Analysis of genetic diversity of Ficus carica L. (Moraceae) collection using simple sequence repeat (SSR) markers

Ilaria Marcotuli

Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Andrea Mazzeo

Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Domenica Nigro

Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Stefania Lucia Giove

Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Angelica Giancaspro

Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Pasqualina Colasuonno

Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Željko Prgomet

Collegium Fluminense Polytechnic of Rijeka, Trpimirova 2/V, 51000 – Rijeka, Croatia

Iva Prgomet

Skink, Valalta bb, 52210 – Rovinj, Croatia

Annalisa Tarantino

Department of Science Agriculture, Food and Environment, University of Foggia, via Napoli 25, 71122 – Foggia, Italy

Giuseppe Ferrara

Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy

Agata Gadaleta

Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy


Abstract

Modern technologies and accurate information on genetic diversity and structure are contributing to improve the plant breeding, in particular for all the minor species with a lack of data. Genetic diversity of 139 different Ficus carica L. genotypes collected from Italy and Croatia, and divided into two subgroups: uniferous (only main crop) and biferous (breba and main crop), was investigated using 49 microsatellite markers.
A total of 70 alleles were generated, of which 64 (91.4%) showed a polymorphic pattern indicating high level of genetic diversity within the studied collection. The mean heterozygosity over the 64 single locus microsatellites was 0.33 and the expected and observed averaged variance were 16.50 and 184.08, respectively.
The 139 fig genotypes formed two clusters in the PCoA analysis, suggesting a division between Italian and Croatian genotypes. Moreover, the fig accessions could be divided into two main clusters based on the STRUCTURE analysis according to the biological type, uniferous or biferous, with partly overlapping varieties. In conclusion, our results demonstrated that molecular markers were able to discriminate among genotypes and useful for the authentication of fig tree varieties (homonymies and synonymies).

Keywords:

fig, breba, SSRs, genetic diversity, population structure

Achtak, H., Oukabli, A., Ater, M., Santoni, S., Kjellberg, F., Khadari, B. (2009). Microsatellite markers as reliable tools for fig cultivar identification. J. Am. Soc. Hortic. Sci., 134, 624–631.

Aradhya, M.K., Stove, E., Velasco, D., Koehmstedt A. (2010). Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica, 138, 681–694.

Aradhya, M.K., Zee, F.T., Manshardt, R.M. (1995). Isozyme variation in lychee (Litchi chinensis Sonn). Sci. Hortic., 63, 21–35.

Baraket, G., Chatti, K., Saddoud, O., Abdelkarim, A.B., Mars, M., Trifi, M., Hannachi, A.S. (2011). 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. Report., 29, 171–184.

Baraket, G., Chatti, K., Saddoud, O., Mars, M., Marrakchi, M., Trifi, M., Salhi-Hannachi, A. (2009). Genetic analysis of Tunisian fig (Ficus carica L.) cultivars using amplified fragment length polymorphism (AFLP) markers. Sci. Hortic., 120, 487–492.

Caliskan, O., Polat, A.A., Celikkol, P., Bakir, M. (2012). Molecular characterization of autochthonous Turkish fig accessions. Span. J. Agric. Res., 10, 130–140.

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. Integr. Plant Biol., 49, 386–391.

Condit, I.J. (1955). Fig varieties: a monograph. Hilgardia, 23, 323–539.

Datwyler, S.L., Weiblen, G.D. (2004). On the origin of the fig: phylogenetic relationships of Moraceae from ndhF sequences. Am. J. Bot., 91, 767–777.

Evanno, G., Regnaut, S., Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. Notes, 14, 2611–2620.

Ferrara, G., Mazzeo, A., Pacucci, C., Matarrese, A.M.S., Tarantino, A., Crisosto, C., Incerti, O., Marcotuli, I., Nigro, D., Blanco, A., Gadaleta, A. (2016). Characterization of edible fig germplasm from Puglia, southeastern Italy: is the distinction of three fig types (Smyrna, San Pedro and Common) still valid? Sci. Hortic., 250, 52–58.

Flaishman, M., Rodov, V., Stover, E. (2008). The fig: botany, horticulture and breeding. Hortic. Rev., 34, 113–96.

Galet, P. (1990). Cepages et Vignobles de France. Tome II L’Ampelographie FranHaise. 2nd ed. Imprimerie Charles Dehan Press, Montpellier, France.

Ganopoulos, I., Xanthopoulou, A., Molassiotis, A., Karagiannis, E., Moysiadis, T., Katsaris, P., Aravanopoulos, F., Tsaftaris, A., Kalivas, A., Madesis, P. (2015). Mediterranean basin Ficus carica L. from genetic diversity and structure to authentication of a Protected Designation of Origin cultivar using microsatellite markers. Trees.Struct. Funct., 29, 1959–1971.

Giraldo, E., Viruel, M.A., Lopez-Corrales, M., Hormaza, J.I. (2005). Characterisation and cross-species transferability of microsatellites in the common fig tree (Ficus carica L.). J. Hortic. Sci. Biotechnol., 80, 217–224.

Ikegami, H., Nogata, H., Hirashima, K., Awamura, M. (2009). Analysis of genetic diversity among European and Asian fig varieties (Ficus carica L.) using ISSR, RAPD, and SSR markers. Genet. Resour. Crop Evol., 56, 201–209.

Lebot, V., Aradhya, K.M. (1991). Isozyme variation in taro [Colocasia esculenta (L.) Schott] from Asia and the Pacific. Euphytica, 56, 55–66.

Machado, C.A., Jousselin, E., Kjellberg, F., Compton, S.G., Herre, E.A. (2001). Phylogenetic relationships, historical biogeography and character evolution of fig pollinating wasps. Proc. R. Soc. B-Biol. Sci., 268, 7–10.

Peakall, R., Smouse, P.E. (2006). GenAlex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes, 6, 288–295.

Peakall, R., Smouse, P.E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research − an update. Bioinformatics, 28, 2537–2539.

Perez-Jiménez, M., López, B., Dorado, G., Pujadas-Salvá, A., Guzmán, G., Hernández, P. (2012). Analysis of genetic diversity of southern Spain fig tree (Ficus carica L.) and reference materials as a tool for breeding and conservation. Hereditas, 149, 108–113.

Prgomet, Ž., Bohač, M. (2003). Smokva (Ficus carica L.). Skink, Rovinj.

Salhi-Hannachi, A., Chatti, K., Mars, M., Marrakchi, M., Trifi, M. (2005). Comparative analysis of genetic diversity in two Tunisian collections of fig cultivars based on random amplified polymorphic DNA and inter simple sequence repeats fingerprints. Genet. Resour. Crop Evol., 52, 563–573.

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, 15–22.

Storey, W.B. (1976). Subtropical and tropical fruit and nut crops in California, USA. I International Symposium on Tropical and Subtropical Fruits, 57, 53–62.

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Published
2019-08-07



Ilaria Marcotuli 
Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Andrea Mazzeo 
Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Domenica Nigro 
Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Stefania Lucia Giove 
Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Angelica Giancaspro 
Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Pasqualina Colasuonno 
Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Željko Prgomet 
Collegium Fluminense Polytechnic of Rijeka, Trpimirova 2/V, 51000 – Rijeka, Croatia
Iva Prgomet 
Skink, Valalta bb, 52210 – Rovinj, Croatia
Annalisa Tarantino 
Department of Science Agriculture, Food and Environment, University of Foggia, via Napoli 25, 71122 – Foggia, Italy
Giuseppe Ferrara 
Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy
Agata Gadaleta 
Department of Environmental and Territorial Sciences, University of Bari “Aldo Moro”, via G. Amendola 165/A, 70126 – Bari, Italy



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