Skip to main content
SpringerLink
Log in

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

  • Chapter
Molecular Systematics of Plants II

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 299.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Literature Cited

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Abrol, S., and V. K. Chaudhary. 1993. Excess PCR primers inhibit DNA cleavage by some restriction endonucle-ases. BioTechniques 15:630–631.

    PubMed  CAS  Google Scholar 

  • Adams, R. P., and T. Demeke. 1993. Systematic relationships in Juniperus based on random amplified polymorphic DNAs (RAPDs). Taxon 42:553–571.

    Article  Google Scholar 

  • Akkaya, M. S., A. A. Bhagwat, and P. B. Cregan. 1992. Length polymorphisms of simple sequence repeat DNA in soybean. Genetics 132:1131–1193.

    PubMed  CAS  Google Scholar 

  • 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 

  • Amos, B., C. Schlötterer, and D. Tautz. 1993. Social structure of pilot whales revealed by analytical DNA profiling. Science 260:670–672.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Asmussen, C., and A. Liston. 1998. Chloroplast DNA characters, phylogeny, and classification of Lathryus (Fabaceae). American Journal of Botany, in press.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Bachmann, K. 1994. Molecular markers in plant ecology. New Phytologist 126:403–418.

    Article  CAS  Google Scholar 

  • Bachmann, K. 1995. Progress and pitfalls in systematics: cladistics, DNA and morphology. Acta Botanica Neerlandica 44:403–419.

    Google Scholar 

  • Bachmann, K. 1997. Nuclear DNA markers in biosystematic research. Opera Botanica, in press.

    Google Scholar 

  • 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 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Becker, J., and M. Heun. 1995. Barley microsatellites: allele variation and mapping. Plant Molecular Biology 27:835–845.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Beckmann, J. S., and J. L. Weber. 1992. Survey of human and rat microsatellites. Genomics 12:627–631.

    Article  CAS  Google Scholar 

  • Bell, C. J., and J. R. Ecker. 1994. Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Bock, J. H., and J. L. Slightom. 1995. Fluorescence-based cycle sequencing with primers selected from a nonamer library. BioTechniques 19:60–62.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Bruford, M. W., and R. K. Wayne. 1993. Microsatellites and their application to population genetic studies. Current Biology 3:939–943.

    CAS  Google Scholar 

  • Brummer, E. C., J. H. Bouton, and G. Kochert. 1995. Analysis of annual Medicago species using RAPD markers. Genome 38:362–367.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Brunei, D. 1994a. A microsatellite marker in Helianthus annuus L. Plant Molecular Biology 24:397–400.

    Article  Google Scholar 

  • 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 

  • 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 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Clark, A. G., and M. S. Lanigan. 1993. Prospects for estimating nucleotide divergence with RAPDs. Molecular Biology and Evolution 10:1096–1111.

    PubMed  CAS  Google Scholar 

  • Clegg, M. T., and M. L. Durbin. 1990. Molecular approaches to the study of plant biosystematics. Australian Systematic Botany 3:1–8.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Condit, R., and S. P. Hubbell. 1991. Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome 34:66–71.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Dean, R., and J. Arnold. 1996. Cytonuclear disequilibria in hybrid zones using RAPD markers. Evolution 50:1702–1705.

    Article  Google Scholar 

  • de la Cruz, M., R. Whitkus, A. Gómez-Pompa, and L. Mota-Bravo. 1995. Origins of cacao cultivation. Nature 375:542–543.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Dieffenbach, C. W., and G. S. Dveksler. 1995. PCR Primer: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, New York.

    Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Chapter  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Doyle, J. J. 1992. Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17:144–163.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Ellsworth, D. L., K. D. Rittenhouse, and R. L. Honeycutt. 1993. Artifactual variation in randomly amplified polymorphic DNA banding patterns. BioTechniques 14:214–217.

    PubMed  CAS  Google Scholar 

  • El Mousadik, A., and R. J. Petit. 1996. Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology 5:547–555.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Erlich, H. A., D. Gelfand, and J. J. Sninsky. 1991. Recent advances in the polymerase chain reaction. Science 252:1643–1651.

    Article  PubMed  CAS  Google Scholar 

  • Estep, P. 1995. Long PCR reagents and guidelines. http://twod.med.harvard.edu/labgc/estep/longPCRprotocol.html

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Golenberg, E. M. 1991. Amplification and analysis of Miocene plant fossil DNA. Philosophical Transactions of the Royal Society B 333:419–427.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • González, J. M., and E. Ferrer. 1993. Random amplified polymorphic DNA analysis in Hordeum species. Genome 36:1029–1031.

    Article  PubMed  Google Scholar 

  • Goodfellow, P. N. 1992. Variation is now the theme. Nature 359:777–778.

    Article  PubMed  CAS  Google Scholar 

  • Gourmet, C., and A. L. Rayburn. 1996. Identification of RAPD markers associated with the presence of B chromosomes. Heredity 77:240–244.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Grist, S. A., F. A. Firgaira, and A. A. Morley. 1993. Dinucleotide repeat polymorphisms isolated by the polymerase chain reaction. BioTechniques 15:304–309.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Hadrys, H., M. Balick, and B. Schierwater. 1992. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology. Molecular Ecology 1:55–63.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Hamada, H., and T. Kakunaga. 1982. Potential Z-DNA forming sequences are highly dispersed in the human genome. Nature 298:396–398.

    Article  PubMed  CAS  Google Scholar 

  • Harris, S. A. 1995. Systematics and randomly amplified polymorphic DNA in the genus Leucaena (Leguminosae, Mimosoideae). Plant Systematics and Evolution 197:195–208.

    Article  CAS  Google Scholar 

  • Haufler, C. H. 1987. Electrophoresis is modifying our concepts of evolution in homosporous pteridophytes. American Journal of Botany 74:953–966.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • He, S., H. Ohm, and S. Mackenzie. 1992. Detection of DNA sequence polymorphisms among wheat varieties. Theoretical and Applied Genetics 84:573–578.

    Article  Google Scholar 

  • Heun, M., and T. Helentjaris. 1993. Inheritance of RAPDs in F1 hybrids of corn. Theoretical and Applied Genetics 85:961–968.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Hilu, K. W. 1994. Evidence from RAPD markers in the evolution of Echinochloa millets (Poaceae). Plant Systematics and Evolution 189:247–257.

    Article  CAS  Google Scholar 

  • Hilu, K. W., 1995. Evolution of finger millet: evidence from random amplified polymorphic DNA. Genome 38:232–238.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Hsiao, J. Y, and L. H. Rieseberg. 1994. Population genetic structure of Yushania niitakayamensis (Bambusoideae, Poaceae) in Taiwan. Molecular Ecology 3:201–208.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Innis, M. A., D. H. Gelfand, and J. J. Sninsky, eds. 1995. PCR Strategies. Academic Press, San Diego.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Jeffreys, A. J., V. Wilson, and S. L. Thein. 1985. Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67–73.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Karp, A., O. Seberg, and M. Buiatti. 1996. Molecular techniques in the assessment of botanical diversity. Annals of Botany 78:143–149.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Kostia, S., S.-L. Varvio, P. Vakkari, and P. Pulkkinen. 1995. Microsatellite sequences in a conifer, Pinus sylvestris. Genome 38:1244–1248.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Lamboy, W. F. 1994a. Computing genetic similarity coefficients from RAPD data: the effects of PCR artifacts. PCR Methods and Applications 4:31–37.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Molecular Biology and Evolution 4:203–221.

    PubMed  CAS  Google Scholar 

  • Liston, A. 1992a. Restriction site mapping of PCR-amplified products. Ancient DNA Newsletter 1:11.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Lynch, M. 1990. The similarity index and DNA fingerprinting. Molecular Biology and Evolution 7:478–484.

    PubMed  CAS  Google Scholar 

  • Lynch, M., and B. G. Milligan. 1994. Analysis of population genetic structure with RAPD markers. Molecular Ecology 3:91–99.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Marillia, E. F., and G. J. Scoles. 1996. The use of RAPD markers in Hordeum phylogeny. Genome 39:646–654.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Messinger, W. 1994. Molecular systematic studies in the genus Ribes (Grossulariaceae). M.Sc. thesis. Oregon State University, Corvallis, Oregon.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Morgante, M., and A. M. Olivieri. 1993. PCR-amplified microsatellites as markers in plant genetics. Plant Journal 3:175–182.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Morin, P. A., and D. G. Smith. 1995. Non-radioactive detection of hypervariable simple sequence repeats in short polyacrylamide gels. BioTechniques 19:223–228.

    PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    Article  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences U.S.A. 70:3321–3323.

    Article  CAS  Google Scholar 

  • Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Neuffer, B. 1996. RAPD analyses in colonial and ancestral populations of Capsella bursa-pastoris (L.) Med. (Brassicaceae). Biochemical Systematics and Ecology 24:393–403.

    Article  CAS  Google Scholar 

  • Newbury, H. J., and B. V. Ford-Lloyd. 1993. The use of RAPD for assessing variation in plants. Plant Growth Regulation 12:43–51.

    Article  CAS  Google Scholar 

  • Nickrent, D. L. 1994. From field to film: rapid sequencing methods for field-collected plant species. BioTechniques 16:470–475.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Nybom, H. 1994. DNA fingerprinting—a useful tool in fruit breeding. Euphytica 77:59–64.

    Article  Google Scholar 

  • Nybom, H., and T. Kraft. 1995. Application of DNA fingerprinting to the taxonomy of European blackberry species. Electrophoresis 16:1731–1735.

    Article  PubMed  CAS  Google Scholar 

  • Ochman, H., A. S. Gerber, and L. H. Hartl. 1988. Genetic application of inverse polymerase chain reaction. Genetics 120:621–623.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • Pillay, M., and S. T. Kenny. 1995. Anomalies in direct pairwise comparisons of RAPD fragments for genetic analysis. BioTechniques 19:694–698.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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 

  • Queller, D. C., J. E. Strassmann, and C. R. Hughes. 1993. Microsatellites and kinship. Trends in Ecology and Evolution 8:285–288.

    Article  PubMed  CAS  Google Scholar 

  • Rafalski, J. A., and S. V. Tingey. 1993. Genetic diagnostics in plant breeding: RAPDs, microsatellites and machines. Trends in Genetics 9:275–280.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Rieseberg, L. H. 1996. Homology among RAPD fragments in interspecific comparisons. Molecular Ecology 5:99–105.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Rieseberg, L. H., H. Choi, R. Chan, and C. Spore. 1993. Genomic map of a diploid hybrid species. Heredity 70:285–293.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Plainview, New York.

    Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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 

  • Schlötterer, C., and D. Tautz. 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Research 20:211–215.

    Article  PubMed  Google Scholar 

  • Schlötterer, C., B. Amos, and D. Tautz. 1991. Conservation of polymorphic simple sequence loci in cetacean species. Nature 354:63–65.

    Article  PubMed  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Skinner, D. Z. 1992. A PCR-based method of identifying species-specific repeated DNAs. BioTechniques 13:210–214.

    PubMed  CAS  Google Scholar 

  • Slatkin, M. 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457–462.

    PubMed  CAS  Google Scholar 

  • Smith, D. N., and M. E. Devey. 1994. Occurrence and inheritance of microsatellites in Pinus radiate. Genome 37:977–983.

    Article  PubMed  CAS  Google Scholar 

  • Smith, J. F., and T. V. Pham. 1996. Genetic diversity of the narrow endemic Allium aaseae (Alliaceae). American Journal of Botany 83:717–726.

    Article  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Sneath, P. H. A., and R. R. Sokal. 1973. Numerical Taxonomy. Freeman, San Francisco.

    Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Soltis, P. S., D. E. Soltis, and J. J. Doyle, eds. 1992a. Molecular Systematics of Plants. Chapman & Hall, New York.

    Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Song, K., and T. C. Osborn. 1994. A method for examining expression of homologous genes in plant polyploids. Plant Molecular Biology 26:1065–1071.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • Strand, A. E., J. Leebens-Mack, and B. G. Milligan. 1997. Nuclear DNA-based markers for plant evolutionary biology. Molecular Ecology 6:113–118.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Swerdlow, H., and R. Gesteland. 1990. Capillary gel electrophoresis for rapid high resolution DNA sequencing. Nucleic Acids Research 18:1415–1420.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Tautz, D. 1989. Hypervariability of simple-sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17:6463–6471.

    Article  PubMed  CAS  Google Scholar 

  • Tautz, D., and M. Renz. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research 12:4127–4138.

    Article  PubMed  CAS  Google Scholar 

  • Tautz, D., M. Trick, and G. A. Dover. 1986. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652–656.

    Article  PubMed  CAS  Google Scholar 

  • Terauchi, R., and A. Konuma. 1994. Microsatellite polymorphism in Dioscorea tokoro, a wild yam species. Genome 37:794–801.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Tracy, T. E., and L. S. Mulcahy. 1991. A simple method for direct automated sequencing of PCR fragments. BioTechniques 11:74–75.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Valdes, A. M., M. Slatkin, and N. B. Freimer. 1993. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133:737–749.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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 

  • 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 

  • 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.

    Article  Google Scholar 

  • 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 

  • 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.

    PubMed  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Waugh, R., and W. Powell. 1992. Using RAPD markers for crop improvement. Trends in Biotechnology 10:186–191.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Weising, K., H. Nybom, K. Wolff, and W. Meyer. 1995. DNA Fingerprinting in Plants and Fungi. CRC Press, Boca Raton, Florida.

    Google Scholar 

  • Welsh, J., and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18:7213–17218.

    Article  PubMed  CAS  Google Scholar 

  • Welsh, J., and M. McClelland. 1991. Genomic fingerprints produced by PCR with consensus transfer RNA gene primers. Nucleic Acids Research 19:861–866.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • Whitton, J., L. H. Rieseberg, and M. C. Ungerer. 1997. Microsatellite loci are not conserved across Asteraceae. Molecular Biology and Evolution 14:204–209.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Wolfe, A. D., and W. J. Elisens. 1993. Diploid hybrid speciation in Penstemon (Scrophulariaceae) revisited. American Journal of Botany 80:1082–1094.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Wu, K.-S., and S. D. Tanksley. 1993. Abundance, polymorphism and genetic mapping of microsatellites in rice. Molecular and General Genetics 241:225–235.

    Article  PubMed  CAS  Google Scholar 

  • Wu, K., R. Jones, L. Danneberger, and P. A. Scolnik. 1994. Detection of microsatellite polymorphisms without cloning. Nucleic Acids Research 22:3257–3258.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Yang, X., and C. Quiros. 1993. Identification and classification of celery cultivars with RAPD markers. Theoretical and Applied Genetics 86:205–212.

    Article  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Zietkiewicz, E., A. Rafalski, and D. Labuda. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

Download references

Authors
  1. Andrea D. Wolfe
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aaron Liston
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Botany, Washington State University, USA

    Douglas E. Soltis  & Pamela S. Soltis  & 

  2. Department of Botany, Cornell University, USA

    Jeff J. Doyle

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Springer Science+Business Media New York

About this chapter

Cite this chapter

Wolfe, A.D., Liston, A. (1998). Contributions of PCR-Based Methods to Plant Systematics and Evolutionary Biology. In: Soltis, D.E., Soltis, P.S., Doyle, J.J. (eds) Molecular Systematics of Plants II. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-5419-6_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4615-5419-6_2

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-0-412-11131-0

  • Online ISBN: 978-1-4615-5419-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation