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 (H O, H E) 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.
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Anderson WF, Holbroook CC, Culbreath AK (1996) Screening the peanut core collection for resistance to tomato spotted wilt virus. Peanut Sci 23:57–61
Aradhya MK, Stover E, Velasco D, Koehmstedt A (2010) Genetic structure an differentiation in cultivated fig (Ficus carica L.). Genetica 138:681–694
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 8:365–378
Berg CC (2003) Flora Malesiana precursor for treatment of Moraceae 1: the main subdivision of Ficus: the subgenera. Blumea 48:167–178
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 45:325–335
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-Ferrand
Brown AHD, Schoen DJ, Speer SS (1987) Designation of a “core” collection of perennial Glycine. Soybean Gent Newsl 14:59–70
Condit IJ (1955) Fig varieties: a monograph. Hilgardia 23:323–538
Diwan N, McIntosh MS, Bauchan GR (1995) Developing a core collection of annual Medicago species. Theor Appl Genet 90:755–761
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 DC
Erksine W, Muehlbauer FJ (1991) Allozyme and morphological variability, outcrossing rate and core collection formation in lentil germplasm. Theor Appl Genet 83:119–125
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 153:25–32
Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50
FAO (1996) Global plan of action for the conservation and sustainable utilization of plant genetic resources for food and agriculture. FAO, Rome
FAOSTAT (2013) faostat.fao.org
Flaishman M, Rodov V, Stover E (2008) The fig: botany, horticulture and breeding. Horticul Revs 34:113–196
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 161–170
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, Winchester
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):217–224
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):69–77
Giraldo E, Hormaza JI, López-Corrales M (2008b) Selection of morphological quantitative variables in the characterization of Ficus carica L. Acta Hort 798:103–108
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 92:93–94
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 101:197–202
Guerrero VM, Gornés (2000) Colonización humana en ambientes insulares: interacción con el medio y adaptación cultural. Universitat Illes Balears, Palma, Spain
Hewitt GM (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J Linnean Soc 58:247–276
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 101:264–268
Huntley B, Birks HJB (1983) An atlas of past and present pollen maps for Europe: 0–13,000 years ago. Cambridge University Press, Cambridge
Kappel F, Granger A, Hrotkó K, Schuster M (2012) Cherry. In: Badenes ML, Byrne DH (eds) Fruit breeding. Springer, USA, pp 459–504
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, Morocco
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 605:69–75
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 52:97–109
Kislev ME, Hartmann A, Bar-Yosef O (2006) Early domesticated fig in the Jordan Valley. Science 312:1372–1374
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 41:693–704
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):102–110
Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 47:515–526
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 195–214
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 62:227–228
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 70:3321–3323
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 30:827–837
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 55–76
Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7:453–464
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, Italy
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
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, Chichester
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 47:273–279
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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.
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Communicated by A. Dandekar
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Data is deposited in the Dryad repository at http://dx.doi.org/10.5061/dryad.2r107.
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Balas, F.C., Osuna, M.D., Domínguez, G. et al. Ex situ conservation of underutilised fruit tree species: establishment of a core collection for Ficus carica L. using microsatellite markers (SSRs). Tree Genetics & Genomes 10, 703–710 (2014). https://doi.org/10.1007/s11295-014-0715-3
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DOI: https://doi.org/10.1007/s11295-014-0715-3