Contributions of PCR-Based Methods to Plant Systematics and Evolutionary Biology

  • Andrea D. Wolfe
  • Aaron Liston


In less than a decade, the polymerase chain reaction (PCR) has evolved into the common denominator of molecular biology for nucleic acid research. The most important impact of PCR in plant molecular systematics has been rapid amplification of DNA regions, facilitating nucleotide sequencing (see Chapter 1). However, there are many other techniques aside from DNA sequencing in which PCR is appropriate and extremely useful. In this chapter we review these applications of PCR in plant systematics and highlight areas of research that have been underused in plant molecular systematics laboratories.


Internal Transcribe Spacer Chloroplast Genome Nucleic Acid Research Intron Loss Apply Genetic 
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Literature Cited

  1. Aagaard, J. E., S. S. Vollmer, F. C. Sorensen, and S. H. Strauss. 1995. Mitochondrial DNA products among RAPD profiles are frequent and strongly differentiated between races of Douglas-fir. Molecular Ecology 4:441–447.PubMedCrossRefGoogle Scholar
  2. Abo-elwafa, A., K. Murai, and T. Shimada. 1995. Intra-and inter-specific variations in Lens revealed by RAPD markers. Theoretical and Applied Genetics 90:335–340.Google Scholar
  3. Abrol, S., and V. K. Chaudhary. 1993. Excess PCR primers inhibit DNA cleavage by some restriction endonucle-ases. BioTechniques 15:630–631.PubMedGoogle Scholar
  4. Adams, R. P., and T. Demeke. 1993. Systematic relationships in Juniperus based on random amplified polymorphic DNAs (RAPDs). Taxon 42:553–571.CrossRefGoogle Scholar
  5. Akkaya, M. S., A. A. Bhagwat, and P. B. Cregan. 1992. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1193.PubMedGoogle Scholar
  6. Amato, G., and J. Gatesy. 1994. PCR assays of variable nucleotide sites for identification of conservation units. In Molecular Ecology and Evolution: Approaches and Applications, eds. B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, pp. 215–226. Birkhäuser Verlag, Basel, Switzerland.Google Scholar
  7. Amos, B., C. Schlötterer, and D. Tautz. 1993. Social structure of pilot whales revealed by analytical DNA profiling. Science 260:670–672.PubMedCrossRefGoogle Scholar
  8. Anderson, J. A., G. A. Churchill, J. E. Autrique, S. D. Tanksley, and M. E. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36:181–186.PubMedCrossRefGoogle Scholar
  9. Apuya, N. R., B. L. Frazier, P. Keim, E. J. Roth, and K. G. Lark. 1988. Restriction fragment length polymorphisms as genetic markers in soybean Glycine max (L.) Merrill. Theoretical and Applied Genetics 75:889–901.Google Scholar
  10. Arnold, M. L., C. M. Buckner, and J. J. Robinson. 1991. Pollen mediated introgression and hybrid speciation in Louisiana irises. Proceedings of the National Academy of Sciences U.S.A. 88:1398–1402.CrossRefGoogle Scholar
  11. Asmussen, C., and A. Liston. 1998. Chloroplast DNA characters, phylogeny, and classification of Lathryus (Fabaceae). American Journal of Botany, in press.Google Scholar
  12. Ayliffe, M. A., G. J. Lawrence, J. G. Ellis, and A. J. Pryor. 1994. Heteroduplex molecules formed between allelic sequences cause nonparental RAPD bands. Nucleic Acids Research 22:1632–1636.PubMedCrossRefGoogle Scholar
  13. Bachmann, K. 1994. Molecular markers in plant ecology. New Phytologist 126:403–418.CrossRefGoogle Scholar
  14. Bachmann, K. 1995. Progress and pitfalls in systematics: cladistics, DNA and morphology. Acta Botanica Neerlandica 44:403–419.Google Scholar
  15. Bachmann, K. 1997. Nuclear DNA markers in biosystematic research. Opera Botanica, in press.Google Scholar
  16. Bachmann, K., and E. J. Hombergen. 1996. Mapping genes for phenotypic variation in Microseris (Lactuceae) with molecular markers. In Compositae: Systematics, Biology, Utilization, eds. D. J. N. Hind and P. D. S. Caligari, Proceedings of the International Compositae Conference, Kew, 1994, Vol. 2, Biology and Utilization, pp. 22–43. Royal Botanical Gardens, Kew, England.Google Scholar
  17. Backeljau, T., L. De Bruyn, H. De Wolf, K. Jordaens, S. Van Dongen, R. Verhagen, and B. Winnepenninckx. 1995. Random amplified polymorphic DNA (RAPD) and parsimony methods. Cladistics 11:119–130.CrossRefGoogle Scholar
  18. Backeljau, T., L. De Bruyn, H. De Wolf, K. Jordaens, S. Van Dongen, and B. Winnepenninckx. 1996. Multiple UPGMA and neighbor-joining trees and the performance of some computer packages. Molecular Biology and Evolution 13:309–313.CrossRefGoogle Scholar
  19. Badenes, M. L., and D. E. Parfitt. 1995. Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation. Theoretical and Applied Genetics 90:1035–1041.CrossRefGoogle Scholar
  20. Baker, R. J., J. L. Longmire, and R. A. Van Den Bussche. 1995. Organization of repetitive elements in the upland cotton genome (Gossypium hirsutum). Journal of Heredity 86:178–185.Google Scholar
  21. Ballvora, A., J. Hesselbach, J. Niewöhner, D. Leister, F. Salamini, and C. Gebhardt. 1995. Marker enrichment and high-resolution map of the segment of potato chromosome VII harbouring the nematode resistance gene Grol. Molecular and General Genetics 249:82–90.PubMedCrossRefGoogle Scholar
  22. Baum, D. A., and K. J. Sytsma. 1994. A phylogenetic analysis of Epilobium (Onagraceae) based on nuclear ribosomal DNA sequences. Systematic Botany 19:363–388.CrossRefGoogle Scholar
  23. Becker, J., and M. Heun. 1995. Barley microsatellites: allele variation and mapping. Plant Molecular Biology 27:835–845.PubMedCrossRefGoogle Scholar
  24. Becker, J., P. Vos, M. Kuiper, F. Salamini, and M. Heun. 1995. Combined mapping of AFLP and RFLP markers in barley. Molecular and General Genetics 249:65–73.PubMedCrossRefGoogle Scholar
  25. Beckmann, J. S., and J. L. Weber. 1992. Survey of human and rat microsatellites. Genomics 12:627–631.CrossRefGoogle Scholar
  26. Bell, C. J., and J. R. Ecker. 1994. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144.PubMedCrossRefGoogle Scholar
  27. Benter, T., S. Papadopoulos, M. Pape, M. Manns, and H. Poliwoda. 1995. Optimization and reproducibility of random amplified polymorphic DNA in human. Analytical Biochemistry 230:92–100.PubMedCrossRefGoogle Scholar
  28. Bock, J. H., and J. L. Slightom. 1995. Fluorescence-based cycle sequencing with primers selected from a nonamer library. BioTechniques 19:60–62.PubMedGoogle Scholar
  29. Boge, A., R. Gerstmeier, and R. Einspanier. 1994. Molecular polymorphism as a tool for differentiating ground beetles (Carabus species): application of ubiquitin PCR/SSCP analysis. Insect Molecular Biology 3:267–271.PubMedCrossRefGoogle Scholar
  30. Borowsky, R. L., M. McClelland, R. Cheng, and J. Welsh. 1995. Arbitrarily primed DNA fingerprinting for phylogenetic reconstruction in vertebrates: the Xiphophorus model. Molecular Biology and Evolution 12:1022–1032.PubMedGoogle Scholar
  31. Boscherini, G., M. Morgante, P. Rossi, and G. G. Vendramin. 1994. Allozyme and chloroplast DNA variation in Italian and Greek populations of Pinus leucodermis. Heredity 73:284–290.PubMedCrossRefGoogle Scholar
  32. Bowcock, A. M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J. R. Kidd, and L. L. Cavalli-Sforza. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455–457.PubMedCrossRefGoogle Scholar
  33. Bradshaw, H. D., S. M. Wilbert, K. G. Otto, and D. W. Schemske. 1995. Genetic mapping of floral traits associated with reproductive isolation in monkeyflowers (Mimulus). Nature 376:762–765.CrossRefGoogle Scholar
  34. Bremer, B. 1991. Restriction data from chloroplast DNA for phylogenetic reconstruction: is there only one accurate way of scoring? Plant Systematics and Evolution 175:39–54.CrossRefGoogle Scholar
  35. Broun, P., and S. D. Tanksley. 1996. Characterization and genetic mapping of simple repeat sequences in the tomato genome. Molecular and General Genetics 250:39–49.PubMedCrossRefGoogle Scholar
  36. Brown, S. M., M. S. Hopkins, S. E. Mitchell, M. L. Senior, T. Y. Wang, R. R. Duncan, F. Gonzalez-Candelas, and S. Kresovich. 1996. Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench.]. Theoretical and Applied Genetics 93:190–198.CrossRefGoogle Scholar
  37. Bruford, M. W., and R. K. Wayne. 1993. Microsatellites and their application to population genetic studies. Current Biology 3:939–943.Google Scholar
  38. Brummer, E. C., J. H. Bouton, and G. Kochert. 1995. Analysis of annual Medicago species using RAPD markers. Genome 38:362–367.PubMedCrossRefGoogle Scholar
  39. Bruneau, A., J. J. Doyle, and J. D. Palmer. 1990. A chloroplast DNA inversion as a subtribal character in the Phaseoleae (Leguminosae). Systematic Botany 15:378–386.CrossRefGoogle Scholar
  40. Brunei, D. 1994a. A microsatellite marker in Helianthus annuus L. Plant Molecular Biology 24:397–400.CrossRefGoogle Scholar
  41. Brunei, D. 1994b. Denaturing gradient gel electrophoresis (DGGE) and direct sequencing of PCR amplified genomic DNA: Rapid and reliable identification of Helianthus annuus L. cultivars. Seed Science and Technology 22:185–194.Google Scholar
  42. Caetano-Anollés, G. and P. M. Gresshoff. 1994. DNA amplification fingerprinting: a general tool with applications in breeding, identification and phylogenetic analysis of plants. In Molecular Ecology and Evolution: Approaches and Applications, eds. B. Schierwater, B. Streit, G. P. Wagner and R. DeSalle, pp. 17–31. Birkhäuser Verlag, Basel, Switzerland.Google Scholar
  43. Caetano-Anollés, G., B. J. Bassam, and P. M. Gresshoff. 1991. DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Bio/Technology 9:553–557.PubMedCrossRefGoogle Scholar
  44. Caetano-Anollés, G., B. J. Bassam, and P. M. Gresshoff. 1993. Enhanced detection of polymorphic DNA by multiple arbitrary amplicon profiling of endonuclease digested DNA: identification of markers linked to the supernodulation locus in soybean. Molecular and General Genetics 241:57–64.PubMedCrossRefGoogle Scholar
  45. Callen, D. F., A. D. Thompson, Y. Shen, H. A. Phillips, R. I. Richards, J. C. Mulley, and G. R. Sutherland. 1993. Incidence and origin of ‘null ‘alleles in the (AC)n microsatellite markers. American Journal of Human Genetics 52:922–927.PubMedGoogle Scholar
  46. Campos, L. P., J. V. Raelson, and W.F. Grant. 1994. Genome relationships among Lotus species based on random amplified polymorphic DNA (RAPD). Theoretical and Applied Genetics 88:417–422.CrossRefGoogle Scholar
  47. Castiglione, S., G. Wang, G. Damiani, C. Bandi, S. Bisoffi, and F. Sala. 1993. RAPD fingerprints for identification and for taxonomic studies of elite poplar (Populus spp.) clones. Theoretical and Applied Genetics 87:54–59.CrossRefGoogle Scholar
  48. Catalan, P., Y. Shi, L. Armstrong, J. Draper, and C. A. Stace. 1995. Molecular phylogeny of the grass genus Brachypodium P. Beauv., based on RFLP and RAPD analysis. Botanical Journal of the Linnean Society 117:263–280.Google Scholar
  49. Cha, R. S., and W. G. Thilly. 1995. Specificity, efficiency, and fidelity of PCR. In PCR Primer: A Laboratory Manual, eds. C. W. Dieffenbach and G. S. Dveksler, pp. 37–51. Cold Spring Harbor Laboratory Press, Plainview, New York.Google Scholar
  50. Chalmers, K. J., R. Waugh, J. I. Sprent, A. J. Simons, and W. Powell. 1992. Detection of genetic variation between and within populations of Gliricidia sepium and G. maculata using RAPD markers. Heredity 69:465–472.PubMedCrossRefGoogle Scholar
  51. Chalmers, K. J., A. C. Newton, R. Waugh, J. Wilson, and W. Powell. 1994. Evaluation of the extent of genetic variation in mahoganies (Meliaceae) using RAPD markers. Theoretical and Applied Genetics 89:504–508.CrossRefGoogle Scholar
  52. Charters, Y M., A. Robertson, M. J. Wilkinson, and G. Ramsay. 1996. PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5’-anchored simple sequence repeat (SSR) primers. Theoretical and Applied Genetics 92:442–447.CrossRefGoogle Scholar
  53. Chase, M., R. Kesseli, and K. Bawa. 1996. Microsatellite markers for population and conservation genetics of tropical trees. American Journal of Botany 83:51–57.CrossRefGoogle Scholar
  54. Cheng, S., C. Fockler, W. Barnes, and R. Higuchi. 1994. Effective amplification of long targets from cloned inserts and human genomic DNA. Proceedings of the National Academy of Sciences U.S.A. 91:5695–5699.CrossRefGoogle Scholar
  55. Cipriani, G., and M. Morgante. 1993. Evidence of chloroplast DNA variation in the genus Actinidia revealed by restriction analysis of PCR-amplified fragments. Journal of Genetics and Breeding 47:319–326.Google Scholar
  56. Clark, A. G., and M. S. Lanigan. 1993. Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution 10:1096–1111.PubMedGoogle Scholar
  57. Clegg, M. T., and M. L. Durbin. 1990. Molecular approaches to the study of plant biosystematics. Australian Systematic Botany 3:1–8.CrossRefGoogle Scholar
  58. Cohen, S. N., A. C. Y. Chang, H. W. Boyer, and R. B. Helling. 1973. Construction of biologically functional bacterial plasmids in vitro. Proceedings of the National Academy of Sciences U.S.A. 70:3240–3244.CrossRefGoogle Scholar
  59. Condit, R., and S. P. Hubbell. 1991. Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66–71.PubMedCrossRefGoogle Scholar
  60. Coruzzi, G., R. Broglie, C. Edwards, and N.-H. Chua. 1984. Tissue-specific and light-regulated expression of a pea nuclear gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. EMBO Journal 3:1671–1679.PubMedGoogle Scholar
  61. Crawford, D. J., S. Brauner, M. B. Cosner, and T. F. Stuessy. 1993. Use of RAPD markers to document the origin of the intergeneric hybrid X Margyracaena skottsbergii (Rosaceae) on the Juan Fernandez islands. American Journal of Botany 80:89–92.CrossRefGoogle Scholar
  62. Davis, T. M., H. Yu, K. M. Haigis, and P. J. McGowan. 1995. Template mixing: a method for enhancing detection and interpretation of codominant RAPD markers. Theoretical and Applied Genetics 91:582–588.CrossRefGoogle Scholar
  63. Dawson, I. K., K. J. Chalmers, R. Waugh, and W. Powell. 1993. Detection and analysis of genetic variation in Hordeum spontaneum populations from Israel using RAPD markers. Molecular Ecology 2:151–159.PubMedCrossRefGoogle Scholar
  64. Dawson, I. K., A. J. Simons, R. Waugh, and W. Powell. 1995. Diversity and genetic differentiation among subpopulations of Gliricidia sepium revealed by PCRbased assays. Heredity 74:10–18.PubMedCrossRefGoogle Scholar
  65. Dawson, I. K., A. J. Simons, R. Waugh, and W. Powell. 1996. Detection and pattern of interspecific hybridization between Gliricidia sepium and G. maculata in Meso-America revealed by PCR-based assays. Molecular Ecology 5:89–98.PubMedCrossRefGoogle Scholar
  66. Dean, R., and J. Arnold. 1996. Cytonuclear disequilibria in hybrid zones using RAPD markers. Evolution 50:1702–1705.CrossRefGoogle Scholar
  67. de la Cruz, M., R. Whitkus, A. Gómez-Pompa, and L. Mota-Bravo. 1995. Origins of cacao cultivation. Nature 375:542–543.CrossRefGoogle Scholar
  68. Demeke, T., R. P. Adams, and R. Chibbar. 1992. Potential taxonomic use of random amplified polymorphic DNA (RAPD): a case study in Brassica. Theoretical and Applied Genetics 84:990–994.CrossRefGoogle Scholar
  69. Démesure, B., N. Sodzi, and R. J. Petit. 1995. A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4:129–131.PubMedCrossRefGoogle Scholar
  70. Demesure, B., B. Comps, and R. J. Petit. 1996. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50:2515–2520.CrossRefGoogle Scholar
  71. Depeiges, A., C. Goubely, A. Lenoir, S. Cocherel, G. Picard, M. Raynal, F. Grellet, and M. Delseny. 1995. Identification of the most represented repeated motifs in Ara-bidopsis thaliana microsatellite loci. Theoretical and Applied Genetics 91:160–168.CrossRefGoogle Scholar
  72. Devos, K. M., and M. D. Gale. 1992. The use of random amplified polymorphic DNA markers in wheat. Theoretical and Applied Genetics 84:567–572.CrossRefGoogle Scholar
  73. Devos, K. M., G. J. Bryan, A. J. Collins, P. Stephenson, and M. D. Gale. 1995. Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theoretical and Applied Genetics 90:247–252.CrossRefGoogle Scholar
  74. Diaz Lifante, Z., and I. Aguinagalde. 1996. The use of random amplified polymorphic DNA (RAPD) markers for the study of taxonomical relationships among species of Asphodelus sect. Verinea (Asphodelaceae). American Journal of Botany 83:949–953.CrossRefGoogle Scholar
  75. Dieffenbach, C. W., and G. S. Dveksler. 1995. PCR Primer: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, New York.Google Scholar
  76. D‘Ovidio, R., O. A. Tanzarella, and E. Porceddu. 1990. Rapid and efficient detection of genetic polymorphism in wheat through amplification by polymerase chain reaction. Plant Molecular Biology 15:169–171.Google Scholar
  77. Dow, B. D., M. V. Ashley, and H. F. Howe. 1995. Characterization of highly variable(GA/CT)n microsatellites in the bur oak, Quercus macrocarpa. Theoretical and Applied Genetics 91:137–141.CrossRefGoogle Scholar
  78. Dowling, T. E., C. Moritz, J. D. Palmer, and L. H. Rieseberg. 1996. Nucleic Acids III: analysis of fragments and restriction sites. In Molecular Systematics, second edition, eds. D. M. Hillis, B. K. Mable, and C. Mortiz, pp. 249–320. Sinauer Associates, Sunderland, Massachusetts.Google Scholar
  79. Downie, S. R., and J. D. Palmer. 1992. Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In Molecular Systematics of Plants, eds. P. S. Soltis, D. E. Soltis, and J. J. Doyle, pp. 14–35. Chapman & Hall, New York.CrossRefGoogle Scholar
  80. Downie, S. R., R. G. Olmstead, G. Zurawski, D. E. Soltis, P. S. Soltis, J. C. Wa, and J. D. Palmer. 1991. Six independent losses of the chloroplast DNA rpl2 intron in dicotyledons. Evolution 45:1245–1259.CrossRefGoogle Scholar
  81. Downie, S. R., D. S. Katz-Downie, K. H. Wolfe, P. J. Calie, and J. D. Palmer. 1994. Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution. Current Genetics 25:367–378.PubMedCrossRefGoogle Scholar
  82. Downie, S. R., E. Lianas, and D. S. Katz-Downie. 1996. Multiple independent losses of the rpoCl intron in angiosperm chloroplast DNAs. Systematic Botany 21:135–151.CrossRefGoogle Scholar
  83. Downie, S. R., D. S. Katz-Downie, and K.-J. Cho. 1997. Relationships in the Caryophyllales as suggested by phylogenetic analyses of partial chloroplast DNA ORF2280 homolog sequences. American Journal of Botany 84:253–273.PubMedCrossRefGoogle Scholar
  84. Doyle, J. J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17:144–163.CrossRefGoogle Scholar
  85. Doyle, J. J., J. I. Davis, R. J. Soreng, D. Garvin, and M. J. Anderson. 1992. Chloroplast DNA inversions and the origin of the grass family (Poaceae). Proceedings of the National Academy of Sciences U.S.A. 89:7722–7726.CrossRefGoogle Scholar
  86. Doyle, J. J., J. L. Doyle, and J. D. Palmer. 1995. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Systematic Botany 20:272–294.CrossRefGoogle Scholar
  87. Doyle, J. J., J. L. Doyle, J. A. Ballenger, and J. D. Palmer. 1996. The distribution and phylogenetic significance of a 50-kb chloroplast DNA inversion in the flowering plant family Leguminosae. Molecular Phylogenetics and Evolution 5:429–438.PubMedCrossRefGoogle Scholar
  88. Dumolin-Lepegue, S., M.-H. Pemonge, and R. J. Petit. 1997. An enlarged set of consensus primers for the study of organeile DNA in plants. Molecular Ecology 6:393–397.CrossRefGoogle Scholar
  89. Dunemann, F., R. Kahnau, and H. Schmidt. 1994. Genetic relationships in Malus evaluated by RAPD ‘fingerprinting’ of cultivars and wild species. Plant Breeding 113:150–159.CrossRefGoogle Scholar
  90. Dweikat, I., S. Mackenzie, M. Levy, and H. Ohm. 1993. Pedigree assessment using RAPD-DGGE in cereal crop species. Theoretical and Applied Genetics 85:497–505.CrossRefGoogle Scholar
  91. Dweikat, I., H. Ohm, S. Mackenzie, F. Patterson, S. Cambron, and R. Ratcliffe. 1994. Association of a DNA marker with Hessian fly resistance gene H9 in wheat. Theoretical and Applied Genetics 89:964–968.CrossRefGoogle Scholar
  92. Edwards, A., A. Civitello, H. A. Hammond, and C. T. Caskey. 1991. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. American Journal of Human Genetics 49:746–756.PubMedGoogle Scholar
  93. Ellsworth, D. L., K. D. Rittenhouse, and R. L. Honeycutt. 1993. Artifactual variation in randomly amplified polymorphic DNA banding patterns. BioTechniques 14:214–217.PubMedGoogle Scholar
  94. El Mousadik, A., and R. J. Petit. 1996. Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology 5:547–555.PubMedCrossRefGoogle Scholar
  95. Epplen, J. T., H. Ammer, C. Epplen, C. Kammerbauer, R. Mitreiter, L. Roewer, W. Schwaiger, V. Steimle, H. Zischler, E. Albert, A. Andreas, B. Beyermann, W. Meyer, J. Buitkamp, I. Nanda, M. Schmid, P. Nürnberg, S. D. J. Pena, H. Pöche, W. Sprecher, M. Schartl, K. Weising, and A. Yassouridis. 1991. Oligonucleotide fingerprinting using simple repeat motifs: a convenient, ubiquitously applicable method to detect hypervariability for multiple purposes. In DNA Fingerprinting: Approaches and Applications, eds. T. Burke, G. Dolf, A. J. Jeffreys, and R. Wolff, pp. 50–69. Birkhäuser Verlag, Basel, Switzerland.CrossRefGoogle Scholar
  96. Erlich, H. A., D. Gelfand, and J. J. Sninsky. 1991. Recent advances in the polymerase chain reaction. Science 252:1643–1651.PubMedCrossRefGoogle Scholar
  97. Estep, P. 1995. Long PCR reagents and guidelines.
  98. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491.PubMedGoogle Scholar
  99. Fabbri, A., J. I. Hormaza, and V. S. Polito. 1995. Random amplified polymorphic DNA analysis of olive (Olea europaea L.) cultivars. Journal American Society Horticultural Science 120:538–542.Google Scholar
  100. Fischer, S. G., and L. S. Lerman. 1983. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proceedings of the National Academy of Sciences U.S.A. 80:1579–1583.CrossRefGoogle Scholar
  101. Foord, O. S., and E. A. Rose. 1995. Long-distance PCR. In PCR Primer: A Laboratory Manual, eds. C. W. Dieffenbach and G. S. Dveksler, pp. 63–77. Cold Spring Harbor Laboratory Press, Plainview, New York.Google Scholar
  102. Fritsch, P., and L. H. Rieseberg. 1992. High outcrossing rates maintain male and hermaphrodite individuals in populations of the flowering plant Datisca glomerata. Nature 359:633–636.CrossRefGoogle Scholar
  103. Fritsch, P., and L. H. Rieseberg. 1996. The use of random amplified polymorphic DNA (RAPD) in conservation genetics. In Molecular Genetic Approaches in Conservation, eds. T.B. Smith and B. Wayne, pp. 54–73. Oxford University Press, New York.Google Scholar
  104. Furman, B. J., D. Grattapaglia, W. S. Dvorak, and D. M. O’Malley. 1997. Analysis of genetic relationships of Central American and Mexican pines using RAPD markers that distinguish species. Molecular Ecology 6:321–331.CrossRefGoogle Scholar
  105. Goldstein, D. B., A. R. Linares, L. L. Cavalli-Sforza, and M. W. Feldman. 1995. An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471.PubMedGoogle Scholar
  106. Golenberg, E. M. 1991. Amplification and analysis of Miocene plant fossil DNA. Philosophical Transactions of the Royal Society B 333:419–427.CrossRefGoogle Scholar
  107. Golenberg, E. M., D. E. Giannasi, M. T. Clegg, C. J. Smiley, M. Durbin, D. Henderson, and G. Zurawski. 1990. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 344:656–658.PubMedCrossRefGoogle Scholar
  108. González, J. M., and E. Ferrer. 1993. Random amplified polymorphic DNA analysis in Hordeum species. Genome 36:1029–1031.PubMedCrossRefGoogle Scholar
  109. Goodfellow, P. N. 1992. Variation is now the theme. Nature 359:777–778.PubMedCrossRefGoogle Scholar
  110. Gourmet, C., and A. L. Rayburn. 1996. Identification of RAPD markers associated with the presence of B chromosomes. Heredity 77:240–244.CrossRefGoogle Scholar
  111. Graham, J., and R. J. McNicol. 1995. An examination of the ability of RAPD markers to determine the relationships within and between Rubus species. Theoretical and Applied Genetics 90:1128–1132.CrossRefGoogle Scholar
  112. Grist, S. A., F. A. Firgaira, and A. A. Morley. 1993. Dinucleotide repeat polymorphisms isolated by the polymerase chain reaction. BioTechniques 15:304–309.PubMedGoogle Scholar
  113. Gupta, M., Y.-S. Chyi, J. Romero-Severson, and J. L. Owen. 1994. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simplesequence repeats. Theoretical and Applied Genetics 89:998–1006.CrossRefGoogle Scholar
  114. Gustafsson, L., and P. Gustafsson. 1994. Low genetic variation in Swedish populations of the rare species Vicia pisiformis (Fabaceae) revealed with RFLP (rDNA) and RAPD. Plant Systematics and Evolution 189:133–148.CrossRefGoogle Scholar
  115. Hadrys, H., M. Balick, and B. Schierwater. 1992. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Molecular Ecology 1:55–63.PubMedCrossRefGoogle Scholar
  116. Hahn, W. J., T. J. Givnish, and K. J. Sytsma. 1995. Evolution of the monocot chloroplast inverted repeat: I. Evolution and phylogenetic implications of the ORF2280 deletion. In Monocotyledons: Systematics and Evolution, eds. P. J. Rudall, P. J. Cribb, D. F. Cutler, and C. J. Humphries, pp. 579–587. Royal Botanic Gardens, Kew, England.Google Scholar
  117. Hamada, H., and T. Kakunaga. 1982. Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature 298:396–398.PubMedCrossRefGoogle Scholar
  118. Harris, S. A. 1995. Systematics and randomly amplified polymorphic DNA in the genus Leucaena (Leguminosae, Mimosoideae). Plant Systematics and Evolution 197:195–208.CrossRefGoogle Scholar
  119. Haufler, C. H. 1987. Electrophoresis is modifying our concepts of evolution in homosporous pteridophytes. American Journal of Botany 74:953–966.CrossRefGoogle Scholar
  120. Haufler, C. H., and D. E. Soltis. 1986. Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid. Proceedings of the National Academy of Sciences U.S.A. 83:4389–4393.CrossRefGoogle Scholar
  121. He, S., H. Ohm, and S. Mackenzie. 1992. Detection of DNA sequence polymorphisms among wheat varieties. Theoretical and Applied Genetics 84:573–578.CrossRefGoogle Scholar
  122. Heun, M., and T. Helentjaris. 1993. Inheritance of RAPDs in F1 hybrids of corn. Theoretical and Applied Genetics 85:961–968.CrossRefGoogle Scholar
  123. Heun, M., J. P. Murphy, and T. D. Phillips. 1994. A comparison of RAPD and isozyme analyses for determining the genetic relationships among Avena sterilis L. accessions. Theoretical and Applied Genetics 87:689–696.CrossRefGoogle Scholar
  124. Hilu, K. W. 1994. Evidence from RAPD markers in the evolution of Echinochloa millets (Poaceae). Plant Systematics and Evolution 189:247–257.CrossRefGoogle Scholar
  125. Hilu, K. W., 1995. Evolution of finger millet: evidence from random amplified polymorphic DNA. Genome 38:232–238.PubMedCrossRefGoogle Scholar
  126. Hilu, K. W., and H. T. Stalker. 1995. Genetic relationships between peanut and wild species of Arachis sect. Arachis (Fabaceae): evidence from RAPDs. Plant Systematics and Evolution 198:167–178.CrossRefGoogle Scholar
  127. Hiratsuka, J., H. Shimada, R. Whittier, T. Ishibashi, M. Sakamoto, M. Mori, C. Kondo, Y. Honji, C. R. Sun, B. Y. Meng, Y.Q. Li, A. Kanno, Y Nishizwa, A. Hirai, K. Shinozaki, and M. Sugiura. 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Molecular and General Genetics 217:185–194.PubMedCrossRefGoogle Scholar
  128. Hiss, R. H., D. E. Norris, C. H. Dietrich, R. F. Whitcombe, D. F. West, C. F. Bosio, S. Kambhampati, J. Piesman, M. F. Antolin, and W. C. I. Black. 1994. Molecular taxonomy using single-strand conformation polymorphism (SSCP) analysis of mitochondrial ribosomal DNA genes. Insect Molecular Biology 3:171–182.PubMedCrossRefGoogle Scholar
  129. Hoot, S. B., and J. D. Palmer. 1994. Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera. Journal of Molecular Evolution 38:274–281.PubMedCrossRefGoogle Scholar
  130. Hormaza, J. I., L. Dollo, and V. S. Polito. 1994. Identification of RAPD marker linked to sex determination in Pistacia vera using bulked segregant analysis. Theoretical and Applied Genetics 89:9–13.CrossRefGoogle Scholar
  131. Hsiao, J. Y, and L. H. Rieseberg. 1994. Population genetic structure of Yushania niitakayamensis (Bambusoideae, Poaceae) in Taiwan. Molecular Ecology 3:201–208.CrossRefGoogle Scholar
  132. Huff, D. R., R. Peakall, and P. E. Smouse. 1993. RAPD variation within and among natural populations of outcrossing buffalograss [Buchloe dactyloides (Nutt.) Engelm.]. Theoretical and Applied Genetics 86:927–934.CrossRefGoogle Scholar
  133. Hughes, C. R., and D. C. Queller. 1993. Detection of highly polymorphic microsatellite loci in a species with little allozyme polymorphism. Molecular Ecology 2:131–137.PubMedCrossRefGoogle Scholar
  134. Innis, M. A., and D. H. Gelfand. 1990. Optimization of PCRs. In PCR Protocols, eds. M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White, pp. 3–12. Academic Press, San Diego.Google Scholar
  135. Innis, M. A., D. H. Gelfand, and J. J. Sninsky, eds. 1995. PCR Strategies. Academic Press, San Diego.Google Scholar
  136. Jacob, H. J., K. Lindpaintner, S. E. Lincoln, K. Kusumi, R. K. Bunker, Y-P Mao, D. Ganten, V. J. Dzau, and E. S. Lander. 1991. Genetic mapping of a gene causing hypertension in the stroke-prone spontaneously hypertensive rat. Cell 67:213–224.PubMedCrossRefGoogle Scholar
  137. Jain, A., S. Bhatia, S. S. Banga, and S. Prakash. 1994. Potential use of random amplified polymorphic DNA (RAPD) technique to study the genetic diversity in Indian mustard (Brassica juncea) and its relationship to heterosis. Theoretical and Applied Genetics 88:116–122.CrossRefGoogle Scholar
  138. Jarret, R. L., D. R. Vuylsteke, N. J. Gawel, R. B. Pimentel, and L. J. Dunbar. 1993. Detecting genetic diversity in diploid bananas using PCR and primers from a highly repetitive DNA sequence. Euphytica 68:69–76.CrossRefGoogle Scholar
  139. Jeffreys, A. J., V. Wilson, and S. L. Thein. 1985. Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73.PubMedCrossRefGoogle Scholar
  140. Jessup, S. L. 1993. Reticulate evolution in Gaudichaudia (Malpighiaceae): phylogenetic and biogeographic analysis of molecular and morphological variation in a polyploid complex of neotropical vines. American Journal of Botany (suppl.) 80:154.Google Scholar
  141. Jordan, W. C., M. W. Courtney, and J. E. Neigel. 1996. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). American Journal of Botany 83:430–439.CrossRefGoogle Scholar
  142. Jork, K. B., and J. W. Kadereit. 1995. Molecular phylogeny of the Old World representatives of Papaveraceae subfamily Papaveroideae with special emphasis on the genus Meconopsis. Plant Systematics and Evolution (suppl.) 9:171–180.Google Scholar
  143. Joshi, C. P., and H. T. Nguyen. 1993. RAPD (random amplified polymorphic DNA) analysis based intervarietal genetic relationships among hexaploid wheats. Plant Science 93:95–103.CrossRefGoogle Scholar
  144. Karihaloo, J. L., S. Brauner, and L. D. Gottlieb. 1995. Random amplified polymorphic DNA variation in the eggplant, Solarium melongena L. (Solanaceae). Theoretical and Applied Genetics 90:767–770.Google Scholar
  145. Karp, A., O. Seberg, and M. Buiatti. 1996. Molecular techniques in the assessment of botanical diversity. Annals of Botany 78:143–149.CrossRefGoogle Scholar
  146. Katayama, H., and Y. Ogihara. 1996. Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Current Genetics 29:572–581.PubMedCrossRefGoogle Scholar
  147. Kijas, J. M. H., J. C. S. Fowler, C. A. Garbett, and M. R. Thomas. 1994. Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles. BioTechniques 16:656–662.PubMedGoogle Scholar
  148. Kijas, J. M. H., J. C. S. Fowler, and M. R. Thomas. 1995. An evaluation of sequence tagged microsatellite site markers for genetic analysis with Citrus and related species. Genome 38:349–355.PubMedCrossRefGoogle Scholar
  149. Kleppe, K., E. Ohtsuka, R. Kleppe, I. Molineux, and H. G. Khorana. 1971. Studies on polynucleotides XCVI. Repair replication of short synthetic DNA’s as catalyzed by DNA polymerases. Journal of Molecular Biology 56:341–361.Google Scholar
  150. Kostia, S., S.-L. Varvio, P. Vakkari, and P. Pulkkinen. 1995. Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244–1248.PubMedCrossRefGoogle Scholar
  151. Lagercrantz, U., H. Ellegren, and L. Andersson. 1993. The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Research 21:1111–1115.PubMedCrossRefGoogle Scholar
  152. Lamboy, W. F. 1994a. Computing genetic similarity coefficients from RAPD data: the effects of PCR artifacts. PCR Methods and Applications 4:31–37.PubMedCrossRefGoogle Scholar
  153. Lamboy, W. F. 1994b. Computing genetic similarity coefficients from RAPD data: Correcting for the effects of PCR artifacts caused by variation in experimental conditions. PCR Methods and Applications 4:38–43.PubMedCrossRefGoogle Scholar
  154. Lavi, U., M. Akkaya, A. Bhagwat, E. Lahav, and P. B. Cregan. 1994. Methodology of generation and characteristics of simple sequence repeat DNA markers in avocado (Persea americana M.). Euphytica 80:171–177.CrossRefGoogle Scholar
  155. Lavin, M., J. J. Doyle, and J. D. Palmer. 1990. Evolutionary significance of the loss of the chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 44:390–402.CrossRefGoogle Scholar
  156. Leebens-Mack, J. 1995. An investigation of the consequence of natural hybridization between two east Texas Baptisia (Fabaceae) species. Austin, Texas, University of Texas.Google Scholar
  157. Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution 4:203–221.PubMedGoogle Scholar
  158. Liston, A. 1992a. Restriction site mapping of PCR-amplified products. Ancient DNA Newsletter 1:11.Google Scholar
  159. Liston, A. 1992b. Variation in the chloroplast genes rpoC1 and rpoCl of the genus Astragalus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. American Journal of Botany 79:953–961.CrossRefGoogle Scholar
  160. Liston, A. 1995. Use of the polymerase chain reaction to survey for the loss of the inverted repeat in the legume chloroplast genome. In Advances in Legume Systematics, Part 7, eds. M. D. Crisp and J. J. Doyle, pp. 31–40. Royal Botanic Gardens, Kew, England.Google Scholar
  161. Liston, A., and J. W. Kadereit. 1995. Chloroplast DNA evidence for introgression and long distance dispersal in the desert annual Senecio flavus (Asteraceae). Plant Systematics and Evolution 197:33–41.CrossRefGoogle Scholar
  162. Liston, A., and J. A. Wheeler. 1994. The phylogenetic position of the genus Astragalus (Fabaceae): evidence from the chloroplast genes rpoCl and rpoCl. Biochemical Systematics and Ecology 22:377–388.CrossRefGoogle Scholar
  163. Liston, A., L. H. Rieseberg, and M. A. Hanson. 1992. Geographic partitioning of chloroplast DNA variation in the genus Datisca (Datiscaceae). Plant Systematics and Evolution 181:121–132.CrossRefGoogle Scholar
  164. Liston, A., W. A. Robinson, J. Oliphant, and E. R. Alvarez Buylia. 1996. Length variation in the nuclear ribosomal internal transcribed spacer region of non-flowering seed plants. Systematic Botany 21:109–120.CrossRefGoogle Scholar
  165. Litt, M., and J. A. Luty. 1989. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. American Journal of Human Genetics 44:397–401.PubMedGoogle Scholar
  166. Livneh, O., E. Vardi, Y. Stram, O. Edelbaum, and I. Sela. 1992. The conversion of a RFLP assay into PCR for the determination of purity in a hybrid pepper cultivar. Euphytica 62:97–102.CrossRefGoogle Scholar
  167. Lorenz, M., A. Weihe, and T. Börner. 1994. DNA fragments of organellar origin in random amplified polymorphic DNA (RAPD) patterns of sugar beet (Beta vulgaris L.). Theoretical and Applied Genetics 88:775–779.CrossRefGoogle Scholar
  168. Lynch, M. 1990. The similarity index and DNA fingerprinting. Molecular Biology and Evolution 7:478–484.PubMedGoogle Scholar
  169. Lynch, M., and B. G. Milligan. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3:91–99.PubMedCrossRefGoogle Scholar
  170. Maier, R. M., K. Neckermann, G. L. Igloi, and H. Kossel. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology 251:614–628.PubMedCrossRefGoogle Scholar
  171. Manhart, J. R., and J. D. Palmer. 1990. The gain of two chloroplast tRNA intron marks the green algal ancestors of land plants. Nature 345:268–270.PubMedCrossRefGoogle Scholar
  172. Marillia, E. F., and G. J. Scoles. 1996. The use of RAPD markers in Hordeum phylogeny. Genome 39:646–654.PubMedCrossRefGoogle Scholar
  173. Marklund, S., R. Chaudhary, L. Marklund, K. Sandberg, and L. Andersson. 1995. Extensive mtDNA diversity in horses revealed by PCR-SSCP analysis. Animal Genetics 26:193–196.PubMedCrossRefGoogle Scholar
  174. Matioli, S. R., and R. A. DeBrito. 1995. Obtaining genetic markers by using double-stringency PCR with microsatellites and arbitrary primers. BioTechniques 19:752–754.PubMedGoogle Scholar
  175. Maughan, P. J., M. A. Saghai Maroof, and G. R. Buss. 1995. Microsatellite and amplified sequence length polymorphisms in cultivated and wild soybean. Genome 38:715–723.PubMedCrossRefGoogle Scholar
  176. McBride, L. J., S. M. Koepf, R. A. Gibbs, W. Salser, P. E. Mayrand, M. W. Hunkapiller, and M. N. Kronick. 1989. Automated DNA sequencing methods involving polymerase chain reaction. Clinical Chemistry 35:2196–2201.PubMedGoogle Scholar
  177. McCauley, D. E., J. E. Stevens, P. A. Peroni, and J. A. Raveill. 1996. The spatial distribution of chloroplast DNA and allozyme polymorphisms within a population of Silene alba (Caryophyllaceae). American Journal of Botany 83:727–731.CrossRefGoogle Scholar
  178. Meksem, K., D. Leister, J. Peleman, M. Zabeau, F. Salamini, and C. Gebhardt. 1995. A high-resolution map of the vicinity of the R1 locus on chromosome V of potato based on RFLP and AFLP markers. Molecular and General Genetics 249:74–81.PubMedCrossRefGoogle Scholar
  179. Messinger, W. 1994. Molecular systematic studies in the genus Ribes (Grossulariaceae). M.Sc. thesis. Oregon State University, Corvallis, Oregon.Google Scholar
  180. Moore, S. S., L. L. Sargeant, T. J. King, J. S. Mattick, M. Georges, and D. J. S. Hetzel. 1991. The conservation of dinucleotide microsatellites among mammalian genomes allows the use of heterologous PCR primer pairs in closely related species. Genomics 10:654–660.PubMedCrossRefGoogle Scholar
  181. Mörchen, M., J. Cuguen, G. Michaelis, C. Hänni, and P. Saumitou-Laprade. 1996. Abundance and length polymorphism of microsatellite repeats in Beta vulgaris L. Theoretical and Applied Genetics 92:326–333.CrossRefGoogle Scholar
  182. Morgante, M., and A. M. Olivieri. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant Journal 3:175–182.PubMedCrossRefGoogle Scholar
  183. Morgante, M., A. Rafalski, P. Biddle, S. Tingey, and A. M. Olivieri. 1994. Genetic mapping and variability of seven soyean simple sequence repeat loci. Genome 37:763–769.PubMedCrossRefGoogle Scholar
  184. Morin, P. A., and D. G. Smith. 1995. Non-radioactive detection of hypervariable simple sequence repeats in short polyacrylamide gels. BioTechniques 19:223–228.PubMedGoogle Scholar
  185. M’Ribu, H. K., and K. W. Hilu. 1994. Detection of interspecific and intraspecific variation in Panicum millets through random amplified polymorphic DNA. Theoretical and Applied Genetics 88:412–416.Google Scholar
  186. Mulcahy, D. L., N. F. Weeden, R. Kesseli and S. B. Carroll. 1992. DNA probes for the Y-chromosome of Silene latifolia, a dioecious angiosperm. Sexual Plant Reproduction 5:86–88.CrossRefGoogle Scholar
  187. Mullis, K. B. 1994. PCR and scientific invention: the trial of Dupont vs. Cetus. In The Polymerase Chain Reaction, eds. K. B. Mullis, F. Ferre, and R. A. Gibbs, pp. 427–441. Birkhäuser, Boston, Massachusetts.CrossRefGoogle Scholar
  188. Mullis, K. B., and F. A. Faloona. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology 155:335–350.PubMedCrossRefGoogle Scholar
  189. Mullis, K., F. Faloona, S. Scharf, R. Saiki, G. Horn, and H. Erlich. 1986. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symposium Quntitative Biology 51:263–273.CrossRefGoogle Scholar
  190. Myers, R. M., S. G. Fischer, T. Maniatis, and L. S. Lerman. 1985. Modification of the melting properties of duplex DNA by attachment of GC-rich DNA sequence as determined by denaturing gradient gel electrophoresis. Nucleic Acids Research 13:3111–3129.PubMedCrossRefGoogle Scholar
  191. Myers, R. M., T. Maniatis, and L. S. Lerman. 1987. Detection and localization of single base changes by denaturing gradient gel electrophoresis. Methods in Enzymology 155:501–527.PubMedCrossRefGoogle Scholar
  192. Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences U.S.A. 70:3321–3323.CrossRefGoogle Scholar
  193. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590.PubMedGoogle Scholar
  194. Nei, M., and W. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences U.S.A. 76:5269–5273.CrossRefGoogle Scholar
  195. Nesbitt, K. A., B. M. Potts, R. E. Vaillancourt, A. K. West, and J. B. Reid. 1995. Partitioning and distribution of RAPD variation in a forest tree species, Eucalyptus globulus (Myrtaceae). Heredity 74:628–637.CrossRefGoogle Scholar
  196. Neuffer, B. 1996. RAPD analyses in colonial and ancestral populations of Capsella bursa-pastoris (L.) Med. (Brassicaceae). Biochemical Systematics and Ecology 24:393–403.CrossRefGoogle Scholar
  197. Newbury, H. J., and B. V. Ford-Lloyd. 1993. The use of RAPD for assessing variation in plants. Plant Growth Regulation 12:43–51.CrossRefGoogle Scholar
  198. Nickrent, D. L. 1994. From field to film: rapid sequencing methods for field-collected plant species. BioTechniques 16:470–475.PubMedGoogle Scholar
  199. Nishio, T., M. Kusaba, M. Watanabe, and K. Hinata. 1996. Registration of S alleles in Brassica campestris L. by the restriction fragment sizes of SLGs. Theoretical and Applied Genetics 92:388–394.CrossRefGoogle Scholar
  200. Nybom, H. 1994. DNA fingerprinting—a useful tool in fruit breeding. Euphytica 77:59–64.CrossRefGoogle Scholar
  201. Nybom, H., and T. Kraft. 1995. Application of DNA fingerprinting to the taxonomy of European blackberry species. Electrophoresis 16:1731–1735.PubMedCrossRefGoogle Scholar
  202. Ochman, H., A. S. Gerber, and L. H. Hartl. 1988. Genetic application of inverse polymerase chain reaction. Genetics 120:621–623.PubMedGoogle Scholar
  203. Ohyama, K., H. Fukuzawa, T. Kohchi, H. Shirai, T. Sano, S. Sano, K. Umesono, Y. Shiki, M. Takeuchi, Z. Chang, S. Aota, H. Inokuchi, and H. Ozeki. 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574.CrossRefGoogle Scholar
  204. Olmstead, R. G., and J. D. Palmer. 1994. Chloroplast DNA systematics: a review of methods and data analysis. American Journal of Botany 81:1205–1224.CrossRefGoogle Scholar
  205. Orita, M., Y. Suziki, T. Sekiya, and K. Hayashi. 1989. Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5:874–879.PubMedCrossRefGoogle Scholar
  206. Orozco-Castillo, C., K. J. Chalmers, R. Waugh, and W. Powell. 1994. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theoretical and Applied Genetics 87:934–940.CrossRefGoogle Scholar
  207. Palumbi, S. R. 1996. Nucleic acids II: the polymerase chain reaction. In Molecular Systematics, second edition, eds. D. M. Hillis, B. K. Mable, and C. Mortiz, pp. 205–247. Sinauer Associates, Sunderland, Massachusetts.Google Scholar
  208. Paran, I., and R. W. Michelmore. 1993. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theoretical and Applied Genetics 85:985–993.CrossRefGoogle Scholar
  209. Peakall, R., P. E. Smouse, and D. R. Huff. 1995. Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloe dactyloides. Molecular Ecology 4:135–147.CrossRefGoogle Scholar
  210. Perez de la Rosa, J., S. A. Harris, and A. Farjon. 1995. Noncoding chloroplast DNA variation in Mexican pines. Theoretical and Applied Genetics 91:1101–1106.Google Scholar
  211. Pillay, M., and S. T. Kenny. 1995. Anomalies in direct pairwise comparisons of RAPD fragments for genetic analysis. BioTechniques 19:694–698.PubMedGoogle Scholar
  212. Poinar, H. N., M. Höss, J. L. Bada, and S. Pääbo. 1996. Amino acid racemization and the preservation of ancient DNA. Science 272:864–866.PubMedCrossRefGoogle Scholar
  213. Poulsen, G. B., G. Kahl, and K. Weising. 1993. Abundance and polymorphism of simple repetitive DNA sequences in Brassica napus L. Theoretical and Applied Genetics 85:994–1000.CrossRefGoogle Scholar
  214. Powell, W., M. Morgante, C. Andre, J. W. McNicol, G. C. Machray, J. J. Doyle, S. V. Tingey, and J. A. Rafalski. 1995a. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Current Biology 5:1023–1029.PubMedCrossRefGoogle Scholar
  215. Powell, W., M. Morgante, R. McDevitt, G. G. Vendramin, and J. A. Rafalski. 1995b. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proceedings of the National Academy of Sciences U.S.A. 92:7759–7763.CrossRefGoogle Scholar
  216. Powell, W., C. Orozco-Castillo, K. J. Chalmers, J. Provan, and R. Waugh. 1995c. Polymerase chain reactionbased assays for the characterization of plant genetic resources. Electrophoresis 16:1726–1730.PubMedCrossRefGoogle Scholar
  217. Procunier, J. D., T. E Townley Smith, S. Fox, S. Prashar, M. Gray, W. K. Kim, E. Czarnecki, and P. L. Dyck. 1995. PCR-based RAPD/DGGE markers linked to rust resistance genes Lr29 and Lr25 in wheat (Triticum aestivum L.). Journal of Genetics and Breeding 49:87–91.Google Scholar
  218. Purps, D. M. L., and J. W. Kadereit. 1998. RAPD evidence for a sister group relationship of the presumed progenitor-derivative species pair Senecio nebrodensis L. and 5. viscosus L. (Asteraceae). Plant Systematics and Evolution, in press.Google Scholar
  219. Queller, D. C., J. E. Strassmann, and C. R. Hughes. 1993. Microsatellites and kinship. Trends in Ecology and Evolution 8:285–288.PubMedCrossRefGoogle Scholar
  220. Rafalski, J. A., and S. V. Tingey. 1993. Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends in Genetics 9:275–280.PubMedCrossRefGoogle Scholar
  221. Ralph, D., and M. McClelland. 1994. Mapped restriction site polymorphisms (MRSPS) in PCR products for rapid identification and classification of genetically distinct organisms. In PCR Technology: Current Innovations, eds. H. G. Griffin and A. M. Griffin, pp. 121–131. CRC Press, Boca Raton, Florida.Google Scholar
  222. Rassmann, K., C. Schlötterer, and D. Tautz. 1991. Isolation of simple-sequence loci for use in polymerase chain reaction-based DNA fingerprinting. Electrophoresis 12:113–118.PubMedCrossRefGoogle Scholar
  223. Ratnaparkhe, M. B., V. S. Gupta, M. R. Ven Murthy, and P. K. Ranjekar. 1995. Genetic fingerprinting of pigeonpea ]Cajanus cajan (L.) Millsp.] and its wild relatives using RAPD markers. Theoretical and Applied Genetics 91:893–898.CrossRefGoogle Scholar
  224. Riedy, M. F, W. J. Hamilton III, and C. F. Aquadro. 1992. Excess of non-parental bands in offspring from known primate pedigrees assayed using RAPD PCR. Nucleic Acids Research 20:918.PubMedCrossRefGoogle Scholar
  225. Rieseberg, L. H. 1996. Homology among RAPD fragments in interspecific comparisons. Molecular Ecology 5:99–105.CrossRefGoogle Scholar
  226. Rieseberg, L. H., M. A. Hanson, and C. T. Philbrick. 1992. Androdioecy is derived from dioecy in Datiscaceae: evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments. Systematic Botany 17:324–336.CrossRefGoogle Scholar
  227. Rieseberg, L. H., H. Choi, R. Chan, and C. Spore. 1993. Genomic map of a diploid hybrid species. Heredity 70:285–293.CrossRefGoogle Scholar
  228. Rieseberg, L. H., C. Van Fossen, D. Arias and R. L. Carter. 1994. Cytoplasmic male sterility in sunflower: origin, inheritance, and frequency in natural populations. Journal of Heredity 85:233–238.PubMedGoogle Scholar
  229. Rieseberg, L. H., B. Sinervo, C. R. Under, M. C. Ungerer, and D. M. Arias. 1996. Role of gene interactions in hybrid speciation: evidence from ancient and experimental hybrids. Science 272:741–745.PubMedCrossRefGoogle Scholar
  230. Röder, M., J. Plaschke, S. U. König, A. Borner, M. E. Sorrells, S. D. Tanksley, and M. W. Ganal. 1995. Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics 246:327–333.PubMedCrossRefGoogle Scholar
  231. Roelofs, D., and K. Bachmann. 1995. Chloroplast and nuclear DNA variation among homozygous plants in a population of the autogamous annual Microseris douglasii (Asteraceae, Lactuceae). Plant Systematics and Evolution 196:185–194.CrossRefGoogle Scholar
  232. Roelofs, D. and K. Bachmann. 1997. Comparison of chloroplast and nuclear phylogeny in the autogamous annual Microseris douglasii (Asteraceae, Lactuceae). Plant Systematics and Evolution 204:49–63.CrossRefGoogle Scholar
  233. Rogers, S. O., and A. J. Bendich. 1985. Extraction of DNA from milligram amounts of fresh, herbarium, and mummified plant tissues. Plant Molecular Biology 5:69–76.CrossRefGoogle Scholar
  234. Rogstad, S. H. 1994. Inheritance in turnip of variable-number tandem-repeat genetic markers revealed with synthetic repetitive DNA probes. Theoretical and Applied Genetics 89:824–830.CrossRefGoogle Scholar
  235. Rogstad, S. H., J. C. Patton II, and B. A. Schaal. 1988. M13 repeat probe detects DNA minisatellite-like sequences in gymnosperms and angiosperms. Proceedings of the National Academy of Sciences U.S.A. 85:9176–9178.CrossRefGoogle Scholar
  236. Rongwen, J., M. S. Akkaya, A. A. Bhagwat, U. Lavi, and P. B. Cregan. 1995. The use of microsatellite DNA markers for soybean genotype identification. Theoretical and Applied Genetics 90:43–48.CrossRefGoogle Scholar
  237. Roy, M. S., E. Geffen, D. Smith, E. A. Ostrander, and R. K. Wayne. 1994. Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci. Molecular Biology and Evolution 11:553–570.PubMedGoogle Scholar
  238. Russell, J. R., F. Hosein, E. Johnson, R. Waugh, and W. Powell. 1993. Genetic differentiation of cocoa (Theobroma cacao L.) populations revealed by RAPD analysis. Molecular Ecology 2:89–97.PubMedCrossRefGoogle Scholar
  239. Saghai Maroof, M. A., R. M. Biyashev, G. P. Yang, Q. Zhang, and R. W. Allard. 1994. Extraordinarily polymorphic microsatellite DNA in barley: Species diversity, chromosomal locations, and population dynamics. Proceedings of the National Academy of Sciences U.S.A. 91:5466–5470.CrossRefGoogle Scholar
  240. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primerdirected enzymatic amplification of DNA with thermostable DNA polymerase. Science 259:487–491.CrossRefGoogle Scholar
  241. Salimath, S. S., A. C. de Oliveira, I. D. Godwin, and J. L. Bennetzen. 1995. Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers. Genome 38:757–763.PubMedCrossRefGoogle Scholar
  242. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, New York.Google Scholar
  243. Sánchez de la Hoz, M. P., J. A. Dávila, Y Loarce, and E. Ferrer. 1996. Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley. Genome 39:112–117.PubMedCrossRefGoogle Scholar
  244. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences U.S.A. 74:5463–5467.CrossRefGoogle Scholar
  245. Savolainen, V., P. Cuenoud, R. Spichiger, M. D. P. Martinez, M. C. Crevecoeur, and J.-F. Manen. 1995. The use of herbarium specimens in DNA phylogenetics: evaluation and improvement. Plant Systematics and Evolution 197:87–98.CrossRefGoogle Scholar
  246. Schlötterer, C., and J. Pemberton. 1994. The use of microsatellites for genetic analysis of natural populations. In Molecular Ecology and Evolution: Approaches and Applications, eds. B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, pp. 203–214. Birkhäuser Verlag, Basel, Switzerland.Google Scholar
  247. Schlötterer, C., and D. Tautz. 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Research 20:211–215.PubMedCrossRefGoogle Scholar
  248. Schlötterer, C., B. Amos, and D. Tautz. 1991. Conservation of polymorphic simple sequence loci in cetacean species. Nature 354:63–65.PubMedCrossRefGoogle Scholar
  249. Schwarzbach, A. E., and J. W. Kadereit. 1995. Rapid radiation of North American desert genera of the Papaveraceae: Evidence from restriction site mapping of PCR-amplified chloroplast DNA fragments. Plant Systematics and Evolution (suppl.) 9:159–170.Google Scholar
  250. Scribner, K. T., J. W. Arntzen, and T. Burke. 1994. Comparative analysis of intra-and interpopulation genetic diversity in Bufu bufo, using allozyme, single-locus microsatellite, minisatellite, and multilocus minisatellite data. Molecular Biology and Evolution 11:737–748.PubMedGoogle Scholar
  251. Senior, M. L., and M. Heun. 1993. Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome 36:884–889.PubMedCrossRefGoogle Scholar
  252. Sharma, P. G, B. Hiittel, P. Winter, G. Kahl, R. C. Gardner, and K. Weising. 1995a. The potential of microsatellites for hybridization-and polymerase chain reactionbased DNA fingerprinting of chickpea. Electrophoresis 16:1755–1761.PubMedCrossRefGoogle Scholar
  253. Sharma, S. K., I. K. Dawson, and R. Waugh. 1995b. Relationships among cultivated and wild lentils revealed by RAPD analysis. Theoretical and Applied Genetics 91:647–654.CrossRefGoogle Scholar
  254. Sharon, D., A. Adato, S. Mhameed, U. Lavi, J. Hillel, M. Gomolka, C. Epplen, and J. T. Epplen. 1995. DNA fingerprints in plants using simple-sequence repeat and minisatellite probes. HortScience 30:109–112.Google Scholar
  255. Shattuck-Eidens, D. M., R. N. Bell, J. T. Mitchell, and V. C. Mcwhorter. 1991. Rapid detection of maize DNA sequence variation. Genetic Analysis, Techniques and Applications 8:240–245.PubMedGoogle Scholar
  256. Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida, T. Matsubayashi, N. Zaita, J. Chunwongse, J. Obokata, K. Yamaguchi-Shinozaki, C. Ohto, K. Torazawa, B. Y. Meng, M. Sugita, H. Deno, T. Kamogashira, K. Yamada, J. Kusuda, F. Takaiwa, A. Kato, N. Tohdoh, H. Shimada, and M. Sugiura. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO Journal 5:2043–2049.PubMedGoogle Scholar
  257. Skinner, D. Z. 1992. A PCR-based method of identifying species-specific repeated DNAs. BioTechniques 13:210–214.PubMedGoogle Scholar
  258. Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462.PubMedGoogle Scholar
  259. Smith, D. N., and M. E. Devey. 1994. Occurrence and inheritance of microsatellites in Pinus radiate. Genome 37:977–983.PubMedCrossRefGoogle Scholar
  260. Smith, J. F., and T. V. Pham. 1996. Genetic diversity of the narrow endemic Allium aaseae (Alliaceae). American Journal of Botany 83:717–726.CrossRefGoogle Scholar
  261. Smith, J. F., C. C. Burke, and W. L. Wagner. 1996. Interspecific hybridization in natural populations of Cyrtandra (Gesneriaceae) on the Hawaiian Islands: evidence from RAPD markers. Plant Systematics and Evolution 200:61–77.CrossRefGoogle Scholar
  262. Smith, J. J., J. S. Scott-Craig, J. R. Leadbetter, G. L. Bush, D. L. Roberts, and D. W. Fulbright. 1994. Characterization of random amplified polymorphic DNA (RAPD) products from Xanthomonas campestris and some comments on the use of RAPD products in phylogenetic analysis. Molecular Phylogenetics and Evolution 3:135–145.PubMedCrossRefGoogle Scholar
  263. Smith, J. S. C., and J. G. K. Williams. 1994. Arbitrary primer mediated fingerprinting in plants: Case studies in plant breeding, taxonomy and phylogeny. In Molecular Ecology and Evolution: Approaches and Applications, eds. B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, pp. 5–15. Birkhäuser Verlag, Basel, Switzerland.Google Scholar
  264. Sneath, P. H. A., and R. R. Sokal. 1973. Numerical Taxonomy. Freeman, San Francisco.Google Scholar
  265. Sobral, B. W. S., and R. J. Honeycutt. 1994. Genetics, plants, and the polymerase chain reaction. In The Polymerase Chain Reaction, eds. K. B. Mullis, F. Ferre, and R. A. Gibbs, pp. 304–319. Birkhäuser, Boston, Massachusetts.CrossRefGoogle Scholar
  266. Soltis, D. E., P. S. Soltis, R. K. Kuzoff, and T. L. Tucker. 1992. Geographic structuring of chloroplast DNA genotypes in Tiarella trifoliata (Saxifragaceae). Plant Systematics and Evolution 181:203–216.CrossRefGoogle Scholar
  267. Soltis, D. E., M. A. Gitzendanner, D. D. Strenge, and P. S. Soltis. 1997. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution 206:353–373.CrossRefGoogle Scholar
  268. Soltis, P. S., D. E. Soltis, and J. J. Doyle, eds. 1992a. Molecular Systematics of Plants. Chapman & Hall, New York.Google Scholar
  269. Soltis, P. S., D. E. Soltis, and C. J. Smiley. 1992b. An rbcL sequence from a Miocene Taxodium (bald cypress). Proceedings of the National Academy of Sciences U.S.A. 89:449–451.CrossRefGoogle Scholar
  270. Song, K., and T. C. Osborn. 1994. A method for examining expression of homologous genes in plant polyploids. Plant Molecular Biology 26:1065–1071.PubMedCrossRefGoogle Scholar
  271. Stammers, M., J. Harris, G. M. Evans, M. D. Hayward, and J. W. Forster. 1995. Use of random PCR (RAPD) technology to analyze phylogenetic relationships in the Loliuml Festuca complex. Heredity 74:19–27.PubMedCrossRefGoogle Scholar
  272. Stewart, C. N., and D. M. Porter. 1995. RAPD profiling in biological conservation: An application to estimating clonal variation in rare and endangered Iliamna in Virginia. Biological Conservation 74:135–142.CrossRefGoogle Scholar
  273. Stiller, J. W., and A. L. Denton. 1995. One hundred years of Spartina alterniflora (Poaceae) in Willapa Bay, Washington: random amplified polymorphic DNA analysis of an invasive population. Molecular Ecology 4:355–363.CrossRefGoogle Scholar
  274. Strand, A. E., B. G. Milligan, and C. M. Pruitt. 1996. Are populations islands? Analysis of chloroplast DNA variation in Aquilegia. Evolution 50:1822–1829.CrossRefGoogle Scholar
  275. Strand, A. E., J. Leebens-Mack, and B. G. Milligan. 1997. Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology 6:113–118.PubMedCrossRefGoogle Scholar
  276. Swensen, S. M., G. J. Allan, M. Howe, W. J. Elisens, S. A. Junak, and L. H. Rieseberg. 1995. Genetic analysis of the endangered island endemic Malacothamnus fasciculaius (Nutt.)Greene var. nesioticus (Rob.) Kearn. (Malvaceae). Conservation Biology 9:404–415.Google Scholar
  277. Swerdlow, H., and R. Gesteland. 1990. Capillary gel electrophoresis for rapid high resolution DNA sequencing. Nucleic Acids Research 18:1415–1420.PubMedCrossRefGoogle Scholar
  278. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. In Molecular Systematics, second edition, eds. D. M. Hillis, B. K. Mable, and C. Mortiz, pp. 407–514. Sinauer Associates, Sunderland, Massachusetts.Google Scholar
  279. Taberlet, P., L. Gielly, G. Pautou, and J. Bouvet. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology Reporter 17:1105–1109.Google Scholar
  280. Tao, Y, J. M. Manners, M. M. Ludlow, and R. G. Henzell. 1993. DNA polymorphisms in grain sorghum (Sorghum bicolor (L.) Moench). Theoretical and Applied Genetics 86:679–688.CrossRefGoogle Scholar
  281. Tautz, D. 1989. Hypervariability of simple-sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17:6463–6471.PubMedCrossRefGoogle Scholar
  282. Tautz, D., and M. Renz. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research 12:4127–4138.PubMedCrossRefGoogle Scholar
  283. Tautz, D., M. Trick, and G. A. Dover. 1986. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652–656.PubMedCrossRefGoogle Scholar
  284. Terauchi, R., and A. Konuma. 1994. Microsatellite polymorphism in Dioscorea tokoro, a wild yam species. Genome 37:794–801.PubMedCrossRefGoogle Scholar
  285. Thomas, M. R., and N. S. Scott. 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theoretical and Applied Genetics 86:985–990.Google Scholar
  286. Thormann, C. E., M. E. Ferreira, L. E. A. Camargo, J. G. Tivang, and T. C. Osborn. 1994. Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species. Theoretical and Applied Genetics 88:973–980.CrossRefGoogle Scholar
  287. To, K.-Y, C.-I. Liu, S.-T. Liu, and Y-S. Chang. 1993. Detection of point mutations in the chloroplast genome by single-stranded conformation polymorphism analysis. Plant Journal 3:183–186.PubMedCrossRefGoogle Scholar
  288. Tracy, T. E., and L. S. Mulcahy. 1991. A simple method for direct automated sequencing of PCR fragments. BioTechniques 11:74–75.Google Scholar
  289. Travis, S. E., J. Maschinski, and P. Keim. 1996. An analysis of genetic variation in Astragalus cremnophylax, a critically-endangered plant, using AFLP markers. Molecular Ecology 5:735–745.PubMedCrossRefGoogle Scholar
  290. Tsumura, Y, K. Yoshimura, N. Tomaru, and K. Ohba. 1995. Molecular phylogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoretical and Applied Genetics 91:1222–1236.CrossRefGoogle Scholar
  291. Tsumura, Y, K. Ohba, and S. H. Strauss. 1996a. Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theoretical and Applied Genetics 92:40–45.CrossRefGoogle Scholar
  292. Tsumura, Y., T. Kawahara, R. Wickneswari, and K. Yoshimura. 1996b. Molecular phylogeny of Dipterocarpaceae in Southeast Asia using RFLP of PCR-amplified chloroplast genes. Theoretical and Applied Genetics 93:22–29.CrossRefGoogle Scholar
  293. Valdes, A. M., M. Slatkin, and N. B. Freimer. 1993. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133:737–749.PubMedGoogle Scholar
  294. Van Buren, R., K. T. Harper, W. R. Andersen, D. J. Stanton, S. Seyoum, and J. L. England. 1994. Evaluating the relationship of autumn buttercup (Ranunculus acriformis var. aestivalis) to some close congeners using random amplified polymorphic DNA. American Journal of Botany 81:514–519.CrossRefGoogle Scholar
  295. Van Coppenolle, B., I. Watanabe, C. Van Hove, G. Second, N. Huang, and S. R. McCouch. 1993. Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers. Genome 36:686–693.PubMedCrossRefGoogle Scholar
  296. van de Zande, L., and R. Bijlsma. 1995. Limitations of the RAPD technique in phylogeny reconstruction in Drosophila. Journal of Evolutionary Biology 8:645–656.CrossRefGoogle Scholar
  297. van Ham, R. C. H. J., H. ‘t Hart, T. H. M. Mes, and J. M. Sandbrick. 1994. Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species. Current Genetics 25:558–566.Google Scholar
  298. Van Heusden, A. W., and K. Bachmann. 1992a. Genetic differentiation of Microseris pygmaea (Asteraceae, Lactuceae) studied with DNA amplification from arbitrary primers (RAPDs). Acta Botanica Neerlandica 41:385–395.Google Scholar
  299. Van Heusden, A. W., and K. Bachmann. 1992b. Genotype relationships in Microseris elegans (Asteraceae, Lactuceae) revealed by DNA amplification from arbitrary primers (RAPDS). Plant Systematics and Evolution 179:221–233.CrossRefGoogle Scholar
  300. Van Heusden, A. W., and K. Bachmann. 1992c. Nuclear DNA polymorphisms among strains of Microseris bigelovii (Asteraceae: Lactuceae) amplified from arbitrary primers. Botanica Acta 105:331–336.Google Scholar
  301. van Pijlen, I. A., B. Amos, and T. Burke. 1995. Patterns of genetic variability at individual minisatellite loci in minke whale Balaenoptera acutorostrata populations from three different oceans. Molecular Biology and Evolution 12:459–472.PubMedGoogle Scholar
  302. Venugopal, G., S. Mohapatra, D. Salo, and S. Mohapatra. 1993. Multiple mismatch annealing: basis for random amplified DNA polymorphic fingerprinting. Biochemical and Biophysical Research Communications 197:1382–1387.PubMedCrossRefGoogle Scholar
  303. Vicario, F., G. G. Vendramin, P. Rossi, P. Liò, and R. Giannini. 1995. Allozyme, chloroplast DNA and RAPD markers for determining genetic relationships between Abies alba and the relic population of Abies nebrodensis. Theoretical and Applied Genetics 90:1012–1018.CrossRefGoogle Scholar
  304. Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. van de Lee, M. Homes, A. Frijiters, J. Pot, J. Peleman, M. Kuiper, and M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23:4407–4414.PubMedCrossRefGoogle Scholar
  305. Wachira, F. N., R. Waugh, C. A. Hackett, and W. Powell. 1995. Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers. Genome 38:201–210.PubMedCrossRefGoogle Scholar
  306. Wakasugi, T., J. Tsudzuki, S. Ito, K. Nakashima, T. Tsudzuki, and M. Sugiura. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergil Proceedings of the National Academy of Sciences U.S.A. 91:9794–9798.CrossRefGoogle Scholar
  307. Wallace, R. S., and J. H. Cota. 1996. An intron loss in the chloroplast gene rpoC1 supports a monophyletic origin for the subfamily Cactoideae of the Cactaceae. Current Genetics 29:275–281.PubMedCrossRefGoogle Scholar
  308. Wang, X.-R., A. E. Szmidt, and M.-Z. Lu. 1996. Genetic evidence for the presence of cytoplasmic DNA in pollen and megagametophytes and maternal inheritance of mitochondrial DNA in Pinus. Forest Genetics 3:37–44.Google Scholar
  309. Wang, Z., J. L. Weber, G. Zhong, and S. D. Tanksley. 1994. Survey of plant short tandem repeats. Theoretical and Applied Genetics 88:1–6.Google Scholar
  310. Watano, Y, [ M. Imazu, and T. Shimuzu. 1995. Chloroplast DNA typing by PCR-SSCP in the Pinus pumila-P parviflora var. pentaphylla complex (Pinaceae). Journal of Plant Research 108:493–499.CrossRefGoogle Scholar
  311. Waugh, R., and W. Powell. 1992. Using RAPD markers for crop improvement. Trends in Biotechnology 10:186–191.CrossRefGoogle Scholar
  312. Wehling, P., B. Hackauf, and G. Wricke. 1994. Identification of S-locus linked PCR fragments in rye (Secale cereale L.) by denaturing gradient gel electrophoresis. Plant Journal 5:891–893.PubMedCrossRefGoogle Scholar
  313. Weising, K., F Weigand, A. J. Driesel, G. Kahl, H. Zischler, and J. T. Epplen. 1989. Polymorphic simple GATA/GACA repeats in plant genomes. Nucleic Acids Research 17:10128.PubMedCrossRefGoogle Scholar
  314. Weising, K., H. Nybom, K. Wolff, and W. Meyer. 1995. DNA Fingerprinting in Plants and Fungi. CRC Press, Boca Raton, Florida.Google Scholar
  315. Welsh, J., and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18:7213–17218.PubMedCrossRefGoogle Scholar
  316. Welsh, J., and M. McClelland. 1991. Genomic fingerprints produced by PCR with consensus transfer RNA gene primers. Nucleic Acids Research 19:861–866.PubMedCrossRefGoogle Scholar
  317. Whitkus, R., J. Doebley, and J. F. Wendel. 1994. Nuclear DNA markers in systematics and evolution. In DNAbased Markers in Plants, eds. R. L. Phillips and I. K. Vasil, pp. 116–141. Kluwer Academic Publishers, Netherlands.CrossRefGoogle Scholar
  318. Whitton, J., L. H. Rieseberg, and M. C. Ungerer. 1997. Microsatellite loci are not conserved across Asteraceae. Molecular Biology and Evolution 14:204–209.PubMedCrossRefGoogle Scholar
  319. Whitty, P. W., W. Powell, and J. I. Sprent. 1994. Molecular separation of genera in Cassiinae (Leguminosae), and analysis of variation in the nodulating species of Chamaecrista. Molecular Ecology 3:507–515.PubMedCrossRefGoogle Scholar
  320. Widjojoatmodjo, M. N., A. C. Fluit, and J. Verhoef. 1994. Rapid identification of bacteria by PCR-single-strand conformation polymorphism. Journal of Clinical Microbiology 32:3002–3007.PubMedGoogle Scholar
  321. Wilkie, S. E., P. G. Isaac, and R. J. Slater. 1993. Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium. Theoretical and Applied Genetics 86:497–504.CrossRefGoogle Scholar
  322. Williams, C. E., and D. A. St. Clair. 1993. Phenetic relationships and levels of variability detected by restriction fragment length polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon esculentum. Genome 36:619–630.PubMedCrossRefGoogle Scholar
  323. Williams, J. G. K., A. R. Kubelik, K. J. Livak, J. A. Rafalski, and S. V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18:6531–6535.PubMedCrossRefGoogle Scholar
  324. Williams, M. N. V., N. Pande, S. Nair, M. Mohan, and J. Bennett. 1991. Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice Oryza sativa L. genomic DNA. Theoretical and Applied Genetics 82:489–498.CrossRefGoogle Scholar
  325. Williams, J. G. K., M. K. Hanafey, J. A. Rafalski, and S. V. Tingey. 1993. Genetic analysis using random amplified polymorphic DNA markers. Methods in Enzymology 218:704–740.PubMedCrossRefGoogle Scholar
  326. Wolfe, A. D., and W. J. Elisens. 1993. Diploid hybrid speciation in Penstemon (Scrophulariaceae) revisited. American Journal of Botany 80:1082–1094.CrossRefGoogle Scholar
  327. Wolfe, A. D., and W. J. Elisens. 1994. Nuclear ribosomal DNA restriction-site variation in Penstemon section Peltanthera (Scrophulariaceae): an evaluation of diploid hybrid speciation and evidence for introgression. American Journal of Botany 81:1627–1635.CrossRefGoogle Scholar
  328. Wolfe, A. D., and W. J. Elisens. 1995. Evidence of chloroplast capture and pollen-mediated gene flow in Penstemon sect. Peltanthera (Scrophulariaceae). Systematic Botany 20:395–412.CrossRefGoogle Scholar
  329. Wolfe, A. D., W. J. Elisens, L. E. Watson, and C. W. de Pamphilis. 1997. Using restriction-site variation of PCRamplified cpDNA genes for phylogenetic analysis: a case study of Cheloneae (Scrophulariaceae). American Journal of Botany 84:555–564.PubMedCrossRefGoogle Scholar
  330. Wolfe, K. H., C. W. Morden, and J. D. Palmer. 1992. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proceedings of the National Academy Sciences U. S. A. 89:10648–10652.CrossRefGoogle Scholar
  331. Wolff, K., E. Zietkiewicz, and H. Hofstra. 1995. Identification of chrysanthemum cultivars and stability of DNA fingerprint patterns. Theoretical and Applied Genetics 91:439–447.CrossRefGoogle Scholar
  332. Wu, K.-S., and S. D. Tanksley. 1993. Abundance, polymorphism and genetic mapping of microsatellites in rice. Molecular and General Genetics 241:225–235.PubMedCrossRefGoogle Scholar
  333. Wu, K., R. Jones, L. Danneberger, and P. A. Scolnik. 1994. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Research 22:3257–3258.PubMedCrossRefGoogle Scholar
  334. Xu, H., D. J. Wilson, S. Arulsekar, and A. T. Bakalinsky. 1995. Sequence-specific polymerase chain-reaction markers derived from randomly amplified polymorphic DNA markers for fingerprinting grape (Vitis) rootstocks. Journal American Society Horticultural Science 120:714–720.Google Scholar
  335. Yang, X., and C. Quiros. 1993. Identification and classification of celery cultivars with RAPD markers. Theoretical and Applied Genetics 86:205–212.CrossRefGoogle Scholar
  336. Yang, G. P., M. A. Saghai Maroof, C. G. Xu, Q. Zhang, and R. M. Biyashev. 1994. Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Molecular and General Genetics 245:187–194.PubMedGoogle Scholar
  337. Yu, J., W. K. Gu, R. Provvidenti, and N. F. Weeden. 1995. Identifying and mapping two DNA markers linked to the gene conferring resistance to pea enation mosaic virus. Journal American Society Horticultural Science 120:730–733.Google Scholar
  338. Zhao, X., and G. Kochert. 1993. Phylogenetic distribution and genetic mapping of a GGCn microsatellite from rice Oryza sativa L. Plant Molecular Biology 21:607–614.PubMedCrossRefGoogle Scholar
  339. Zietkiewicz, E., A. Rafalski, and D. Labuda. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183.PubMedCrossRefGoogle Scholar
  340. Zurawski, G., B. Perrot, W. Bottomley, and P. R. Whitfeld. 1981. The structure of the gene for the large subunit of ribulose-l,5-bisphosphate carboxylase from spinach chloroplast DNA. Nucleic Acids Research 9:3251–3270.PubMedCrossRefGoogle Scholar
  341. Zurawski, G., M. T. Clegg, and A. H. D. Brown. 1984. The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics 106:735–749.PubMedGoogle Scholar

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© Springer Science+Business Media New York 1998

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  • Andrea D. Wolfe
  • Aaron Liston

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