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Genetic Resources and Crop Evolution

, Volume 65, Issue 5, pp 1337–1348 | Cite as

Identification and characterization of Italian common figs (Ficus carica) using nuclear microsatellite markers

  • Margherita Rodolfi
  • Tommaso GaninoEmail author
  • Benedetta Chiancone
  • Raffaella Petruccelli
Research Article

Abstract

Common fig (Ficus carica L.) is one of the most ancient domesticated species, originated, supposedly in Arabia, from where it diffused to the Middle East and Asia, and to the Mediterranean basin, where it greatly diffused. More than 600 fig varieties have been described, but it is conceivable that this number is underestimated. Along all the Italian territory, there is a rich germplasm of fig composed of a large number of varieties (approximately 300) of very not well defined origin. Effectively, during several centuries of cultivation and propagation by seed, a large number of genotypes appeared and were selected, leading to the generation of an uncountable number of genotypes, different in numerous traits, particularly in those related to leaves and fruits features. Unfortunately, the extensive existing fig genetic patrimony is facing genetic erosion; for this reason, it is extremely important to study and valorised it, in order to preserve the remaining biodiversity. The purpose of this study was to genetically characterize, with nSSR markers, 79 fig accessions, collected in several areas in Italy. The set of chosen markers resulted highly polymorphic, and allowed the characterization of all the studied accessions. Data were analysed by cluster analysis, and the results demonstrated a great genetic variability within the population. The nSSR used, moreover, allowed us to identify all accessions and to recognised possible homonyms and synonyms, and cases of intravarietal clones.

Keywords

nSSR Ficus carica L. Biodiversity Germplasm Cultivar identification Genetic variability 

Notes

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10722_2018_617_MOESM1_ESM.docx (25 kb)
Supplementary material 1 (DOCX 24 kb)

References

  1. Abou-Ellail M, Mahfouze SA, El-Enay MAM, Mustafa NSA (2014) Using biochemical and simple sequence repeats (SSR) markers to characterize (Ficus carica L.) cultivars. World Appl Sci J 29(3):313–321.  https://doi.org/10.5829/idosi.wasj.2014.29.03.13835 Google Scholar
  2. 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(6):624–631.  https://doi.org/10.1007/s10681-010-0286-9 Google Scholar
  3. Aradhya MK, Stover E, Velasco D, Koehmstedt A (2010) Genetic structure and differentiation in cultivated fig (Ficus carica L.). Genetica 138:681–694.  https://doi.org/10.1007/s10709-010-9442-3 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Baldini E (1953) Alcuni aspetti della coltura del fico nella provincia di Firenze. Riv Ortoflorfrutt Ital 7–8:185–203Google Scholar
  5. Baraket G, Chatti K, Saddoud O, Abdelkarim AB, Mars M, Trifi M, Hannachi AS (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 Rep 29(1):171–184.  https://doi.org/10.1007/s11105-010-0217-x CrossRefGoogle Scholar
  6. Barberis A, Chessa I, Nieddu G (2001) Analisi multivariata dei descrittori primari del germoplasma di fico della Sardegna. Italus Hortus 8(5):12–15Google Scholar
  7. Basso M (1960a) Contributo allo studio della coltura del fico nella provincia di Pisa. Riv Ortoflorfrutt Ital 3–4:1–17Google Scholar
  8. Basso M (1960b) Contributo allo studio della coltura del fico nella provincia di Livorno. Riv Ortoflorfrutt Ital 5–6:194–208Google Scholar
  9. Beghé D, Ganino T, Dall’Asta C, Silvanini A, Cirlini M, Fabbri A (2013) Identification and characterization of ancient Italian chestnut using nuclear microsatellite markers. Sci Hortic 164:50–57.  https://doi.org/10.1016/j.scienta.2013.09.009 CrossRefGoogle Scholar
  10. Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology 5(3):453-455.  https://doi.org/10.1046/j.1365-294X.1996.00098x CrossRefPubMedGoogle Scholar
  11. Brown AHD, Weir BS (1983) Measuring genetic variability in plant populations. In: Tanksley SD, Orton PA (eds) Isozymes in plant genetics and breeding. Elsevier Science Publications, AmsterdamGoogle Scholar
  12. Buonincontri M, Moser D, Allevato E, Basile B, Di Pasquale G (2014) Farming in a rural settlement in central Italy: cultural and environmental implications of crop production through the transition from Lombard to Frankish influence (8th–11th centuries A.D.). Veg Hist Archaeobot 23:775–788.  https://doi.org/10.1007/s00334-013-0429-8 CrossRefGoogle Scholar
  13. Cabrita LF, Aksoy U, Hepaksoy S, Leitão JM (2001) Suitability of isozyme, RAPD and AFLP markers to assess genetic differences and relatedness among fig (Ficus carica L.) clones. Sci Hortic 87:261–273.  https://doi.org/10.1016/S0304-4238(00)00181-3 CrossRefGoogle Scholar
  14. Çalişkan O, Polat AA (2012) Morphological diversity among fig (Ficus carica L.) accessions sampled from the Eastern Mediterranean Region of Turkey. Turk J Agric For 36:179–193.  https://doi.org/10.3906/tar-1102-33 Google Scholar
  15. Chessa I, Erre P, Nieddu M, Satta D, Nieddu G (2001) Applicazione di marcatori molecolari RAPD in una collezione di germoplasma sardo di fico (Ficus carica L.). Italus Hortus 8(5):16–19Google Scholar
  16. Ciarmiello LF, Piccirillo P, Carillo P, De Luca A, Woodrow P (2015) Determination of the genetic relatedness of fig (Ficus carica L.) accessions using RAPD fingerprint and their agro-morphological characterization. S Afr J Bot 97:40–47.  https://doi.org/10.1016/j.sajb.2014.11.012 CrossRefGoogle Scholar
  17. Cipriani G, Marrazzo MT, Marconi R, Cimato A, Testolin R (2002) Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars. Theor Appl Genet 104(2–3):223–228.  https://doi.org/10.1007/s001220100685 CrossRefPubMedGoogle Scholar
  18. Condit IJ (1955) Fig varieties: a monograph. Calif Agric 23(11):323–538Google Scholar
  19. De Masi L, Cipollaro M, Di Bernardo G, Galderisi U, Galano G, Pavone E, Grassi G, Simeone A, Cascino A (2003) Clonal selection and molecular characterization by RAPD analysis of the fig (Ficus carica L.) “Dottato” and “Bianco del Cilento” cultivars in Italy. Acta Hortic 605:65–68CrossRefGoogle Scholar
  20. do Val ADB, Souza CS, Ferreira EA, Salgado SML, Pasqual M, Cançado GMA (2013) Evaluation of genetic diversity in fig accessions by using microsatellite markers. Genet Mol Res 12(2):1383–1391.  https://doi.org/10.4238/2013.April.25.9 CrossRefPubMedGoogle Scholar
  21. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  22. Ercisli S, Tosun M, Karlidag H, Dzubur A, Hadziabulic S, Aliman Y (2012) Color and antioxidant characteristics of some fresh fig (Ficus carica L.) genotypes from Northeastern Turkey. Plant Foods Hum Nutr 67:271–276.  https://doi.org/10.1007/s11130-012-0292-2 CrossRefPubMedGoogle Scholar
  23. Essid A, Aljane F, Ferchichi A, Hormaza JI (2015) Analysis of genetic diversity of Tunisian caprifig (Ficus carica L.) accessions using simple sequence repeat (SSR) markers. Hereditas 152:1.  https://doi.org/10.1186/s41065-015-0002-9 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Falistocco E (2009) Presence of triploid cytotypes in the common fig (Ficus carica L.). Genome 52:919–925.  https://doi.org/10.1139/g09-068 CrossRefPubMedGoogle Scholar
  25. Ferrara G, Mazzeo A, Pacucci C, Mataresse AMS, 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 205:52–58.  https://doi.org/10.1016/j.scienta.2016.04.016 CrossRefGoogle Scholar
  26. Gaaliche B, Saddoud O, Mars M (2012) Morphological and pomological diversity of fig (Ficus carica L.) cultivars in Northwest of Tunisia. ISRN Agron 2012, Article ID 326461.  https://doi.org/10.5402/2012/326461
  27. Giraldo E, López-Corrales M (2008) Optimization of the management of an ex situ germplasm bank in common fig with SSRs. J Am Soc Hortic Sci 133(1):69–77Google Scholar
  28. Giraldo E, Viruel MA, Lòpez-Corrales M, Hormaza JI (2005) Characterisation and cross-species transferability of microsatellites in the common fig (Ficus carica L.). J Hortic Sci Biotechnol 80:217–224.  https://doi.org/10.1080/14620316.2005.11511920 CrossRefGoogle Scholar
  29. Giraldo E, López-Corrales M, Roger JP, Khadari B, Hochu I, Santoni S, Hormaza JI (2008) Standardization of experimental protocols and SSR markers for the management of fig germplasm collections. Acta Hortic (ISHS) 798:213–216.  https://doi.org/10.17660/ActaHortic.2008.798.29 CrossRefGoogle Scholar
  30. Giraldo E, López-Corrales M, Hormaza JI (2010) Selection of the most discriminating morphological qualitative variables for characterization of fig germplasm. J Am Soc Hortic Sci 135(3):240–249Google Scholar
  31. Grassi G (1998) Studies of Italian fig germplasm. Acta Hortic (ISHS) 480:97–102CrossRefGoogle Scholar
  32. Hocquigny S, Pelsy F, Dumas V, Kindt S, Heloir MC, Merdinoglu D (2004) Diversification within grapevine cultivars goes through chimeric states. Genome 47(3):579–589.  https://doi.org/10.1139/g04-006 CrossRefPubMedGoogle Scholar
  33. Jakše J, Satovic Z, Javornik B (2004) Microsatellite variability among wild and cultivated hops (Humulus lupulus L.). Genome 47:889–899.  https://doi.org/10.1139/g04-054 CrossRefPubMedGoogle Scholar
  34. Khadari B (2012) Ex situ management of fig (Ficus carica L.) genetic resources: towards the establishment of the Mediterranean reference collection. Acta Hortic (ISHS) 940:67–74. http://www.actahort.org/books/940/940_7.htm
  35. Khadari B, Lashermes P, Kjellberg F (1995) RAPD fingerprints for identification and genetic characterization of fig (Ficus cairica L.) genotypes. J Genet Breed 49:77–86Google Scholar
  36. Khadari B, Hochu I, Santoni S, Kjellberg F (2001) Identification and characterisation of microsatellite loci in the common fig (Ficus carica L.) and representative species of genus Ficus. Mol Ecol Notes 1:191–193.  https://doi.org/10.1046/j.1471-8278.2001.00072.x CrossRefGoogle Scholar
  37. Khadari B, Hochu I, Bouzid L, Roger JP, Kjellberg F (2003) The use of microsatellite markers for identification and genetic diversity evaluation of fig collection in CBNMP. Acta Hortic 605:77–86CrossRefGoogle Scholar
  38. Khadari B, Grout C, Santoni S, Kjellberg F (2005) Contrasted genetic diversity and differentiation among Mediterranean populations of Ficus carica L.: a study using mtDNA RFLP. Genet Resour Crop Evol 52:97–109.  https://doi.org/10.1007/s10722-005-0290-4 CrossRefGoogle Scholar
  39. Kirby LT (1990) DNA fingerprinting. An introduction. Stockton Press, New YorkCrossRefGoogle Scholar
  40. Knap T, Jakše J, Cregeen S, Javornik B, Hladnik M, Bandelj D (2016) Characterization and defining of a core set of novel microsatellite markers for use in genotyping and diversity study of Adriatic fig (Ficus carica L.) germplasm. Braz J Bot 39(4):1095–1102.  https://doi.org/10.1007/s40415-016-0299-2 CrossRefGoogle Scholar
  41. Laddomada B, Gerardi C, Mita G, Lumare D, Minonne F, Marchiori S, Fiocchetti F (2008) Molecular characterization of Apulian fig (Ficus carica L.) germplasm collection using fluorescence-based AFLP markers. Acta Hortic 798:205–212CrossRefGoogle Scholar
  42. Mariotti Lippi M, Bellini C, Mori Secci M, Gonnelli T (2009) Comparing seeds/fruits and pollen from a Middle Bronze age pit in Florence (Italy). J Archaeol Sci 36(5):1135–1141.  https://doi.org/10.1016/j.jas.2008.12.017 CrossRefGoogle Scholar
  43. Mariotti Lippi M, Bellini C, Mori Secci M, Gonnelli T, Pallecchi P (2015) Archaeobotany in Florence (Italy): landscape and urban development from the late Roman to the Middle Ages. Plant Biosyst 149(1):216–227.  https://doi.org/10.1080/11263504.2013.822433 CrossRefGoogle Scholar
  44. Mawa S, Husain K, Jantan I (2013). Ficus carica L. (Moraceae): phytochemistry, traditional uses and biological activities. Evid Based Complement Altern Med, Article ID 974256.  https://doi.org/10.1155/2013/974256
  45. Minonne F, Ippolito I, Marchiori S (2001) L’attività dell’orto botanico di Lecce nel reperimento e la propagazione delle vecchie cultivar di Ficus carica L. Italus Hortus 8(5):30–33Google Scholar
  46. Paetkau D, Calvert W, Stirling I, Stroberck C (1995) Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4:347–354.  https://doi.org/10.1111/j.1365-294X.1995.tb00227.x CrossRefPubMedGoogle Scholar
  47. Papadopoulou K, Ehaliotis C, Tourna M, Kastanis P, Karydis I, Zervakis G (2002) Genetic relatedness among dioecious Ficus carica L. cultivars by random amplified polymorphic DNA analysis, and evaluation of agronomic and morphological characters. Genetica 114:183–194.  https://doi.org/10.1023/A:1015126319534 CrossRefPubMedGoogle Scholar
  48. R Development Core Team (2005) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org
  49. Rattighieri E, Rinaldi R, Bowes K, Mercuri AM (2013) Land use from seasonal archaeological sites: the archaeobotanical evidence of small Roman farmhouses in Cinigiano, South-Eastern Tuscany-Central Italy. Ann Bot 3:207–215.  https://doi.org/10.4462/annbotrm-10267 Google Scholar
  50. 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(4):149–157.  https://doi.org/10.1111/j.2007.0018-0661.01967.x CrossRefPubMedGoogle Scholar
  51. Saddoud O, Baraket G, Chatti K, Trifi M (2011) Using morphological characters and simple sequence repeat (SSR) markers to characterize tunisian fig (Ficus carica L.) cultivars. Acta Biol Crac 53:7–14.  https://doi.org/10.2478/v10182-011-0019-y Google Scholar
  52. Storey WB (1976) Fig Ficus carica (Moraceae). In: Simmonds NW (ed) Evolution of crop plants, 2nd edn. Wiley-Blackwell, London, pp 205–208Google Scholar
  53. Turfa JM (2012) Background on agriculture, agronomy in prehistoric Italy. In: Turfa JM (ed) Divining the etruscan world: the brontoscopic calendar and religious practice. Cambridge University Press, Cambridge, pp 152–153CrossRefGoogle Scholar
  54. UPOV (2010) Guidelines for the conduct of tests for distinctness, homogeneity and stability, fig edn. International union for the protection of new varieties of plants, GenéveGoogle Scholar
  55. Veberic R, Mikulic-Petkovsek M (2016) Phytochemical composition of common fig (Ficus carica L.) cultivars. In: Simmons MSJ, Preedy VR (eds) Nutritional composition of fruit cultivars. Elsevier, Amsterdam, pp 235–255CrossRefGoogle Scholar
  56. Wagner HW, Sefc KM (1999) Identity 1.0: freeware program for the analysis of microsatellite data. Vienna. http://www.boku.ac.at/zag/forsch/identity.htm

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Food and DrugUniversity of ParmaParmaItaly
  2. 2.Istituto per la Valorizzazione del Legno e delle Specie Arboree (IVaLSA)Consiglio Nazionale delle RicercheSesto FiorentinoItaly

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