Tree Genetics & Genomes

, Volume 10, Issue 3, pp 703–710 | Cite as

Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs)

  • F. C. Balas
  • M. D. Osuna
  • G. Domínguez
  • F. Pérez-Gragera
  • M. López-Corrales
Original Paper

Abstract

Ex situ germ plasm collections of woody crops are necessary to ensure the optimal use of plant genetic resources. The fig tree (Ficus carica L.) germ plasm bank, consisting of 229 accessions, is located in Centro de Investigación ‘La Orden’. Despite great progress in conservation, ex situ collections face size and organization problems. Core collections obtained from structured samples of bigger collections are a useful tool to improve germ plasm management. In this work, we used simple sequence repeat (SSR) markers to establish a core collection in this underutilised Mediterranean fruit tree species. Four approaches have been carried out (random sampling, maximization, simulated annealing and stepwise clustering) to determine the best method to develop a core collection in this woody plant. The genetic diversity obtained with each subset was compared with that of the complete collection. It was found that the most efficient way to achieve the maximum diversity was the maximization strategy, which, with 30 accessions, recovers all the SSR alleles and does not show significant differences in allele frequency distribution in any of the loci or in the variability parameters (HO, HE) between the whole and core collections. Thus, this core collection, a representative of most fig diversity conserved in the germ plasm bank, could be used as a basis for plant material exchange among researchers and breeders.

Keywords

Ex situ conservation Germ plasm bank Fig tree SSRs Core collection Plant genetic resources 

Notes

Acknowledgments

Financial support for this research was provided by the Spanish Ministry of Economy and Competitiveness–European Regional Development Fund (Project Grant RF2010-00009) and agreement with the Spanish Ministry of Agriculture, Food and Environment.

References

  1. Anderson WF, Holbroook CC, Culbreath AK (1996) Screening the peanut core collection for resistance to tomato spotted wilt virus. Peanut Sci 23:57–61CrossRefGoogle Scholar
  2. Aradhya MK, Stover E, Velasco D, Koehmstedt A (2010) Genetic structure an differentiation in cultivated fig (Ficus carica L.). Genetica 138:681–694PubMedCentralCrossRefGoogle Scholar
  3. Belaj A, Dominguez-García MC, Attienza SG et al (2012) Developing a core collection of olive (Olea europaea L.) based on molecular markers (DarTs, SSRs, SNPs) and agronomic traits. Tree Genet Genomes 8:365–378CrossRefGoogle Scholar
  4. Berg CC (2003) Flora Malesiana precursor for treatment of Moraceae 1: the main subdivision of Ficus: the subgenera. Blumea 48:167–178Google Scholar
  5. Bisht IS, Mahajan RK, Lokknathan TR, Agrawal RC (1998) Diversity in Indian sesame collection and stratification of germplasm accessions in different diversity groups. Gent Resour Crop Evol 45:325–335CrossRefGoogle Scholar
  6. Boukema IW, van Hintum TJL (1994) Brassica oleracea, a case of an integrated approach to genetic resources conservation. In: Balfourier F, Perretant MR (eds) Evaluation and exploitation of genetic resources: pre-breeding. Porc. Genetic Resources Section Meeting of Eucarpia, Clermont-FerrandGoogle Scholar
  7. Brown AHD, Schoen DJ, Speer SS (1987) Designation of a “core” collection of perennial Glycine. Soybean Gent Newsl 14:59–70Google Scholar
  8. Condit IJ (1955) Fig varieties: a monograph. Hilgardia 23:323–538Google Scholar
  9. Diwan N, McIntosh MS, Bauchan GR (1995) Developing a core collection of annual Medicago species. Theor Appl Genet 90:755–761CrossRefGoogle Scholar
  10. Eisen GA (1901) The fig: history, culture and curing with a descriptive catalogue of the known varieties of fig. Bulletin no. 9. U.S. Department of Agriculture, Division of Pomology, Washington DCGoogle Scholar
  11. Erksine W, Muehlbauer FJ (1991) Allozyme and morphological variability, outcrossing rate and core collection formation in lentil germplasm. Theor Appl Genet 83:119–125Google Scholar
  12. Escribano P, Viruel MA, Hormaza JI (2008) Comparison of different methods to construct a core germplasm collection in woody perennial species with simple sequence repeat markers. A case study in cherimoya (Annona cherimola, Annonaceae), an underutilised subtropical fruit tree species. Ann Appl Biol 153:25–32CrossRefGoogle Scholar
  13. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50Google Scholar
  14. FAO (1996) Global plan of action for the conservation and sustainable utilization of plant genetic resources for food and agriculture. FAO, RomeGoogle Scholar
  15. FAOSTAT (2013) faostat.fao.orgGoogle Scholar
  16. Flaishman M, Rodov V, Stover E (2008) The fig: botany, horticulture and breeding. Horticul Revs 34:113–196Google Scholar
  17. Frankel OH (1984) Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock WJ, Starlinger P (eds) Genetic manipulation: impact on man and society. Cambridge University Press, Cambridge, pp 161–170Google Scholar
  18. Frankel OH, Brownn AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden JHW, Williams JT (eds) Crop genetic resources: conservation and evaluation. Allen and Unwin, WinchesterGoogle Scholar
  19. Giraldo E, Viruel MA, López-Corrales M, Hormaza JI (2005) Characterisation and cross-species transferability of microsatellites in common fig (Ficus carica L.). J Hortic Sci Biotech 80(2):217–224Google Scholar
  20. Giraldo E, López-Corrales M, Hormaza JI (2008a) Optimization of the management of an ex-situ germplasm bank in common fig with SSRs. J Amer Sco Hort Sci 133(1):69–77Google Scholar
  21. Giraldo E, Hormaza JI, López-Corrales M (2008b) Selection of morphological quantitative variables in the characterization of Ficus carica L. Acta Hort 798:103–108Google Scholar
  22. Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: at algorithm for building germ plasm core collection by maximizing allelic or phenotypic richness. J Hered 92:93–94CrossRefGoogle Scholar
  23. Grenier C, Bramel-Cox PJ, Noirot M, Rao KEP, Hamon P (2000) Assessment of genetic diversity in three subsets constituted from the ICRISAT sorghum collection using random and non-random sampling procedures A. Using morpho-agronomical and passport data. Theor Appl Genet 101:197–202CrossRefGoogle Scholar
  24. Guerrero VM, Gornés (2000) Colonización humana en ambientes insulares: interacción con el medio y adaptación cultural. Universitat Illes Balears, Palma, SpainGoogle Scholar
  25. Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linnean Soc 58:247–276CrossRefGoogle Scholar
  26. Hu J, Zhu J, Xu HM (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101:264–268CrossRefGoogle Scholar
  27. Huntley B, Birks HJB (1983) An atlas of past and present pollen maps for Europe: 0–13,000 years ago. Cambridge University Press, CambridgeGoogle Scholar
  28. Kappel F, Granger A, Hrotkó K, Schuster M (2012) Cherry. In: Badenes ML, Byrne DH (eds) Fruit breeding. Springer, USA, pp 459–504Google Scholar
  29. Khadari B, Kjellberg F (2009) Tracking the genetic signature to identify fig origins: insights for evolution before and during domestication processes. Acta Horticulturae (Forthcoming) IV International Symposium on Fig. Méknes, MoroccoGoogle Scholar
  30. Khadari B, Hochu I, Santoni S, Oukabli A, Ater M, Roger JP, Kjellberg F (2001) Which molecular markers are best suited to identify fig cultivars: a comparison of RAPD, ISSR and microsatellite markers. Acta Horticult 605:69–75Google Scholar
  31. 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. Gen Resour Crop Ev 52:97–109CrossRefGoogle Scholar
  32. Kislev ME, Hartmann A, Bar-Yosef O (2006) Early domesticated fig in the Jordan Valley. Science 312:1372–1374CrossRefGoogle Scholar
  33. Kjellberg F, Gouyon PH, Igrahim M, Raymond M, Valdeyron G (1987) The stability of the symbiosis between dioecious figs and their pollinators: a study of Ficus carica L. and Blastophaga psenes L. Int J Org Evol 41:693–704CrossRefGoogle Scholar
  34. Li TH, Li YX, Li ZC, Zhang HL, Qi YW, Wang T (2008) Simple sequence repeat analysis of genetic diversity in primary core collection of peach (Prunus persica L.). J Integr Plant Biol 50(1):102–110CrossRefGoogle Scholar
  35. Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 47:515–526Google Scholar
  36. López A (2000) El poblament inicial de l’illa de Menorca. In: Guerrero VM, Gornés S (eds) Colonización humana en medios insulares. Interacción con el medio y adaptación cultural. Universitat Illes Balears, Palma, pp 195–214Google Scholar
  37. López-Corrales M, Balas F, Domínguez G, Osuna MD, Serradilla MJ, Pérez F (2012) Protocolo de Incorporación de nuevas accesiones al banco de germoplasma de higuera. Actas de Horticultura 62:227–228Google Scholar
  38. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  39. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 70:3321–3323CrossRefGoogle Scholar
  40. Potts SM, Han Y, Khan MA et al (2012) Genetic diversity and characterization of a core collection of Malus germplasm using simple sequence repeats (SSRs). Plant Mol Biol Rep 30:827–837CrossRefGoogle Scholar
  41. Schoen DJ, Brown AHD (1995) Maximizing genetic diversity in core collections of relatives of crop species. In: Hodgkin T, Brown ADH, van Hintum TJL (eds) Core collection of plant genetic resources. Wiley, Chichester, pp 55–76Google Scholar
  42. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453–464CrossRefGoogle Scholar
  43. van Hintum TJL, Brown AHD, Spillane C, Hodgkin T (2003) Colecciones núcleo de recursos fitogenéticos. Boletín Técnico No. 3 del IPGRI. International Plant Genetic Resources Institute, Rome, ItalyGoogle Scholar
  44. Watson L, Dallwitz MJ (2004) The families of flowering plants: descriptions, illustrations, identification, and information retrieval. http://delta-intkey.com/angio/www/inedx.htm. Accessed 29 June 2007
  45. Yonezawa K, Nomura T, Morishima H (1995) Sampling strategies for use in stratified germplasm collections. In: Hodgkin T, Brown AHD, van Hintum TJL, Morales EAV (eds) Core collections of plant genetic resources. Wiley, ChichesterGoogle Scholar
  46. Zhang X, Zhao Y, Cheng Y, Feng X, Guo Q, Zhou M, Hodgkin T (2000) Establishment of sesame germplasm core collection in China. Genet Resour Crop Evol 47:273–279CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • F. C. Balas
    • 1
  • M. D. Osuna
    • 1
  • G. Domínguez
    • 1
  • F. Pérez-Gragera
    • 1
  • M. López-Corrales
    • 1
  1. 1.Centro de Investigación ‘La Orden’BadajozSpain

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