Plant Molecular Biology Reporter

, Volume 29, Issue 1, pp 171–184 | Cite as

Comparative Assessment of SSR and AFLP Markers for Evaluation of Genetic Diversity and Conservation of Fig, Ficus carica L., Genetic Resources in Tunisia

  • Ghada Baraket
  • Khaled Chatti
  • Olfa Saddoud
  • Ahmed Ben Abdelkarim
  • Messaoud Mars
  • Mokhtar Trifi
  • Amel Salhi HannachiEmail author


This study characterises the genetic variability of fig, Ficus carica L., using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. It compares the efficiency and utility of the two techniques in detecting variation and establishing genetic relationships among Tunisian fig cultivars. Our results show that using both marker systems, the Tunisian fig germ plasm is characterised by having a large genetic diversity at the deoxyribonucleic acid level, as most of AFLP bands were detected and all SSR markers were polymorphic. In fact, 351 (342 polymorphic) and 57 (57 polymorphic) bands were detected using AFLP and SSR primers, respectively. SSR markers were the most polymorphic with an average polymorphic information content value of 0.94, while AFLP markers showed the highest effective multiplex ratio (56.9) and marker index (45.2). The effective marker index was recorded highest (4.19) for AFLP markers and lowest (0.70) for the SSR ones. Our results demonstrate that (1) independent as well as combined analyses of cluster analyses of SSR and AFLP fragments showed that cultivars are clustered independently from their geographical origin, horticultural classifications and tree sex; (2) the analysis of molecular variance allowed the partitioning of genetic variation within and among fig groups and showed greater variation within groups and (3) AFLP and SSR markers datasets showed positive correlation. This study suggests the SSR and AFLP markers are suitable for diversity analysis and cultivars fingerprinting. An understanding of the genetic diversity and population structure of F. carica in Tunisia can also provide insight into the conservation and management of this species.


AFLP Genetic diversity Fig, Ficus carica L. SSR Tunisia 



Simple sequence repeat


Amplified fragment length polymorphism


Random amplified polymorphic DNA


Inter simple sequence repeats


Randomly amplified microsatellite polymorphism


Restriction fragment length polymorphism


Internal transcribed spacer


Effective multiplex ratio


Effective marker index


Marker index


Multiplex ratio


Qualitative nature of data


Documentation capability


Quality of marker


Percent reproducibility


Polymorphic information content


Deoxyribonucleic acid


Polymerase chain reaction


Unweighted pair group method with the arithmetic averaging algorithm


Principal component analysis


Analysis of molecular variance



This work was supported by grants from the Tunisian “Ministère de l’Enseignement Supérieur et de la Recherche Scientifique”.


  1. Baraket G, Saddoud O, Chatti K, Mars M, Marrakchi M, Trifi M, Salhi Hannachi A (2009a) Sequence analysis of the internal transcribed spacers (ITS) region of the nuclear ribosomal DNA (nrDNA) in fig cultivars (Ficus carica L.). Sci Hortic 120:34–40CrossRefGoogle Scholar
  2. Baraket G, Chatti K, Saddoud O, Mars M, Marrakchi M, Salhi TM, Hannachi A (2009b) Genetic analysis of Tunisian fig (Ficus carica L.) cultivars using amplified fragment length polymorphism (AFLP) markers. Sci Hortic 120:487–492CrossRefGoogle Scholar
  3. Barker JHA, Matthes M, Arnold GM, Edwards KJ, Ahman I, Larsson S, Karp A (1999) Characterisation of genetic diversity in potential biomass willows (Salix spp.) by RAPD and AFLP analyses. Genome 42:173–183CrossRefPubMedGoogle Scholar
  4. Cabrita LF, Aksoy U, Hepaksoy S, Leitao JM (2001) Suitability of isozyme, RAPD and AFLP markers to assess genetic differences and relatedness among fig (Ficus carica L.) clones. Sci Hort 87(4):261–273CrossRefGoogle Scholar
  5. Cai Q, Aitken KS, Fan YH, Piperidis G, Jackson P, McIntyre CL (2005) A preliminary assessment of the genetic relationship between Erianthus rockii and the “Saccharum complex” using microsatellite (SSR) and AFLP markers. Plant Sci 169:976–984CrossRefGoogle Scholar
  6. Chatti K, Salhi Hannachi A, Mars M, Marrakchi M, Trifi M (2004a) Analyse de la diversité génétique de cultivars tunisiens de figuier (Ficus carica L.) à l’aide de caractères morphologiques. Fruits 59:49–61CrossRefGoogle Scholar
  7. Chatti K, Salhi Hannachi A, Mars M, Marrakchi M, Trifi M (2004b) Genetic diversity and phylogenic relationships in Tunisian fig (Ficus carica L.) cultivars mediated by RAPD. Biol Tunis 1(2):1–4Google Scholar
  8. Chatti K, Saddoud O, Salhi Hannachi A, Mars M, Marrakchi M, Trifi M (2007) Inferring of genetic diversity and relationships in a Tunisian fig (Ficus carica L.) germplasm collection by random amplified microsatellite polymorphisms. J Int Plant Biol 49(3):386–391CrossRefGoogle Scholar
  9. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1:19–21CrossRefGoogle Scholar
  10. Excoffier L (1993) Analysis of molecular variance. Version 1.5.5. Genetics and Biometry Laboratory, University of Geneva, GenevaGoogle Scholar
  11. Felsenstein J (1995) PHYLIP (Phylogeny Interference Package) ver. 3,5 c. Department of Genetics, University of Washington, SeattleGoogle Scholar
  12. Goulao L, Cabrita L, Oliveira CM, Leitao JM (2001) Comparing RAPD and AFLP analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh.) cultivars. Euphytica 119:259–270CrossRefGoogle Scholar
  13. Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185CrossRefGoogle Scholar
  14. Hamrick JL, Godt MJW (1996) Conservation genetics of endemic plant species. In: Avise JC, Hamrick JL (eds) Conservation genetics. Chapman and Hall, New York, pp 281–304Google Scholar
  15. Hedfi J, Trifi M, Salhi Hannachi A, Ould Mohamed Salem A, Marrakchi M (2003) Morphological and isoenzymatic polymorphism in Tunisian fig (Ficus carica L.) collection. Acta Horticulturae 605:319–325Google Scholar
  16. Ikegami H, Nogata H, Hirashima K, Awamura M, Nakahara T (2008) Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genet Resour Crop Evol. doi: 10.1007/S10722-008-9355-5 Google Scholar
  17. Khadari B, Hochu I, Santoni S, Kjellberg F (2001) Identification and characterization of microsatellite loci in the common fig (Ficus carica L.) and representative species of the genus Ficus. Mol Ecol Notes 1:191–193CrossRefGoogle Scholar
  18. Lefebvre V, Goffinet B, Chauvet JC, Caromel B, Signoret P, Brand R, Palloix A (2001) Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theor Appl Genet 102:741–750CrossRefGoogle Scholar
  19. Lynch M, Walsh JB (1998) Genetics and analysis of quantitative traits. Sinauer Assocs., Inc., SunderlandGoogle Scholar
  20. Machado CA, Jousselin E, Kjellberg F, Compton SG, Herre EA (2001) Phylogenetic relationships, historical biogeography and character evolution of fig pollinating wasps. Proc Royal Soc London Biol Sci 268:7–10Google Scholar
  21. Mars M, Marrakchi M (1998) Conservation et valorisation des ressources génétiques du grenadier (Punica granatum L.) en Tunisie. Plant Genet Resour Newsl 114:35–39Google Scholar
  22. Mars M, Chatti K, Saddoud O, Salhi Hannachi A, Trifi M, Marrakchi M (2008) Fig cultivation and genetic ressources in Tunisia, an overview. Proc. IIIrd IS on fig. Acta Horticulturae 798:27–32Google Scholar
  23. Nei M, Li WH (1979) Mathematical models for studying genetic variation in terms of restriction endonucléases. Proc Natl Acad Sci USA 76:5269–5273CrossRefPubMedGoogle Scholar
  24. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  25. Pejic I, Ajmone Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor Appl Genet 97:1248–1255CrossRefGoogle Scholar
  26. Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238CrossRefGoogle Scholar
  27. Rafalski A (2002) Application of single nucleotide polymorphsims in crop genetics. Curr Opin Plant Biol 5:94–100CrossRefPubMedGoogle Scholar
  28. Ridout CJ, Donini P (1999) Use of AFLP in cereal research. Trends Plant Sci 4:76–79CrossRefPubMedGoogle Scholar
  29. Russel JR, Fuller JD, Macaulay M, Hatz BGB, Jahoor A, Powell W, Waugh R (1997) Direct comparisons of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722CrossRefGoogle Scholar
  30. Saddoud O, Salhi Hannachi A, Chatti K, Rhouma A, Mars M, Marrakchi M, Trifi M (2005) Tunisian Fig (Ficus carica L.) genetic diversity and cultivars identification mediated by microsatellites markers. Fruits 60(2):143–153CrossRefGoogle Scholar
  31. Saddoud O, Chatti K, Salhi Hannachi A, Mars M, Rhouma A, Marrakchi M, Trifi M (2007) Genetic diversity of Tunisian figs (Ficus carica L.) as revealed by nuclear microsatellites. Hereditas 144:149–157CrossRefPubMedGoogle Scholar
  32. Saddoud O, Baraket G, Chatti K, Trifi M, Marrakchi M, Salhi Hannachi A, Mars M (2008) Morphological variability of fig (Ficus carica L.) cultivars. Int J Fruit Sci 8:35–51CrossRefGoogle Scholar
  33. Sadhu MK (1990) Fig. In: Kose TK, Mitra SK (eds) Fruits: tropical and subtropical. Naya Prokash, Calcutta, pp 650–663Google Scholar
  34. Salhi Hannachi A, Mars M, Chatti K, Marrakchi M, Trifi M (2003) Specific genetic markers for Tunisian fig germplasm: evidence of morphological traits, random amplified polymorphic DNA and inter simple sequence repeats markers. J Genet Breed 5:125–136Google Scholar
  35. Salhi Hannachi A, Trifi M, Zehdi S, Mars M, Rhouma A, Marrakchi M (2004) Inter simple sequence repeat fingerprintings to assess genetic diversity in Tunisian fig (Ficus carica L.). Genet Res Crop Evol 51(3):269–275CrossRefGoogle Scholar
  36. Salhi Hannachi A, Chatti K, Mars M, Marrakchi M, Trifi M (2005) Comparative analysis of genetic diversity in two collections figs cultivars based on random amplified polymorphic DNA and inter simple sequence repeats fingerprints. Genet Res Crop Evol 52(5):563–573CrossRefGoogle Scholar
  37. Salhi Hannachi A, Chatti K, Saddoud O, Mars M, Rhouma A, Marrakchi M, Trifi M (2006) Genetic diversity of different Tunisian fig (Ficus carica L.) collections revealed by RAPD fingerprints. Hereditas 143:15–22CrossRefPubMedGoogle Scholar
  38. Sambrook J, Frithsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New YorkGoogle Scholar
  39. SAS (1990) SAS user’s guide: SAS/STAT, SAS BASIC. Version 6.07, 4th edn. SAS Inc., Cary, pp 27512–28000Google Scholar
  40. Siegel S, Castellan NJ (1988) Nonparametric statistics for the behavioral sciences, 2nd edn. McGraw-Hill, New YorkGoogle Scholar
  41. Sneath PMA, Sokal RR (1973) Numerical taxonomy. W.H. Freeman and Company, San FranciscoGoogle Scholar
  42. StatSoft Inc (2001) STATISTICA (data analysis software systems), version 6. StatSoft, Inc, Tulsa ( Scholar
  43. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471CrossRefPubMedGoogle Scholar
  44. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers: features and applications. Trends Biotechnol 23:48–55CrossRefPubMedGoogle Scholar
  45. Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A (2007) Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci 173:638–649CrossRefGoogle Scholar
  46. Virk PS, Zhu J, Bryan GJ, Jackson MT, Ford-Lloyd BV (2000) Effectiveness of different classes of markers for classifying and revealing variation in rice (Oryza sativa) germplasm. Euphytica 112:275–284CrossRefGoogle Scholar
  47. Vos P, Hogers R, Bleeker M, Reijans M, De Lee T, Hornes M, Frijters A, Pot J, Poleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414CrossRefPubMedGoogle Scholar
  48. Weiblen GD (2000) Phylogenetic relationships of functionally diocious Ficus (Moraceae) based on ribosomal DNA sequences and morphology. Am J Bot 87(9):1342–1357CrossRefPubMedGoogle Scholar
  49. Woodhed W, Russell J, Squirell J, Hollingsworth PM, Mackenzie K, Gibby M, Powell W (2005) Comparative analysis of population genetic structure in Althyrium distentifolium (Pteridophyta) using AFLPs and SSRs from anonymous and transcribed gene regions. Mol Ecol 14(6):1681–1695CrossRefGoogle Scholar
  50. Yee E, Kidwell KK, Sills GR, Lumpkin TA (1999) Diversity among selected Vigna angularis (Azuki) accessions on the basis of RAPD and AFLP markers. Crop Sci 39:268–275CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Ghada Baraket
    • 1
  • Khaled Chatti
    • 1
  • Olfa Saddoud
    • 1
  • Ahmed Ben Abdelkarim
    • 1
  • Messaoud Mars
    • 2
  • Mokhtar Trifi
    • 1
  • Amel Salhi Hannachi
    • 1
    Email author
  1. 1.Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of TunisCampus UniversityTunisTunisia
  2. 2.U.R. Agro-biodiversityHigher Agronomic InstituteSousseTunisia

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