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

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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.

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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

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Acknowledgements

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

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Authors and Affiliations

  1. Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, Campus University, 2092 El Manar, Tunis, Tunisia

    Ghada Baraket, Khaled Chatti, Olfa Saddoud, Ahmed Ben Abdelkarim, Mokhtar Trifi & Amel Salhi Hannachi

  2. U.R. Agro-biodiversity, Higher Agronomic Institute, 4042 Chott Mariem, Sousse, Tunisia

    Messaoud Mars

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  1. Ghada Baraket
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  2. Khaled Chatti
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  4. Ahmed Ben Abdelkarim
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  5. Messaoud Mars
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  6. Mokhtar Trifi
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  7. Amel Salhi Hannachi
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Correspondence to Amel Salhi Hannachi.

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Baraket, G., Chatti, K., Saddoud, O. et al. Comparative Assessment of SSR and AFLP Markers for Evaluation of Genetic Diversity and Conservation of Fig, Ficus carica L., Genetic Resources in Tunisia. Plant Mol Biol Rep 29, 171–184 (2011). https://doi.org/10.1007/s11105-010-0217-x

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