THE DISCRIMINATING CAPACITY OF SSR, RAPD AND AFLP MARKERS AND THEIR EFFECTIVENESS IN ESTABLISHING GENETIC RELATIONSHIPS IN OLIVE (Olea europaea L.)
Abstract
RAPDs, AFLPs and SSRs were compared in terms of their informativeness and efficiency in a study of genetic diversity and relationships among eleven olive cultivars (Olea europaea L.) cultivated in Siwa oasis. SSRs presented a higher level of polymorphism and greater information content, as assessed by the expected heterozygosity, than AFLPs and RAPDs. The lowest values of expected heterozygosity were obtained for AFLPs, which nevertheless were the most efficient marker system due to their capacity to reveal the highest number of bands per reaction and because of the high values achieved for a considerable number of indexes. All three techniques discriminated the genotypes effectively, but SSRs were able to discriminate the cultivars Chemlali, Wetagen, Picual and Kalamata. For all markers, a similarity in dendrogram topologies was obtained although some differences were observed. Both, RAPDs and AFLPs, were efficient in detecting genetic similarities in olive, while the codominant nature of SSRs will make it the marker of choice for segregation studies and genome mapping in olive. A better understanding of the effectiveness of the different molecular markers is considered a priority step toward olive germplasm characterisation and classification, and a prerequisite for more effective breeding programs.References
Baali-Cherif, D. and G. Besnard (2005). High genetic diversity and clonal growth in relict populations of Olea europaea subsp. laperrinei (Oleaceae) from Hoggar, Algeria. Ann. Bot., 96: 823-830.
Baldoni, L., N. Tosti, C. Ricciolini, A. Belaj, S. Arcioni and G. Pannelli (2006). Genetic structure of wild and cultivated olives in the Central Mediterranean Basin. Ann. Bot., 98: 935-942.
Bandelj, D., J. Jakse and B. Javornik (2002). DNA Fingerprinting of Olive Varieties, Food Technol. Biotechnol., 40: 185-190.
Bartolini, G., G. Prevost, C. Messeri and G. Carignani (2005). Olive germplasm: cultivars and wordwide collections. Web site FAO: http://www.apps3.fao.org/wiews/olive/oliv.jsp.
Besnard, G. and A. Berville´ (2000). Multiple origins for Mediterranean olive (Olea europaea L. ssp. europaea) based upon mitochondria DNA polymorphisms. Life Science, 323: 173-181.
Besnard, G., B. Khadari, P. Baradat and A. Berville (2002). Combination of chloroplast and mitochondrial DNA polymorphisms to study cytoplasm genetic differentiation in the olive complex (Olea europaea L.). Theor. Appl. Genet., 105: 139-144.
Carriero, F., G. Fontanazza, F. Cellini and G. Giorio (2002). Identification of sample sequence repeats (SSRs) in olive (Olea europaea L.). Theor. Appl. Genet., 104: 301-307.
Casas, R., G. Besnard, P. Scho, L. Balaguer and P. Vargas (2006). Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L. Theor. Appl. Genet., 113: 575–583.
Cipriani, G., M. Marrazzo, R. Marconi, A. Cimato and R. Testolin (2002). Microsatellite markers isolated in olive are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars (Olea europaea L.). Theor. Appl. Genet., 104: 223-228.
Diaz Bermudez, A. (2005). Desarrollo y caracterizacio´n de nuevos microsate´ lites y SNPs y aplicacio´n en la mejora gene´ tica del olivo (Olea europaea L.), PhD. tesis, Departamento de Gene´ tica, Universidad de Co´rdoba ETSIAM, Spain, pp 180.
Fragaki, G., A. Spyros, G. Siragakis, E. Salivaras, P. Dais (2005) Detection of extra vergin olive oil adulteration with lampante olive oil and refined olive oil using nuclear magnetic resonance spectroscopy and multivariate statistical analysis. J. Agric. Food Chem., 53: 2810-2816.
Fuentes, J., F. Escobar, A. Alvarez, G. Gallego, M. Duque, M. Ferrer, J. Deus and M. Tohme (1999). Analyses of genetic diversity in Cuban rice varieties using isozyme, RAPD and AFLP markers. Euphytica, 109: 107-115.
Ganino, T., A. Bartolini and A. Fabbri (2006). A The classification of olive germplasm- a review. J Hortic Sci Biotech., 81: 319-334.
Ganino, T., D. Beghe, S. Valenti and A. Fabbri (2007). RAPD and SSR markers for characterization and identification of ancient cultivars of Olea europaea L. in the Emilia region, Northern Italy. Genet Resour Crop Evol., 54: 1531-1540.
Garcia-Mas, J., M. Oliver, H. Gomez- Paniagua and M. de Vicente (2000). Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon. Theor. Appl. Genet., 101: 860-864.
Grati-Kamoun, N., F. Mahmoud, A. Rebai, A. Gargouri, O. Panaud and A. Saar (2006). Genetic diversity of Tunisian olive tree (Olea europaea L.) cultivars assessed by AFLP markers. Genetic Resources and Crop Evolution, 53: 265-275.
Hemeida, A., A. Sanaa, M. Taha and M. Nassr (2007). Characterization of some Siwan olive cultivars (Olea europaea L.) using agronomic and molecular markers. Egypt. J. Genet. Cytol., 36: 267-284.
Jaccard, P. (1908) Nouvelle recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles, 44: 223-270.
Jones, C., K. Edwards, S. Castaglione, M. Winfield, F. Sala, C. Wiel, 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 and A. Karp (1997). Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol. Breed., 3: 381- 390.
Khadari, B., J. Charafi, A. Moukhli and M. Ater (2008). Substantial genetic diversity in cultivated Moroccan olive despite a single major cultivar: a paradoxical situation evidenced by the use of SSR loci. Tree Genetics & Genomes, 4: 213- 221.
Masini, A., H. F. El-wakil and M. Th. Hassan (2003). Study of flora composition and distribution in Siwa Oasis. J. Adv. Agric. Res., 8: 241-245.
McGregor, C., C. Lambert, M. Greyling, J. Louw and L. Warnich (2000). A comparative assessment of DNA fingerprinting techniques (RAPD, ISSR, AFLP and SSR) in tetraploid potato (Solanum tuberosum L.) germplasm. Euphytica, 113: 135-144.
Minelli, S., F. Maggini, M. Gelati, A. Angiolillo and P. Cionini (2000). The chromosome complement of Olea europaea L.: characterization by differential staining of the chromatin and in situ hybridization of highly repeated DNA sequences. Chromosome Res., 8: 615-619.
Morgante, M., A. Rafalski, P. Biddle, S. Tingey and A. Olivieri (1994). Genetic mapping and variability of seven soybean sample sequence repeat loci. Genome, 37: 763-769.
Ozkaya, M., E. Cakir, Z. Gokbayrak, H. Ercan and N. Taskin (2006). Morphological and molecular characterization of Derik Halhali olive (Olea europaea L.) accession grown in Derik-Mardin province of Turkey. Sci. Hortic., 108: 205- 209.
Pejic, I., P. Ajmone-Marsan, M. Morgante, V. Kozumplik, P. Castiglioni, G. Taramino and 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.
Powell, W., M. Morgante, C. Andre, M. Hanafey, J. Vogel, S. Tingey and A. Rafalski (1996). The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed., 2: 225-238.
Rohlf, F. J. (2000). On the use of shape spaces to compare morphometric method. Hystrix Italian J. Mammology (n.s.), 11: 8-24.
Russell, J., J. Fuller, M. Macaulay, B. Hatz, A. Jahoor, W. Powell and R. Waugh (1997). Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet., 95: 714-722.
Samaee, Z., S. Shobbar, H. Ashrafi and M. Hosseini-Mazinani (2003). Molecular characterization of olive germplasm in Iran by use of Random Amplified Polymorphic DNA (RAPD): Correlation with phenotypic studies. Acta Hort., 623: 169-175.
Sanz-Cortes, F., M. Badenes, S. Paz, A. Iniguez and G. Llacer (2001). Molecular characterization of olive cultivars using RAPD markers. J. Am. Soc. Hort. Sci., 126: 7-12.
Sefc, K. M., M. Lopes, D. Mendonca, M. Rodrigues Dos Santos, M. Laimer Da Camara Machado and A. Da Camara Machado (2000). Identification of microsatellite loci in olive (Olea europaea) and their characterization in Italian and Iberian olive trees. Mol. Ecol., 9: 1171-1173.
Taamalli, W., F. Geuna, R. Banfi, D. Bassi, D. Daoud and M. Zarrouk (2006). Agronomic and molecular analyses for the characterization of accessions in Tunisian olive germplasm collections. Electronic J. Biotechnology, 9: 467-481.
Tessier, C., J. David, P. This, J. Boursiquot and A. Charrier (1999). Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor. Appl. Genet., 98: 171-177.
Trujillo, I., L. Rallo and P. Arus (1995). Identifying olive cultivars by isozyme analysis. J. Am. Soc. Hort. Sci., 120: 318-324.
