Diversity in Natural Fern Populations: Dominant Markers as Genetic Tools

  • E. L. Peredo
  • A. Revilla
  • M. Méndez
  • V. Menéndez
  • H. Fernández


Our aim, in the present chapter, is to provide a synthesis of the use of dominant markers in the Pteridophytes’ genetics. We try to provide a ­comprehensive review of the advantages and disadvantages of the selection of dominant markers as genetic tools, when compared to other molecular techniques ­available. Dominant markers fulfill most of the ideal characteristics of a fingerprinting ­technique as they are usually technically simple procedures, inexpensive, and allow fast data ­acquisition. In addition, dominant markers are based in one of the fundamental characteristic of the DNA, the probability of sequence repetition due to the ­existence of only four nucleotides, so these techniques are easily ­transferable from one ­organism to another as no prior genetic knowledge of each species is needed. However, the increasing availability of sequenced data due to the relative price decrease and apparition of new sequencing techniques together with their drawbacks have forced to ask: are dominant markers still useful?

We do not try here to give a definitive answer to this question. We just want to point out that there is no perfect fingerprinting technique. Its choice is often a ­compromise that depends on a number of material and species-related factors. The existence of previous genetic data in the species, the knowledge of close relatives, and the complexity of the genome are other factors that dramatically influence our selection. The resources of the laboratory, financial constraints, available expertise, time limitations, and, more importantly, the research pursued usually define our opinion about dominant markers. Our purpose in the present chapter is to provide a detailed review of strong points and drawbacks as well the areas where the ­application of dominant markers has succeeded in answering questions in the genetically complex Pteridophytes.


Dominant Marker Codominant Marker Reproductive Barrier Fern Species AFLP Data 



Amplified fragment length polymorphism


Fast isolation by AFLP of sequences containing repeats


Inter-retrotransposon amplified polymorphism


Inter-simple sequence repeats


Methylation-sensitive amplified polymorphism


Polymerase chain reaction


Random amplified polymorphic DNA


Retrotransposon-microsatellite amplified polymorphism


Sequence-characterized amplified regions


Single nucleotide polymorphisms


Single sequence repeat


  1. Ares Jiménez, A., Quintanilla, L.G., Pajarón, S., and Pangua, E. 2009. Genetic Variation in the allotetraploid Dryopteris corleyi (Dryopteridaceae) and its diploid parental species in the lberian Peninsula. Am. J. Bot. 96:1880-1886.Google Scholar
  2. Cook, L.M., Soltis, P.S., Brunsfeld, S.J., and Soltis, D.E. 1998. Multiple independent formations of Tragopogon tetraploids (Asteraceae): Evidence from RAPD markers. Mol. Ecol. 7: 1293–1302.CrossRefGoogle Scholar
  3. Feldman, M., Liu, B., Segal, G., Abbo, S., Levy, A.A., and Vega, J.M. 1997. Rapid elimination of low-copy DNA sequences in polyploid wheat: A possible mechanism for differentiation of homoeologous chromosomes. Genetics 147: 1381–1387.PubMedGoogle Scholar
  4. Given, D.R. 1993. Changing aspects of endemism and endargerment in Pteridophyta. J. Biogeog. 20: 293–302.CrossRefGoogle Scholar
  5. Gong, H.Y., Liu, A.H., and Wang, J.B. 2006. Genomic evolutionary changes in Aegilops allopolyploids revealed by ISSR markers. Act Phytotax. Sin. 44: 286–295. doi: 10.1360/aps040169CrossRefGoogle Scholar
  6. Herrero, A., Pajarón, S., and Prada C. 2001. Isozyme variation and genetic relationships among taxa in the Asplenium obovatum group (Aspleniaceae, Pteridophyta). Am. J. Bot. 88: 2040–2050.CrossRefGoogle Scholar
  7. Hooper, E.A., and Haufler, C.H. 1997. Genetic diversity and breeding system in a group of neotropical epiphytic ferns (Pleopeltis; Polypodiaceae). Am. J. Bot. 84: 1664–1674.CrossRefGoogle Scholar
  8. Hunt, H.V., Ansell, S.W., Russell, S.J., Schneider, H., and Vogel J.C. 2009. Genetic diversity and phylogeography in two diploid ferns, Asplenium fontanum subsp. fontanum and A. petrarchae subsp. bivalens, in the western Mediterranean. Mol. Ecol. 18: 4940–4954.CrossRefPubMedGoogle Scholar
  9. Kingston, N., Waldren, S., and Smyth, N. 2004. Conservation genetics and ecology of Angiopteris chauliodonta Copel. (Marattiaceae), a critically endangered fern from Pitcairn Island, South Central Pacific Ocean. Biol. Cons. 117: 309–319.CrossRefGoogle Scholar
  10. Kang, M., Ye, Q., and Huang, H. 2005. Genetic consequence of restricted habitat and population decline in endangered Isoetes sinensis (Isoetaceae). Ann. Bot. 96: 1265–1274.CrossRefPubMedGoogle Scholar
  11. Keiper, F.J., and McConchie, R. 2000. An analysis of genetic variation in natural populations of Sticherus flabellatus [R. Br. (St John)] using amplified fragment length polymorphism (AFLP) markers. Mol. Ecol. 9: 571–581.CrossRefPubMedGoogle Scholar
  12. Korpelainen, H., Britto, J., Doublet, J., and Pravin, S. 2005. Four tropical, closely related fern species belonging to the genus Adiantum L. are genetically distinct as revealed by ISSR fingerprinting. Genetica 125: 283–291.CrossRefPubMedGoogle Scholar
  13. Korpelainen, H., Kostamo, K., and Virtanen, V. 2007. Microsatellite marker identification using genome screening and restriction-ligation. Biotechniques 42: 479–486.CrossRefPubMedGoogle Scholar
  14. Korpelainen, H., and Pietiläinen, M. 2008. Effort to reconstruct past population history in the fern Blechnum spicant. J. Plant. Res. 121: 293–298.CrossRefPubMedGoogle Scholar
  15. Landergott, U., Holderegger, R., Kozlowski, G., and Schneller, J.J. 2001. Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata. Heredity 87: 344–355.CrossRefPubMedGoogle Scholar
  16. Meudt H.M., and Clarke A.C. 2007. Almost forgotten or latest practice? AFLP applications, analyses and advances. Trends Plant Sci. 12: 106–117.CrossRefPubMedGoogle Scholar
  17. Murphy, R.W., Sites, J.W., Buth, D.G., and Haufler, C.H. 1996. Proteins: Isozyme electrophoresis. In: Molecular Systematics. 2nd edn (eds Hillis DM, Moritz C, Mable BK) Sinauer Associates, Sunderland, MA.Google Scholar
  18. Nakazato, T., Jung, M.K., Housworth, E.A., Rieseberg, L.H., and Gastony, G.J. 2006. Genetic map-based analysis of genome structure in the homosporous fern Ceratopteris richardii. Genetics 173: 1585–1597.CrossRefPubMedGoogle Scholar
  19. Nakazato, T., Jung, M.K., Housworth, E.A., Rieseberg, L.H., and Gastony, G.J. 2007. A genome wide study of reproductive barriers between allopatric populations of a homosporous fern, Ceratopteris richardii. Genetics 177: 1141–1150.CrossRefPubMedGoogle Scholar
  20. Orita, M., Iwahana H., Kanazawa H., Hayashi K., and Sekiya T. 1989. Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2766–2770.CrossRefPubMedGoogle Scholar
  21. Otto, S.P., and Whitton J. 2000. Polyploid incidence and evolution. Annu. Rev. Genet. 34: 401–437.CrossRefPubMedGoogle Scholar
  22. Pajarón, S., Pangua, E., and García-Álvarez, L. 1999. Sexual expression and genetic diversity in populations of Cryptogramma crispa (Pteridaceae). Am. J. Bot. 86: 964–973.CrossRefPubMedGoogle Scholar
  23. Park, Y.J., Lee, J.K., and Kim, N.S. 2009. Simple Sequence Repeat Polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 14: 4546–4569.CrossRefPubMedGoogle Scholar
  24. Parokonny, A.S., and Kenton, A.Y. 1995. Comparative physical mapping and evolution of the Nicotiana tabacum L. karyotype. In: Brandham, P.E., and Bennett, M.D., eds. Kew Chromosome Conference IV. London: Royal Botanic Garden, Kew. pp. 301–320.Google Scholar
  25. Peredo, E.L., Revilla, M.A., Reed, B.M., Javornik, B., and Arroyo-García, R. 2010. The influence of the European and American wild germplasm in hop cultivars. Gen. Res. Crop Evol. doi: 10.1007/s10722-009-9495-2.Google Scholar
  26. Perrie, L.r., and Brownsey P.J. 2005. Genetic variation is not concordant with morphological variation in the fern Asplenium hookerianum sensu lato (Aspleniaceae Am. J. Bot. 92:1559–1564.Google Scholar
  27. Pryor, K.V., Young, J.E., Rumsey, F.J., Edwards, K.J., Bruford, M.W., and Rogers, H.J. 2001. Diversity, genetic structure and evidence of outcrossing in British populations of the rock fern Adiantum capillus-veneris using microsatellites. Mol. Ecol. 10: 1881–1894.CrossRefPubMedGoogle Scholar
  28. Soltis, P.S., and Soltis D.E. 2000. The role of genetic and genomic attributes in the success of polyploids. Proc. Natl. Acad. Sci. USA 97: 7051–7057.CrossRefPubMedGoogle Scholar
  29. Song, K., Lu, P., Tang, K., and Osborn, T.C. 1995. Rapid genomic change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 92: 7719–7723.CrossRefPubMedGoogle Scholar
  30. Schneller, J., and Liebst, B. 2007. Patterns of variation of a common fern (Athyrium filix-femina; Woodsiaceae): Population structure along and between altitudinal gradients. Am. J. Bot. 94: 965–971.CrossRefGoogle Scholar
  31. Sood, A., Prasanna, R., Prasanna, B.M., and Singh, P.K. 2008. Genetic diversity among and within cultured cyanobionts of diverse species of Azolla. Folia Microbiol. 53: 35–43.CrossRefGoogle Scholar
  32. Stebbins, G. L. 1947. Types of polyploids: Their classification and significance. Adv. Genet. 1: 403–429.CrossRefPubMedGoogle Scholar
  33. Vitalis, R., Colas, B., Riba, M., and Olivieri I. 1998. Marsilea strigosa Willd.: Statut génétique et démographique d’une espèce menaceé. Ecol. Mediterranea 24: 145–157.Google Scholar
  34. Vitalis, R., Riba, M., Colas, B., Grillas, P., and Olivieri, I. 2002. Multilocus genetic structure at contrasted spatial scales of the endangered water fern Marsilea strigosa willd. (Marsileaceae, Pteridophyta). Am. J. Bot. 89: 1142–1155.CrossRefGoogle Scholar
  35. Volkov, R.A., Borisjuk, N.V., Panchuk, I.I., Schweizer, D., and Hemleben, V. 1999. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Mol. Biol. Evol. 16: 311–320.PubMedGoogle Scholar
  36. Vos, P., Hogers, R., Bleeker, M., Van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., and Kuiper M. 1995. AFLP: a new tchnique for DNA fingerprinting. Nucleic Acids Res. 23:4407–4414.Google Scholar
  37. Wood, T.E., Takebayashi, N., Barker, M.S., Mayrosee, I., Greenspoon, P.B., and Rieseberg L.H. 2009. The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. USA 106: 13875–13879.CrossRefPubMedGoogle Scholar
  38. Woodhead, M., Russell, J., Squirrell, J., Hollingsworth, P.M., Mackenzie, K., Gibby, M., and Powell, W. 2005. Comparative analysis of population genetic structure in Athyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Mol. Ecol. 14: 1681–1695 doi: 10.1111/j.1365-294x.2005.02543.xCrossRefPubMedGoogle Scholar
  39. Zane, L., Bargelloni, L., and Patarnello, T. 2002. Strategies for microsatellite isolation: A review. Mol. Ecol. 11: 1–16.CrossRefPubMedGoogle Scholar
  40. Zhang, Y., He, J., Zhao, P.X., Bouton, J.H., and Monteros, M.J. 2008. Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Meth. 4: 19 doi:  10.1186/1746-4811-4-19 CrossRefGoogle Scholar
  41. Zheng, W.W., Nilsson, M., Bergman, B., and Rasmussen U. 1999. Genetic diversity and classification of cyanobacteria in different Azolla species by the use of PCR fingerprinting. Theor. Appl. Genet. 99: 1187–1193.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • E. L. Peredo
  • A. Revilla
  • M. Méndez
  • V. Menéndez
  • H. Fernández
    • 1
  1. 1.Area Plant Physiology, Departamento de Biología de Organismos y SistemasUniversidad de OviedoOviedoSpain

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