufferfish of genus {biTakifugu} by RAPD analysis. Chinese Journal of Oceanology and Limnology 2001, 19:128-134.
86. Stott W., Ihssen P.E., White B.N. Inheritance of RAPD molecular markers in lake trout {biSalvelinus namaycush}. Molecular Ecology 1997, 6:609-613.
87. Sun J., Lou Y., Yao J. Application of RAPD technology to analyze the genetic diversity of three breeds of red carp. Shangai Shuichan Daxue Xuebao 2001, 10:207-212.
88. Tassanakajon A., Pongsomboon S., Rimphanitchayakit V., Jarayabhand P., Boonsaeng V. Random amplified polymorphic DNA (RAPD) markers for determination of genetic variation in wild populations of the black tiger prawn ({biPenaeus monodon}) in Thailand. Molecular Marine Biology and Biotechnology 1997, 6:110-115.
89. Tassanakajon A., Pongsomboon S., Jarayabhand P., Klinbunga S., Boonsaeng V. Genetic structure in wild populations of the black tiger shrimp ({biPenaeus monodon}) using randomly amplified polymorphic DNA analysis. Journal of Marine Biotechnology 1998, 6:249-254.
90. Ulrich I., Muller J., Schutt C., Buchholz F. A study of population genetics in the European lobster {biHomarus gammarus} (Decapoda, Nephropidae). Crustaceana 2001, 74:825-837.
91. Warnke K., Soeller R., Blohm D., Saint-Paul U. Rapid differentiation between {biOctopus vulgaris} Cuvier (1797) and {biOctopus mimus} Gould (1852) using randomly amplified polymorphic DNA. Journal of Zoological Systematics and Evolutionary Research 2000, 38:119-122.
92. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 1990, 18:7213-7218.
93. Welsh J., Peterson C., McClelland M. Polymorphisms generated by arbitrarily primed PCR in the mouse: application to strain identification and genetic mapping. Nucleic Acids Research 1991, 19:303-306.
94. Wetton J.H., Carter R.E., Parkin D.T., Walters D. Demographic study of a wild house sparrow population by DNA fingerprinting. Nature 1987, 327:147-149.
95. Williams J.G.K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V. DNA polymorphisms amplified by arbitrary primers are useful genetic markers. Nucleic Acids Research 1990, 18:6531-6535.
96. Xia D., Cao Y., Wu T., Wang T. A study on genetic variation of tilapia fish with RAPD analysis and its application to heterosis. Journal of Fisheries of China 1999, 23:27-32.
97. Zhang H., Rongzong L., Zhang X., Chen T., Xiao T., Jinheng L. Assessment of population genetic variation of grass carp and common carp using RAPD fingerprints. Acta Hydrobiologica Sinica 1998, 22:168-173.