Amplified Fragment Length Polymorphism (AFLP) is Useful for Finding Markers Associated with QTL for Architectural Trait in Hedysarum coronarium L.


Amplified fragment length polymorphism (AFLP) has been proposed as a valuable tool for finding molecular markers linked to QTL controlling architectural trait. Segregation of polymorphic AFLP fragments was followed in F2 offsprings Hedysarum coronarium derived from two native wild accesions crossing: Jebel Zit × El Haouaria, which had previously characterised by morphological and AFLP markers. A comparison of profiles from the morphologically contrasted parental individuals and F2 offspring has been assessed using five AFLP primer combinations. These generated 178 bands revealed by silver-stained denaturing polyacrylamide gels, of which 150 were polymorphic. Several AFLP markers appeared to be implied in the orthotropic form that can assist the selection and improve Hedysarum forage crop.


  1. 1.

    Bassam, B. J., Caetano-Anolles, G., Gresshoff P. M. (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196, 80–83.

    CAS  Article  Google Scholar 

  2. 2.

    Becker, J., Vos, P., Kuiper, M., Salamini, F., Heun, M. (1995) Combined mapping of AFLP and RFLP markers in barley. Mol. Gen. Genet. 249, 65–73.

    CAS  Article  Google Scholar 

  3. 3.

    Beckmann, J. S., Soller, M. (1988) Detection of linkage between marker loci affecting quantitative traits in crosses between segregating populations. Theor. Appl. Genet. 76, 228–236.

    CAS  Article  Google Scholar 

  4. 4.

    Bonierbale, M. W., Plaisted, R. L., Tanksley, S. D. (1988) RFLP maps based on common set of clones reveal modes of chromosomal evolution in potato and tomato. Genetics 120, 1095–1103s.

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Boussaïd, M., Ben Fadhel, N., Trifi-Farah, N., Abdelkefi, A., Marrakchi, M. (1995) Mediterranean species of Hedysarum genus. Genet. Res. For. Grass Plants (Ed. I.N.R.A. et B.R.G.), France, 115–130.

    Google Scholar 

  6. 6.

    Brahm, L., Röcher, T., Friedt, W. (2000) PCR-based markers facilitating marker assisted selection in sunflower for resistance to downy mildew. Crop Sci. 40, 676–682.

    CAS  Article  Google Scholar 

  7. 7.

    Chalhoub, B. A., Thibault, S., Laucou, V., Rameau, C., Hofte, H., Cousin, R. (1997) Silver staining and recovery of AFLPtm amplification products on large denaturing polyacrylamide gels. Biotechniques 22, 216–220.

    CAS  Article  Google Scholar 

  8. 8.

    Cho, Y. G., Blair, M. W., Panaud, O., McCouch, S. R. (1996) Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained polyacrylamide gels. Genome 39, 373–378.

    CAS  Article  Google Scholar 

  9. 9.

    Cho, Y. G., McCouch, S. R., Kuiper, M., Kang, M. R., Pot, J., Groenen, J. T. M., Eun, M. Y. (1998) Integrated map of AFLP, SSLP and RFLP markers using inbred population of rice (Oryza sativa L.). Theor. Appl. Genet. 97, 370–380.

    CAS  Article  Google Scholar 

  10. 10.

    Chong, J., Reimer, E., Somers, D., Aung, T., Penner, G. A. (2004) The Canad. J. Plant Pathol. 26, 89–96.

    CAS  Google Scholar 

  11. 11.

    Figier, J., Espagnac, H., Combes, D., Francillon, G. (1978) Mise en évidence de types mor-phologiques dans les populations naturelles de H. coronarium de Tunisie par analyse multivariable. Rev. Gen. Bot. 85, 21–62.

    Google Scholar 

  12. 12.

    Gebhardt, C., Ritter, E., Debener, T., Schachtschabel, U., Walkemeier, B., Uhrig, H., Salamini, F. (1989) RFLP analysis and linkage mapping in Solanum tuberosum. Theor. Appl. Genet. 78, 65–75.

    CAS  Article  Google Scholar 

  13. 13.

    Maheswaran, M., Subudhi, P. K., Nandi, S., Xu, J. C., Parco, A., Yang, D. C., Huang, N. (1997) Polymorphism, distribution, and segregation of AFLP markers in a doubled haploid rice population. Theor. Appl. Genet. 94, 39–45.

    CAS  Article  Google Scholar 

  14. 14.

    Marghali, S., Panaud, O., Ghariani, S., Lamy, F., Sarr, A., Marrakchi, M., Trifi-Farah, N. (2005) Exploration of intra- and inter-population genetic diversity in Hedysarum coronarium L. revealed by AFLP markers. Genet. Res. Crop Evol. 52, 277–284.

    CAS  Article  Google Scholar 

  15. 15.

    McCouch, S. R., Kochert, G., Yu, Z. H., Wang, Z. Y., Khush, G. S., Coffman, W. R., Tanksley, S. D. (1988) Molecular mapping of rice chromosomes. Theor. Appl. Genet. 76, 815–829.

    CAS  Article  Google Scholar 

  16. 16.

    Mendel, G. (1866) Versuche über Pflanzen-Hybriden. Verhandlungen des naturforschenden Vereines in Brünn 4, pp. 3–47. In: Peters, J. A. (ed.) Classic Papers in Genetics (1959). Translated as “Experiments in plant hybridization”, and reprinted Prentice-Hall, Englewood Cliffs, New Jersey.

    Google Scholar 

  17. 17.

    Norusis, M. J. (1993) SPSS for Windows advanced statistics, Release 6.0. Chicago: SPSS Inc.

    Google Scholar 

  18. 18.

    Paran, I., Michelmore, R. W. (1993) Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor. Appl. Genet. 85, 985–993.

    CAS  Article  Google Scholar 

  19. 19.

    Sambrook, K. J., Fritsch, E. F., Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, Second Edition.

    Google Scholar 

  20. 20.

    SAS (Statistical Analysis System) (1990) SAS User’s Guide. Version 6,07. SAS. Circl. Bow 800 Cary, NC 27 512-8000, Cary NC: SAS Institute INC, Fourth Edition.

    Google Scholar 

  21. 21.

    Simons, G., Van der Lee, T., Diergaarde, P., van Daelen, R., Groenendijk, J., Frijters, A., Buschges, R., Hollricher, K., Topsch, S., Shulze-Lefert, P., Salamini, F., Zabeau, M., Vos, P. (1997) AFLP-based fine mapping of the Mlo gene to a 30-kb DNA segment of the barley genome. Genomic. 44, 61–70.

    CAS  Article  Google Scholar 

  22. 22.

    Suiter, K. A., Wendel, J. F., Case, J. S. (1983) LINKAGE-1. a PASCAL computer program for the detection and analysis of genetic linkage. J. Heredit. 74, 203–204.

    CAS  Article  Google Scholar 

  23. 23.

    Tang, S., Heesacker, A., Kishore, V. K., Fernandez, A., Sadik, E. S., Cole, G., Knapp, S. J. (2003) Genetic Mapping of the Or5 Gene for Resistance to Orobanche Race E in Sunflower. Crop Sci. 43, 1021–1028.

    CAS  Article  Google Scholar 

  24. 24.

    Tanksley, S. D., Young, N. D., Paterson, A. H., Bonierbale, M. W. (1989) RFLP mapping in plant breeding. New tool for an old science. Biotechnol. 7, 257–264.

    CAS  Google Scholar 

  25. 25.

    Thomas, C. M., Vos, P., Zabeau, M., Jones, D. A., Norcott, K. A., Chadwick, B. P., Jones, J. D. G. (1995) Identification of amplified restriction fragment polymorphism (AFLP) markers tightly linked to the tomato Cf-9 gene for resistance to Cladosporium fulvum. Plant J. 8, 785–794.

    CAS  Article  Google Scholar 

  26. 26.

    Trifi-Farah, N., Chatti, W. S., Marrakchi, M., Pernes, J. (1989) Analyse de la variabilité mor-phologique et enzymatique des formes cultivées et spontanées de Hedysarum coronarium L. en Tunisie. Agronomi. 9, 591–598.

    Article  Google Scholar 

  27. 27.

    Trifi-Farah, N., Marrakchi, M. (2001) Hedysarum phylogeny mediated by RFLP analysis of nuclear ribosomal DNA. Genet. Res. Crop Evol. 48, 339–345.

    Article  Google Scholar 

  28. 28.

    Trifi-Farah, N., Marrakchi, M. (2002) Intra- and inter-specific genetic variability in Hedysarum revealed rDNA-RFLP markers. J. Genet. Breedin. 56, 1–9.

    Google Scholar 

  29. 29.

    Trifi-Farah, N., Baatout, H., Boussaïd, M., Combes, D., Figier, J., Salhi-Hannachi, A., Marrakchi, M. (2002) Evaluation des ressources génétiques des espe`ces du genre Hedysarum dans le bassin méditer-ranéen. Plant Genet. Res. Newslette. 130, 1–6.

    Google Scholar 

  30. 30.

    Vos, P., Hoger, R., Bleeker, M., Rejans, M., Vandelee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kuiper, M., Zabeau, M. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407–4414

    CAS  Article  Google Scholar 

  31. 31.

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

    CAS  Article  Google Scholar 

Download references


This research was supported by grants in Tunisia from the “Ministère de la Recherche Scientifique, de la Technologie et du Développement des Compétences”. We are grateful to Pr Rebai A (CB Sfax, Tunisia) for his fruitful help.

Author information



Corresponding author

Correspondence to N. Trifi-Farah.

Rights and permissions

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Reprints and Permissions

About this article

Cite this article

Marghali, S., Chennaoui, H., Bourguiba, H. et al. Amplified Fragment Length Polymorphism (AFLP) is Useful for Finding Markers Associated with QTL for Architectural Trait in Hedysarum coronarium L.. BIOLOGIA FUTURA 57, 459–471 (2006).

Download citation


  • AFLP markers
  • QTL
  • association
  • architecture
  • Hedysarum