Plant Molecular Biology Reporter

, Volume 29, Issue 1, pp 171–184

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 Hannachi
Article

DOI: 10.1007/s11105-010-0217-x

Cite this article as:
Baraket, G., Chatti, K., Saddoud, O. et al. Plant Mol Biol Rep (2011) 29: 171. doi:10.1007/s11105-010-0217-x

Abstract

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.

Keywords

AFLP Genetic diversity Fig, Ficus carica L. SSR Tunisia 

Abbreviations

SSR

Simple sequence repeat

AFLP

Amplified fragment length polymorphism

RAPD

Random amplified polymorphic DNA

ISSR

Inter simple sequence repeats

RAMPO

Randomly amplified microsatellite polymorphism

RFLP

Restriction fragment length polymorphism

ITS

Internal transcribed spacer

E

Effective multiplex ratio

EMI

Effective marker index

MI

Marker index

n

Multiplex ratio

QND

Qualitative nature of data

DC

Documentation capability

QM

Quality of marker

PR

Percent reproducibility

PIC

Polymorphic information content

DNA

Deoxyribonucleic acid

PCR

Polymerase chain reaction

UPGMA

Unweighted pair group method with the arithmetic averaging algorithm

PCA

Principal component analysis

AMOVA

Analysis of molecular variance

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
  1. 1.Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of TunisCampus UniversityTunisTunisia
  2. 2.U.R. Agro-biodiversityHigher Agronomic InstituteSousseTunisia