Nuclear DNA markers in plant biosystematic research

Opera Botanica

Volumn , Issue 132, 1997, Pages 137-148

  Bachmann, Konrad ^a,b  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0030832596     PISSN: 00785237     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Conference Paper

References (80)

1. Adams, R. P. & Demeke, T. 1993. Systematic relationships in Juniperus based on random amplified polymorphic DNAs (RAPDs). - Taxon 42: 553-571.
2. Akkaya, M. S., Bhagwat, A. A. & Cregan, P. B. 1992. Length polymorphisms of simple sequence repeat DNA in soybean. - Genetics 132: 1131-1139.
3. Aldrich, P. & Doebley, J. 1992. Restriction fragment variation in the nuclear ans chloroplast genomes of cultivated and wild Sorghum bicolor. - Theor. Appl. Genet. 85: 293-302.
4. Bachmann, K. 1992. Nuclear DNA markers in angiosperm taxonomy. - Acta Bot. Neerl. 41: 369-384.
5. _ 1994. Molecular markers in plant ecology. - New Phytol. 126: 403-418.
6. _ & Hombergen, E. J. in press. Mapping genes for phenotypic variation in Microseris (Lactuceae) with molecular markers. - In: Hind, D. J. N. (ed.), Compositae. Systematics. Biology, Uitilization. Kew Gardens, London, vol. 2: 23-43.
7. Baldwin, B. G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. - Mol. Phyl. Evol. 1: 3-16.
8. _, Sanderson, M. J., Porter, J. M., Wojciechowski, M. F., Campbell, C. S. & Donoghue, M. J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. - Ann. Miss. Botanical Garden 82: 247-277.
9. Beckmann, J. S. & Soller, M. 1990. Toward a unified approach to the genetic mapping of eukaryotes based on sequence-tagged microsatellite sites. - Bio/Technology 8: 930-932.
10. Brauner, S., Crawford, D. J. & Stuessy, T. F. 1992.Ribosomal DNA & RAPD variation in the rare plant family Lactoridaceae. - Amer. J. Bot. 79: 1436-1439.
11. Brochmann, C., Nilsson, T. & Gabrielsen, T. M. 1996. A classic example of postglacial allopolyploid speciation confirmed by nucleotide sequences and RAPD markers: Saxifraga osloensis. - Acta Univ. Ups. Symb. Bot. Ups. 31: 75-89.
12. Brubaker, C. L.& Wendel, J. F. 1994. Reevaluating the origin of domesticated cotton (Gossypium hirsutum, Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). - Amer. J. Bot. 81: 1309-1326.
13. Chambers, K. L. 1955. A biosystemtic study of the annual species of Microseris. - Contrib. Dudley Herbarium 4: 207-312.
14. Clark, A. G. & Lanigan, C. M. S. 1993. Prospects for estimating nucleotide divergence with RAPDs. - Mol. Biol. Evol. 10: 1096-1111.
15. Clegg, M. T. & Zurawski, G. 1992. Chloroplast DNA and the study of plant phylogeny. - In: Soltis, P. S., Soltis, D. E. & Doyle, J. J.(eds), Molecular Systematics of Plants.Chapman & Hall, New York, pp. 1-13.
16. Condit, R. & Hubbell, S. P. 1991. Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. - Genome 34: 66-71.
17. Cooke, P. H. & Oakshott, J. G. 1989. Amino acid polymorphisms for esterase-6 in Drosophila melanogaster. - Proc. Natl. Acad. Sci. USA 86: 1426-1430.
18. Crawford, D. J. 1990. Plant Molecular Systematics. - Wiley, New York.
19. _, Brauner, S., Cosner, M. B. & Stuessy, T. F. 1993. Use of RAPD markers to document the origin of the intergeneric hybrid xMargyracaena skottsbergii (Rosaceae) on the Juan Fernandez Islands. - Amer. J. Bot. 80: 89-92.
20. Dallas, J. F. 1988. Detection of DNA 'fingerprints' of cultivated rice by hybridization with a human minisatellite probe. - Proc. Natl. Acad. Sci. USA 85: 6831-6835.
21. Ellsworth, D. L., Rittenhouse, K. D. & Honeycutt, R. L. 1993. Artifactual variation in randomly amplified polymorphic DNA banding patterns. - Biotechniques 14: 214-217.
22. Excoffier, L., Smouse, P. E. & Quattro, J. M. 1992. Aalysis of molecular variance inferred from metric distances among DNA haplotypes: application to human DNA mitochondrial restriction data. - Genetics 131: 479-491.
23. Fritsch, P. & Rieseberg, L. H. 1992. High outcrossing rates maintain male and hermaphrodite individuals in populations of the flowering plant Datisca glomerata. - Nature 359: 633-636.
24. Goldstein, D. B., Ruiz Linares, A., Cavalli-Sforza, L. L. & Feldman, M. W. 1995. An evaluation of genetic distances for use with microsatellite loci. - Genetics 139: 463-471.
25. Hadrys, H., Balick, M. & Schierwater, B. 1992. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. - Mol. Ecol. 1: 55-63.
26. Halward, T. M., Stalker, H. T., La Rue, E. A. & Kochert, G. 1991. Genetic variation detectable with molecular markers among unadapted germplasm resources of cultivated peanut and relative wild species. - Genome 34: 1013-1020.
27. Hemleben, V. & Zentgraf, U. 1994. Structural organization and regulation of transcription by RNA polymerase I of plant nuclear ribosomal RNA genes. - In: Nover, L. (ed.) Plant Promoters and Transcription Factors, Springer, Berlin, pp. 1-24.
28. Heun, M., Murphy, J. P. & Phillips, T. D. 1994. A comparison of RAPD and isozyme analyses for determining the genetic relationships among Avena sterilis L. accessions. - Theor. Appl. Genet. 87: 689-696.
29. Huff, D. R., Peakall, R. & Smouse, P. E. 1993. RAPD variation within and among natural populations of outcrossing buffalograss [Buchlöe dactylides (Nutt.) Engelm.]. - Theor. Appl. Genet. 86: 927-934.
30. Jeffreys, A. J., Turner, M. & Debenham, P. 1991. The efficiency of multilocus DNA fingerprint probes for the individualization and establishment of family relationships determined from extensive casework. - Am. J. Human Genet. 48: 824-840.
31. _, Wilson, V. & Thein, S. L. 1985. Hypervariable 'minisatellite' regions in human DNA. - Nature (London) 314: 67-73.
32. Kijas, J. M. H., Fowler, J. C. S. & Thomas, M. R. 1995. An evaluation of sequence tagged microsatellite site markers for genetic analysis within citrus and related species. - Genome 38: 349-355.
33. Kim, K.-J. & Jansen, R. K. 1994. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia, Asteraceae): additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. - Plant Syst. Evol. 190: 157-185.
34. Lewontin, R. C. 1974. The Genetic Basis of Evolutionary Change. - Columbia University Press. New York.
35. Liu, Z. & Furnier, G. R. 1993. Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variation within and between trembling aspen and bigtooth aspen. - Theor. Appl. Genet. 87: 97-105.
36. Lynch, M. 1990. The similarity index and DNA fingerprinting. - Mol. Biol. Evol. 7: 478-484.
37. _ & Milligan, B. G. 1994. Analysis of population genetic structure with RAPD markers. - Mol. Ecol. 3: 91-99.
38. Macpherson, J. M., Eckstein, P. E., Scoles, G. J. & Gajadhar, A. A. 1993. Variability of the random amplified polymorphic DNA assay among thermal cyclers, and effects of primer and DNA concentration. - Mol. Cell. Probes 7: 293-299.
39. Marsolais, J. V., Pringle, J. S. & White, N. B. 1993. Assessment of random amplified polymorphic DNA (RAPD) as genetic markers for determining the origin of interspecific lilac hybrids. - Taxon 42: 531-537.
40. Martienssen, R. A. & Baulcombe, D. C. 1989. An unusual wheat insertion sequence (WIS1) lies upstream of an aamylase gene in hexaploid wheat and carries a minisatellite array. - Mol. Gen. Genet. 217: 401-410.
41. Meunier, J. R. & Grimont, P. A. D. 1993. Factors affecting reproducibility of random amplified polymorphic DNA fingerprinting. - Res. Microbiol. 144: 373-379.
42. Michelmore, R. W., Peran, I. & Kesseli, R. V. 1991. Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genome regions using segregating populations. - Proc. Natl. Acad. Sci. USA 88: 9828-9832.
43. Miller, J. C. & Tanksley, S. D. 1990. RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. - Theor. Appl. Genet. 80: 437-448.
44. Morgante, M. & Olivieri, A. M. 1993. PCR amplified microsatellites as markers in plant genetics. - Plant J. 3: 175-182.
45. Mosseler, A. J., Egger, K. N. & Innes, D. J. 1993. Life history and the loss of genetic diversity in red pine. - Amer. J. Bot. 80: abstract 240.
46. Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G. & Erlich, H. 1986. Specific amplification of DNA in vitro: the polymerase chain reaction. - Cold Spring Harbor Symp. Quant. Biol. 51: 263-273.
47. Oakeshott, J. G., Boyce, T. M., Rusell, R. J. & Healy, M. 1995. Molecular insights into the evolution of an enzyme; esterase 6 in Drosophila. - Trends Ecol. Evol. 10: 103-110.
48. Paran, I. & Michelmore, R. W. 1993. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. - Theor. Appl. Genet.85: 985-993.
49. Peakall, R., Smouse, P. E. & Huffs, D. R. 1995. Evolutionary implications of allozyme & RAPD variation in diploid populations of dioecious buffalograss Buchloë dactylides. - Mol. Ecol. 4: 135-147.
50. Penner, G. A., Bush, A., Wise, R., Kim, W., Domier, L., Kasha, K., Laroche, A., Scoles, G., Molner, S. & Fedak, G. 1993. Reproducibility of random amplified polymorphic DNA (RAPD) analysis among laboratories. - PCR Meth. Applic. 2: 341-345.
51. Poulsen, G. B., Kahl, G. & Weising, K. 1993. Abundance & polymorphisms of simple repetitive DNA sequences in Brassica napus L. - Theor. Appl. Genet. 85: 994-1000.
52. Rafalski, J. A. & Tingey, S. V. 1993. Genetic diagnosis in plant breeding: RAPDs. microsatellites and machines. - Trends in Genetics 9: 275-280.
53. Richardson, T., Cato, S., Ramser, J., Kahl, G. & Weising, K. 1995. Hybridization of microsatellites to RAPD: a new source of polymorphic markers. - Nucleic Acids Res. 23: 3789-3799.
54. Rieseberg, L., Choi, H., Chan, R. & Spore, C. 1993. Genomic map of a diploid hybrid species. - Heredity 70: 285-293.
55. Roelofs, D. & Bachmann, K. 1995. Chloroplast & nuclear DNA variation amog homozygous plants in a population of the autogamous annual Microseris douglasii (Asteraceae, Lactuceae). - Plant Syst. Evol. 196:185-194.
56. Rogstad, S. H., Patton, J. C. & Schaal, B. A. 1988. A human minisatellite probe reveals RFLPs among individuals of two angiosperms. - Nucl. Acids Res. 16: 11378.
57. Rossetto, M., Weaver, P. K. & Dixon, K. W. 1995. Use of RAPD analysis in devising conservation strategies for the rare and endangered Grevillea scapigera (Proteaceae). - Mol. Ecol. 4: 321-329.
58. Ryskov, A. P., Jincharadze, A. G., Prosnyak, M. I., Ivanov, P. L. & Limborskaya, S. A., 1988. M13 phage DNA as a universal marker for DNA fingerprinting of animals, plants, and microorganisms. - FEBS Letters 233: 388-392.
59. Schierwater, B. & Ender, A. 1993. Different thermostable DNA polymerases may amplify different RAPD products. - Nucl. Acids Res. 21: 4647-4648.
60. Sneath, P. H. A. & Sokal., R. R. 1973. Numerical Taxonomy. - Freeman, San Francisco.
61. Song, K. M., Osborn, T. C. & Williams, P. H. 1988. Brassica taxonomy based on nuclear restriction fragment length polymorphisms (RFLPs). 1. Genome evolution of diploid and amphidiploid species. - Theor. Appl. Genet. 75: 784-794.
62. Swofford, D. L. 1991. PAUP, phylogenetic analysis using parsimony, version 3.0. - Natural History Survey, Champaign, IL.
63. Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. - Nucleic Acids Res. 17: 6463-6471.
64. _, Trick, M. & Dover, G. A. 1986. Cryptic simplicity in DNA is a major source of genetic variation. - Nature 322: 652-656.
65. Thomas, M. R. & Scott, N. S. 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). - Theor. Appl. Genet. 86: 985-990.
66. Van Buren, R., Harper, K. T., Andersen, W. R., Stanton, D. J., Seyoum, S. & England, J. L. 1994. Evaluating the relationship of autumn buttercup (Ranunculus acriformis var. aestivalis) to some close congeners using random amplified polymorphic DNA. - Amer. J. Bot. 81: 514-519.
67. Van Heusden, A. W. & Bachmann, K. 1992a. Genotype relationships in Microseris elegans (Asteraceae, Lactuceae) revealed by DNA amplification from arbitrary primers (RAPDs). - Plant Syst. Evol. 179: 221-233.
68. _ & Bachmann, K. 1992b. Nuclear DNA polymorphisms among strains of Microseris bigelovii (Asteraceae, Lactuceae) amplified from arbitrary primers. - Botanica Acta 105: 331-336.
69. _ & Bachmann, K. 1992c. Genetic differentiation of Microseris pygmaea (Asteraceae, Lactuceae) studied with DNA amplification from arbitrary primers (RAPDs). - Acta Bot. Neerl. 41: 385-395.
70. Van Houten, W. H., van Heusden, A. W., Rouppe v.d. Voort, J., Raijmann, L. & Bachmann, K. 1991. Hypervariable DNA fingerprint loci in Microseris pygmaea (Asteraceae, Lactuceae). - Bot. Acta 104: 252-256.
71. _, Scarlett, N. & Bachmann, K. 1993. Nuclear DNA markers of the Australian tetraploid Microseris scapigera and its North American diploid relatives. - Theor. Appl. Genet. 87: 498-505.
72. Veuille, M. & King, L. M. 1995. The molecular bases of Est5B polypmorphism in Drosophila pseudoobscura. - Genetics 141: 255-262.
73. Vos, P., Hogers, R., Bleeker, M., Reijans, M., Van der Lee, M., Homes, M. Frijters, A., Post, J., Peleman, J., Kuiper, M. & Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. - Nucl. Acids Res. 23: 4407-4414.
74. Weising, K., Nybom, H., Wolff, K. & Meyer, W. 1995. DNA Fingerprinting in Plants & Fungi. - CRC Press, Boca Raton.
75. Welsh, S. L. & McClelland, M. 1990. Fingerprinting genomes using PCR with arbitrary primers. - Nucl. Acids Res. 18: 7213-7218.
76. Wendel, J. F., Schnabel, A. & Seelanan, T. 1995. Bi-directional interlocus concerted evolution following allopolyploidization in cotton (Gossvpium). - Proc. Natl. Acad. Sci. USA 92: 280-284.
77. White, T. J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. - In: Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J. (eds), PCR Protocols, Academic Press, San Diego, pp. 315-322.
78. Whitkus, R., Doebley, J. & Wendel, J. F. 1994. Nuclear DNA markers in systematics and evolution. - In: Phillips, R. L. & Vasil, I. K. (eds), DNA-Based Markers in Plants. Kluwer, Dordrecht, pp. 116-141.
79. Williams, J. G. K., Hanafey, M. K., Rafalski, J. A. & Tingey, S. V. 1993. Genetic analysis using random amplified polymorphic DNA markers. - Methods in Enzymology 218: 704-740.
80. _, Kubelik, A. R., Livak, J. K., Rafalski, J. A. & Tingey, S. V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. - Nucl. Acids Res. 18: 6531-6535.