Skip to main content
SpringerLink
Log in

Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.)

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

The use of bulked leaf samples from individual plants for amplified fragment length polymorphism (AFLP) analysis was evaluated as a tool for assessment of genetic diversity in white clover (Trifolium repens L.). Bulking of leaf samples produced slightly simpler AFLP profiles compared to the combined profiles of individual plants from the same cultivar. Approximately 90% of bands which were present in individual plants were present in bulked samples of the same cultivar. The majority of those absent were rare bands, shared by less than 25% of individual plants. Replicate bulk samples gave almost identical banding patterns, demonstrating the robustness of the bulked AFLP technique. Cluster analysis of AFLP data derived from individual plants resulted in a phenogram similar to that produced from data derived from bulked samples of the same plants. AFLP analysis of bulked samples detected significant amounts of genetic variability among 52 cultivars and accessions with genetic similarity values ranging from 0.42 to 0.92. However, cluster analysis of AFLP data only partially reflected the geographic origin of cultivars and accessions and was not congruent with cluster analysis based on variation for morphophysiological characters. Bulked AFLP analysis provides a powerful tool for rapid assessment of genetic variability in white clover and may also be used for cultivar identification.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Atwood, S.S., 1940. Genetics of cross-incompatibility among selfincompatible plants of Trifolium repens. J Am Soc Agron 32: 955–968.

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Beer, S.C., J. Goffreda, T.D. Phillips, J.P. Murphy & M.E. Sorrells, 1993. Assessment of genetic variation in Avena sterilis using morphological traits, isozymes and RFLPs. Crop Sci 33: 1386–1393.

    Article  CAS  Google Scholar 

  • Carnahan, H.L., 1960. A comparison of 1st and 2nd synthetic generation forage yields of ladino white clover in association with bromegrass. Agron J 52: 302.

    Article  Google Scholar 

  • Carnahan, H.L., H.D. Hill, A.A. Hanson & K.G. Brown, 1955. Inheritance and frequencies of leaf markings in white clover. J Hered 46: 109–114.

    Google Scholar 

  • Chowdari, K.V., S.R. Venkatachalam, A.P. Davierwala, V.S. Gupta, P.K. Ranjekar & O.P. Govila, 1998. Hybrid performance and genetic distance as revealed by the (GATA)(4) microsatellite and RAPD markers in pearl millet. Theor Appl Genet 97: 163–169.

    Article  CAS  Google Scholar 

  • Crawford, D.J., E.J. Esselman, J.L. Windus & C.S. Pabin, 1998. Genetic variation in running buffalo clover (Trifolium stoloniferum - Fabaceae) using random amplified polymorphic DNA markers (RAPDs). Ann MO Bot Gard 85: 81–89.

    Article  Google Scholar 

  • Divaret, I., E. Margale & G. Thomas, 1999. RAPD markers on seed bulks efficiently assess the genetic diversity of a Brassica oleracea L. collection. Theor Appl Genet 98: 1029–1035.

    Article  CAS  Google Scholar 

  • Dulson, J., L.S. Kott & V.L. Ripley, 1998. Efficacy of bulked DNA samples for RAPD DNA fingerprinting of genetically complex Brassica napus cultivars. Euphytica 102: 65–70.

    Article  CAS  Google Scholar 

  • Excoffier, L., P.E. Smouse & 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 

  • Fernando, W.M.U., M.D. Hayward & M.J. Kearsey, 1997. Isozyme and quantitative traits polymorphisms in European provenances of perennial ryegrass (Lolium perenne L.). Euphytica 93: 263–269.

    Article  CAS  Google Scholar 

  • Fulton, T.M., J. Chunwongse & S.D. Tanskley, 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molec Biol Rep 13: 207–209.

    CAS  Google Scholar 

  • Gilbert, J.E., R.V. Lewis, M.J. Wilkinson & P.D.S. Caligari, 1999. Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theor Appl Genet 98: 1125–1131.

    Article  CAS  Google Scholar 

  • Golembiewski, R.C., T.K. Danneberger & P.M. Sweeney, 1997. Potential of RAPD markers for use in the identification of creeping bentgrass cultivars. Crop Sci 37: 212–214.

    Article  CAS  Google Scholar 

  • Gustine, D.L. & D.R. Huff, 1999. Genetic variation within and among white clover populations from managed permanent pastures of the northeastern USA. Crop Sci 39: 524–530.

    Article  Google Scholar 

  • Huff, D.R., 1997. RAPD characterisation of heterogeneous perennial ryegrass cultivars. Crop Sci 37: 557–564.

    Article  CAS  Google Scholar 

  • Jahufer, M.Z.Z., M. Cooper & L.A. Brien, 1994. Genotypic variation for stolen and other morphological attributes of white clover (Trifolium repens L.) populations and their influence on herbage yield in the summer rainfall region of New South Wales. Aust J Agric Res 45: 703–720.

    Google Scholar 

  • Jones, C.J., K.J. Edwards, S. Castaglione, M.O. Winfield, F. Sala, C. Vandewiel, G. Bredemeijer, B. Vosman, M. Matthes, A. Daly, R. Brettschneider, P. Bettini, M. Buiatti, E. Maestri, A. Malcevschi, N. Marmiroli, R. Aert, G. Volckaert, J. Rueda, R. Linacero, A. Vazquez & A. Karp, 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol Breed 3: 381–390.

    Article  CAS  Google Scholar 

  • Joyce, T.A., M.T. Abberton, T.P.T. Michaelson-Yeates & J.W. Forster, 1999. Relationships between genetic distance measured by RAPD-PCR and heterosis in inbred lines of white clover (Trifolium repens L.). Euphytica 107: 159–165.

    Article  Google Scholar 

  • Kidwell, K.K., E.T. Bingham, D.R. Woodfield & T.C. Osborn, 1994. Relationships among genetic distance, forage yield and heterozygosity in isogenic diploid and tetraploid alfalfa populations. Theor Appl Genet 89: 323–328.

    Article  Google Scholar 

  • Kölliker, R., F.J. Stadelmann, B. Reidy & J. Nösberger, 1999. Genetic variability of forage grass cultivars: A comparison of Festuca pratensis Huds., Lolium perenne L. and Dactylis glomerata L. Euphytica 106: 261–270.

    Article  Google Scholar 

  • Kongkiatngam, P., M.J. Waterway, B.E. Coulman & M.G. Fortin, 1996. Genetic variation among cultivars of red clover (Trifolium pratense L.) detected by RAPD markers amplified from bulk genomic DNA. Euphytica 89: 355–361.

    CAS  Google Scholar 

  • Kongkiatngam, P., M.J. Waterway, M.G. Fortin & B.E. Coulman, 1995. Genetic variation within and between two cultivars of red clover (Trifolium pratense L.) - Comparisons of morphological, isozyme, and RAPD markers. Euphytica 84: 237–246.

    Article  CAS  Google Scholar 

  • Kraft, T. & T. Sall, 1999. An evaluation of the use of pooled samples in studies of genetic variation. Heredity 82: 488–494.

    Article  PubMed  Google Scholar 

  • Lee, C.K., H.A. Eagles, N.M. McFarlane & K.B. Kelly, 1993. Genetic variation within white clover (Trifolium repens L.) populations from North-Central Victoria. Aust J Exp Agric 33: 333–336.

    Article  Google Scholar 

  • Michelmore, R.W., I. Paran & R.V. Kesseli, 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88: 9828–9832.

    Article  PubMed  CAS  Google Scholar 

  • Moreno-Gonzalez, J. & J.I. Cubero, 1993. Selection strategies and choice of breeding materials. In: M.D. Hayward, N.O. Bosemark & I. Romagosa (Eds.), Plant Breeding: Principles and Prospects, pp. 281–313. Chapman & Hall, London.

    Google Scholar 

  • Mytton, L.R., 1975. Plant genotype x rhizobium strain interaction in white clover. Ann Appl Biol 80: 103–107.

    Article  PubMed  CAS  Google Scholar 

  • Nei, M. & W.H. Li, 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76: 5269–5273.

    Article  PubMed  CAS  Google Scholar 

  • Pejic, I., P. Ajmone-Marsan, M. Morgante, V. Kozumplick, P. Castiglioni, G. Taramino & M. Motto, 1998. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97: 1248–1255.

    Article  CAS  Google Scholar 

  • Rafalski, J.A., J.M. Vogel, M. Morgante, W. Powell, C. Andre & S.V. Tingey, 1996. Generating and using DNA markers in plants. In: B. Birren & E. Lai (Eds.), Non-Mammalian Genomic Analysis: A Practical Guide, pp. 75–135. Academic Press, Inc., San Diego.

    Google Scholar 

  • Rohlf, F.J., 1993. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. Exter Publishers, Setauket, NY.

    Google Scholar 

  • Sambrook, J., E.F. Fritsch & T. Maniatis, 1989. Molecular Cloning: A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press, Plainview, New York.

    Google Scholar 

  • Staub, J.E., F.C. Serquen & M. Gupta, 1996. Genetic markers, map construction, and their application in plant breeding. Hortscience 31: 729–741.

    CAS  Google Scholar 

  • Sweeney, P.M. & T.K. Danneberger, 1995. RAPD characterization of Poa annua L. populations in golf course greens and fairways. Crop Sci 35: 1676–1680.

    Article  CAS  Google Scholar 

  • Tohme, J., D.O. Gonzalez, S. Beebe & M.C. Duque, 1996. AFLP analysis of gene pools of a wild bean core collection. Crop Sci 36: 1375–1384.

    Article  CAS  Google Scholar 

  • Turkington, R., M.A. Cahn, A. Vardy & J.L. Harper, 1979. The growth, distribution, and neighbor-relationships of Trifolium repens in a permanent pasture. III. The establishment and growth of Trifolium repens in natural and perturbed sites. J Ecol 67: 231–243.

    Article  Google Scholar 

  • Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Vandelee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper & M. Zabeau, 1995. AFLP - a new technique for DNA fingerprinting. Nucleic Acids Res 23: 4407–4414.

    PubMed  CAS  Google Scholar 

  • Williams, W.M., 1987. Genetics and breeding. In: M.J. Baker & W.M. Williams (Eds.), White Clover, pp. 343–419. CAB International, Wallingford, Oxon.

    Google Scholar 

  • Woodfield, D.R. & J.R. Caradus, 1990. Estimates of heritability for, and relationship between root and shoot characters of white clover. II. Regression progeny on mid parent. Euphytica 46: 211–215.

    Article  Google Scholar 

  • Xu, W.W., D.A. Sleper & G.F. Krause, 1991. Genetic diversity of tall fescue germplasm based on RFLPs. Crop Sci 34: 246–252.

    Article  Google Scholar 

  • Yu, K.F. & K.P. Pauls, 1993. Rapid estimation of genetic relatedness among heterogeneous populations of alfalfa by random amplification of bulked genomic DNA samples. Theor Appl Genet 86: 788–794.

    CAS  Google Scholar 

Download references

Author information

Author notes

  1. R. Kölliker

    Present address: Swiss Federal Research Station for Agroecology and Agriculture, Reckenholzstrasse 191, 8046, Zurich, Switzerland

Authors and Affiliations

  1. Plant Biotechnology Centre, Agriculture Victoria, La Trobe University, Bundoora, Victoria, 3083, Australia

    R. Kölliker, E.S. Jones & J.W. Forster

  2. Pastoral and Veterinary Institute, Agriculture Victoria, Hamilton, Victoria, 3300, Australia

    M.Z.Z. Jahufer

Authors
  1. R. Kölliker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E.S. Jones
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M.Z.Z. Jahufer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J.W. Forster
    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

Kölliker, R., Jones, E., Jahufer, M. et al. Bulked AFLP analysis for the assessment of genetic diversity in white clover (Trifolium repens L.). Euphytica 121, 305–315 (2001). https://doi.org/10.1023/A:1012048103585

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1012048103585

Search

Navigation