Skip to main content
Download PDF

Phylogenetic analyses within three sections of the genus Vicia

Cellular & Molecular Biology Letters volume 11, pages 594–615 (2006)Cite this article

Abstract

The averaged genomic similarities based on multilocus randomly amplified polymorphic DNA (RAPD) were calculated for eight species representing three sections of the genus Vicia: faba, bithynica and narbonensis. The frequency of appearance of the sequences corresponding to 25 decamers selected at random from genomes of different Fabace species was checked, and a high correlation with the frequency observed for Vicia allowed us to assume their similar weight in typing Vicia species. The RAPD-based similarity coefficients compared with those related to whole genome hybridization with barley rDNA and those based on restriction fragment length polymorphism (RFLP) revealed similar interspecies relationships. The averaged RAPD-based similarity coefficient (Pearson’s) was 0.68 for all the species, and was sectionspecific: 0.43 (bithynica), 0.50 (faba) and 0.73 (narbonensis). The averaged similarity coefficient for V. serratifolia (0.63) placed it apart from the rest (0.75) of its section. The results correspond to the interspecies relationships built upon non-genetic data. The averaged similarity coefficient for particular RAPD was related to the presence and type of tandemly repeated motif in a primer: 0.7–0.8 for heterodimers (GC, AG, CA, GT, CT), 0.5–0.6 for homodimers (CC, GG) and 0.6 for no repeat, indicating the sensitivity of diversity range to the type of target sequences.

Abbreviations

AFLP:

amplified fragment length polymorphism

BLAST:

basic local alignement search tool

EDTA:

ethylene diamine tetraacetic acid

HTGS:

high throughput genomic sequences

ICARDA:

International Center for Agricultural Research in the Dry Areas

ITS:

internal transcribed spacers

Mb:

mega base

Nr:

‘non redundant’

QTL:

quantitative trait loci

RAPD:

randomly amplified polymorphic DNA

RFLP:

restriction fragment length polymorphism

UPGMA:

unweighted pairs group method using mathematical avarages

References

  1. 1.

    Allkin, R., Goyder, D.J., Bisby, F.A. and White, R.J. Names and synonymus of species and subspecies in the Viciae. Issue 3 Vicieae Database Project Publication No 7 Southampton, 1986.

  2. 2.

    Harlan, J.R. Theory and dynamics of grassland agriculture. (Van Nostrand, D. Ed), Princeton, New Jersey, USA, 1956.

    Google Scholar 

  3. 3.

    Buntier, J.B., Sørensen, A.P. and Peleman, J.D. Haplotype diversity: the link between statistical and biological association. Trends Plant Sci. 10 (2005) 1360–1385.

    Google Scholar 

  4. 4.

    Gepts, P., Beavis, W.D., Brummer, E.Ch., Shoemaker, R.C., Stalker, H.T., Weeden, N.F. and Young, N.D. Legumes as a model plant family. Genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol. 137 (2005) 1228–1235.

    PubMed  CAS  Article  Google Scholar 

  5. 5.

    Lee, J.M., Grant, D., Vallejos, C.E. and Shoemaker, R.C. Genome organization in dicots. II. Arabidopsis as a ‘bridging species’ to resolve genome evolution events among legumes. Theor. Appl. Genet. 103 (2001) 765–773.

    CAS  Article  Google Scholar 

  6. 6.

    Paterson, A.H., Bowers, J.E., Burow, M.D., Draye, X., Elsik, Ch.G., Jiang, Ch-X., Katsar, C.S., Lan, T.-H., Lin, Y.-R. and Wright, R.J. Comparative genomics of plant chromosomes. Plant Cell 12 (2000) 1021–1029.

    Article  Google Scholar 

  7. 7.

    Zhu, H., Choi, H.-K., Cook, D.R. and Shoemaker, R.C. Bridging model and crop legumes through comparative genomics. Plant Physiol. 137 (2005) 1189–1196.

    PubMed  CAS  Article  Google Scholar 

  8. 8.

    Bennetzen, J.L. Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12 (2000) 1021–1029.

    PubMed  CAS  Article  Google Scholar 

  9. 9.

    Choi, H.K., Mun, J.H., Kim, D.J., Zhu, H., Baek, J.M., Mudge, J., Roe, B., Ellis, N., Doyle, J., Kiss, G.B., Young, N.D. and Cook, D.R. Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA 101 (2004) 15289–15294.

    PubMed  CAS  Article  Google Scholar 

  10. 10.

    McCouch, S.R. Genomics and synteny. Plant Physiol. 125 (2001) 152–155.

    PubMed  CAS  Article  Google Scholar 

  11. 11.

    Yan, H.H., Mudge, J., Kim, D.-J., Shoemaker, R.C. and Young, N.D. Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana. Genome 47 (2004) 141–155.

    PubMed  CAS  Article  Google Scholar 

  12. 12.

    Grant, D., Cregan, P. and Shoemaker, R.C. Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc. Natl. Acad. Sci. USA 97 (2000) 4168–4173.

    PubMed  CAS  Article  Google Scholar 

  13. 13.

    Frediani, M., Caputo, P., Venora, G., Ravelli, C., Ambrosio, M. and Cremonini, R. Nuclear DNA contents, rDNAs, and karyotype evolution in Vicia subgenus Vicia: II. Section Peregrinae. Protoplasma 226 (2005) 181–190.

    PubMed  CAS  Article  Google Scholar 

  14. 14.

    Fuchs, J., Strehl S., Brandes, A., Schweizer, D. and Schubert, I. Molecular-cytogenetic characterization of the Vicia faba genome, heterochromatin differentiation, replication patterns and sequence localization. Chromosome Res. 6 (1998) 219–230.

    PubMed  CAS  Article  Google Scholar 

  15. 15.

    Leht, M. and Jaaska, V. Cladistic and phenetic analysis of relationships in Vicia subgenus Vicia (Fabaceae) by morphology and isozymes. Plant Syst. Evol. 232 (2001) 237–260.

    Article  Google Scholar 

  16. 16.

    Przybylska, J. and Zimniak-Przybylska, Z. Electrophoretic seed albumin patterns and species relationships in Vicia sect Faba (Fabaceae). Plant. Syst. Evol. 198 (1995) 179–194.

    CAS  Article  Google Scholar 

  17. 17.

    Van de Ven, W.T.G., Duncan N., Ramsay, G., Philips, M., Powell, M. and Waugh, R. Taxonomic relationships between V. faba and relatives based on nuclear and mitochondrial RFLPs and PCR analysis. Theor. Appl. Genet. 86 (1993) 71–80.

    Article  Google Scholar 

  18. 18.

    Venora, G., Blangifirti, S., Frediani, M., Maggini, F., Castiglione, M.R. and Cremonini, R. Nuclear DNA contents, rDNAs, chromatin organization, and karyotype evolution in Vicia sect Faba. Protoplasma 213 (2000) 118–125.

    CAS  Article  Google Scholar 

  19. 19.

    Wojciechowski, M.F. In Advances in legume systematics. Part 10. Higher level systematics. Edited by Klitgaard, B.B. and Bruneau, A. Royal Botanic Gardens, Kew, U.K. (2003) 5–35.

    Google Scholar 

  20. 20.

    Raina, S.N. Genome organization and evolution in the genus Vicia. In: Biological approaches and evolutionary trends in plants. Academic Press, New York, NY (1990) 183–201.

    Google Scholar 

  21. 21.

    Pozarkova, D., Kublizkova, A., Roman, B., Torres, A.M., Lucretti, S., Lysak, M., Dolezel, J. and Macas, J. Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. Biol. Plant. 45 (2002) 337–345.

    CAS  Article  Google Scholar 

  22. 22.

    Román, B., Torres, A.M., Rubiales, D., Cubero, J.I. and Satovic, Z. Mapping of quantitative trait loci controlling broomrape (Orobanche crenata Forsk) resistance in faba bean (Vicia faba L). Genome 45 (2002) 1057–1063.

    PubMed  Article  Google Scholar 

  23. 23.

    Bennett, M.D. and Leitch, I.J. Angiosprm DNA C-values database (release5.0 dec.2004) http://www.rbgkew.org.uk/cval/homepage.html (2004).

  24. 24.

    Román, B., Satovic, Z., Pozarkova, D., Macas, J., Dolezel, J. and Torres, A.M. Development of a composite map in Vicia faba, breeding applications and future prospects. Theor. Appl. Genet. 108 (2004) 1079–1088.

    PubMed  Article  Google Scholar 

  25. 25.

    Torres, A.M., Weeden, N.F. and Martín, A. Linkage among isozyme, RFLP and RAPD markers in Vicia faba. Theor. Appl. Genet. 85 (1993) 937–945.

    CAS  Article  Google Scholar 

  26. 26.

    Heslop-Harrison, J.S. Comparative genome organization in plants: from sequence and markers to chromatin and chromosomes. Plant Cell 12 (2000) 617–635.

    PubMed  CAS  Article  Google Scholar 

  27. 27.

    Avila, C.M., Sillero, J.C., Rubiales, D., Moreno, M.T. and Torres, A.M. Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (Uromyces Viciae-fabae) in Vicia faba L. Theor. Appl. Genet. 107 (2003) 353–358.

    PubMed  CAS  Article  Google Scholar 

  28. 28.

    Weder, J.K.P. Identifcation of Food and Feed Legumes by RAPD-PCR. Lebensm-Wiss u-Technol. 35 (2002) 504–511.

    CAS  Article  Google Scholar 

  29. 29.

    Raina, S.N. and Ogihara, A. Ribosomal DNA repeat unit polymorphism in 49 Vicia species. Theor. Appl. Genet. 90 (1995) 477–486.

    CAS  Article  Google Scholar 

  30. 30.

    Potokina, E., Tomooka, N., Vaughan, D.A., Alexandrowa, T. and Xu, R.Q. Phylogeny of Vicia subgenus Vicia (Fabaceae) based on analysis of RAPDs and RFLP of PCR-amplified chloroplast genes. Genet. Res. Crop. Evol. 46 (1999) 149–161.

    Article  Google Scholar 

  31. 31.

    Potokina, E., Blattner, F.R., Alexandrova, T. and Bachmann, K. AFLP diversity in the common vetch (Vicia sativa L) on the world scale. Theor. Appl. Genet. 105 (2002) 58–67.

    PubMed  CAS  Article  Google Scholar 

  32. 32.

    Peakall, R., Gilmore, S., Keys, W., Morgante, M. and Rafalski, A. Cross-Species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15 (1998) 1275–1287.

    PubMed  CAS  Google Scholar 

  33. 33.

    Frediani, M., Galati, M.T., Maggini, F., Galasso, I., Minelli, S., Ceccarelli, M. and Cionini, P.G. A family of dispersed repeats in the genome of V. faba: structure, chromosomal organization, redundancy modulation, and evolution. Chromosoma 108 (1999) 317–324.

    PubMed  CAS  Article  Google Scholar 

  34. 34.

    Macas, J., Navratilova, A. and Meszaros, T. Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes. Chromosoma 112 (2003) 152–158.

    PubMed  CAS  Article  Google Scholar 

  35. 35.

    Pearce, S.R., Harrison, G., Li, D., Heslop-Harrison, J.S., Flavell, A. and Kumar, A. The Ty-1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localization. Mol. Gen. Genet. 250 (1996) 305–315.

    PubMed  CAS  Google Scholar 

  36. 36.

    Naumann, P., Koblizkova, A., Navratilova, A. and Macas, J. Significant expansion of Vicia pannonica genome size mediated by amplification of a single type of giant retroelement. Genetics 173 (2006) 1047–1056.

    Article  Google Scholar 

  37. 37.

    Macas, J., Neumann, P. and Pozarkova, D. Zaba: a novel miniature transposable element present in genomes of legume plants. Mol. Gen. Genomics 269 (2003) 624–631.

    CAS  Article  Google Scholar 

  38. 38.

    Maxted, N., Khettab, M.A. and Bisby, F.A. The newly discovered relatives of Vicia faba do little to resolve the enigma of its origin. Bot. Chron. 10 (1991) 435–465.

    Google Scholar 

  39. 39.

    Gerlach, W.L. and Bedbrook, J.R. Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 8 (1979) 1869–1885.

    Google Scholar 

  40. 40.

    Sambrook, J., Fritsch, E.F. and Maniatis, T. Molecular Cloning A Laboratory Manual, 2nd Ed. Edited by Cold Spring Harbor Laboratory Press, New York, 1989.

    Google Scholar 

  41. 41.

    Williams, J.G.K., Kubelik, A.R., Livak, A.J., Rafalski, J.A. and Tingey, S.V. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18 (1990) 6531–6535.

    PubMed  CAS  Google Scholar 

  42. 42.

    Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389–3402.

    PubMed  CAS  Article  Google Scholar 

  43. 43.

    Sokal, R.R. and Sneath, P.H.A., Principles of Numerical Taxonomy. WH Freeman & Co, San Francisco, CA USA, 1963.

    Google Scholar 

  44. 44.

    Francki, M.G. and Mullan, D.J. Application of comparative genomics to narrowleafed lupin (Lupinus angustifolius L.) using sequence information from soybean and Arabidopsis. Genome 47 (2004) 623–632.

    PubMed  CAS  Article  Google Scholar 

  45. 45.

    Hecht, V., Foucher, F., Ferrandiz, C., Macknight, R., Vardy, M.E., Ellis, N., Beltran, J.P., Rameau, C. and Weller, J.L. Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol. 137 (2005) 142–1434.

    Article  Google Scholar 

  46. 46.

    Kalo, P., Seres, A., Taylor, S.A., Jakab, J., Kevei, Z., Kereszt, A., Endre, G., Ellis, T.H.N. and Kiss, G.B. Comparative mapping between Medicago sativa and Pisum sativum. Mol. Genet. Genomics 272 (2004) 235–246.

    PubMed  CAS  Article  Google Scholar 

  47. 47.

    Hill, P., Burford, D., Martin, D.M. and Flavell, A.J. Retrotranspozon populations of Vicia species with varying genome size. Mol. Genet. Genomics 273 (2005) 371–381.

    PubMed  CAS  Article  Google Scholar 

  48. 48.

    SanMiguel, P. and Bennetzen, J.L. Evidence that recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82 Suppl A (1998) 37–44.

    CAS  Article  Google Scholar 

  49. 49.

    Menacio-Hautea, D., Fatokum, C.A., Kumar, L., Danesh, D. and Young, N.D. Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata) using RFLP analysis. Theor. Appl. Genet. 86 (1993) 797–810.

    Article  Google Scholar 

  50. 50.

    Bennett, M.D. and Smith, J.B. Nuclear DNA amounts in angiosperms. Phil. Trans. of the Royal Society of London B 334 (1991) 309–345.

    CAS  Google Scholar 

  51. 51.

    Olszewska, M.J. and Osiecka, R. The relationship between 2C DNA content, life-cycle type, systematic position and the dynamics of DNA endoreplication in parenchyma nuclei during growth and differentiation of roots in some dicotyledonous-herbaceous species. Biochemie und Physiologie der Pflanzen 178 (1983) 581–599.

    CAS  Google Scholar 

  52. 52.

    Naranjo, C.A., Ferrari, M.R., Palermo, A.M. and Poggio, L. Karyotype, DNA content and meiotic behaviour in five south american species of Vicia (Fabaceae). Ann. Bot. 82 (1998) 757–764.

    Article  Google Scholar 

Download references

Author information

Affiliations

  1. Department of Cytogenetics and Plant Molecular Biology, University of Łódź, 90-237, Łódź, Banacha 12/16, Poland

    Tomasz Sakowicz

  2. Centre for Medical Biology Polish Academy of Sciences, 93-232, Łódź, Lodowa 106, Poland

    Tomasz Cieślikowski

Authors
  1. Tomasz Sakowicz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tomasz Cieślikowski
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Sakowicz, T., Cieślikowski, T. Phylogenetic analyses within three sections of the genus Vicia . Cell Mol Biol Lett 11, 594–615 (2006). https://doi.org/10.2478/s11658-006-0047-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.2478/s11658-006-0047-x

Key words

  • Vicia
  • Average similarity
  • Multilocus diversity
  • RAPD

Cellular & Molecular Biology Letters

ISSN: 1689-1392

Contact us