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Assessing inter- and intra-cultivar variation in Greek Prunus avium by SSR markers

Published online by Cambridge University Press:  24 September 2010

Ioannis V. Ganopoulos
Affiliation:
Laboratory of Forest Genetics and Forest Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, PO Box 238, Thessaloniki 54124, Greece Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Aristotle University of Thessaloniki, PO Box 261, Thessaloniki 54124, Greece
Evagellia Avramidou
Affiliation:
Laboratory of Forest Genetics and Forest Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, PO Box 238, Thessaloniki 54124, Greece
Dionisia A. Fasoula
Affiliation:
Laboratory of Genetics and Plant Breeding, Faculty of Agriculture, Aristotle University of Thessaloniki, PO Box 261, Thessaloniki 54124, Greece
Grigorios Diamantidis
Affiliation:
Laboratory of Agricultural Chemistry, Faculty of Agriculture, Aristotle University of Thessaloniki, PO Box 261, Thessaloniki 54124, Greece
Filippos A. Aravanopoulos*
Affiliation:
Laboratory of Forest Genetics and Forest Tree Breeding, Faculty of Forestry and Natural Environment, Aristotle University of Thessaloniki, PO Box 238, Thessaloniki 54124, Greece
*
*Corresponding author. E-mail: [email protected]

Abstract

Prunus avium cultivars widely used in northern Greece were investigated in terms of inter- and intra-cultivar genetic variation and DNA fingerprinting. Based on 11 simple sequence repeats loci, the average number of alleles per locus (Na = 2.82), probability of identity (PID = 0.327), polymorphic information content (0.451) and expected heterozygosity (He = 0.494) were within the range reported in similar studies. The most informative markers were BPPCT039 and EMPa018. The cultivars were clearly separated in both an unweighted pair group method with arithmetic mean dendrogram and a multivariate space ordination. Any two cultivars differed on the average at 6.30 loci. The null hypothesis of zero intra-cultivar variability was tested and could not be rejected. Two cultivars (Tragana Edessis and Tragana Sarakinon) were genetically similar, but not identical. This study, the first of its kind for sweet cherry in Greece, presents a useful molecular tool for resolving issues of intra-cultivar variability and synonimity and provides a warranty of genetic identity in the handling and management of local traditional germplasm.

Type
Research Article
Copyright
Copyright © NIAB 2010

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References

Aravanopoulos, F (1999) Fingerprinting genetically improved forest genetic material by using molecular genetic markers. Scientific Annals Faculty of Forestry and Natural Environment, vol. 42. Thessaloniki: Aristotle University of Thessaloniki, pp. 645656.Google Scholar
Avramidou, E, Ganopoulos, I and Aravanopoulos, F (2007) A molecular study of wild cherry (Prunus avium L.) clones selected by using SSR markers. In: Proceedings of 13th Conference Hellenic Forest Science Society, vol. 1, pp. 400405.Google Scholar
Beaver, JA, Iezzoni, AF and Ramm, CW (1995) Isozyme diversity in sour, sweet and ground cherry. Theoretical and Applied Genetics 90: 847852.CrossRefGoogle ScholarPubMed
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314331.Google ScholarPubMed
Chatzicharisis, I, Mainou-Plerou, A, Chatzitheodorou, I and Kazantzis, K (2000) Monograph of Sweet Cherry and Sour Cherry Cultivars Evaluated and Cultivated in Greece. Naousa: Institute of Pomology.Google Scholar
Cipriani, G, Lot, G, Huang, WG, Marrazzo, MT, Peterlunger, E and Testolin, R (1999) AC/GT and AG/CT microsatellite repeats in peach [Prunus persica (L.) Batsch]: isolation, characterisation and cross-species amplification in Prunus. Theoretical and Applied Genetics 99: 6572.CrossRefGoogle Scholar
Clarke, JB and Tobutt, KR (2003) Development and characterization of polymorphic microsatellites from Prunus avium ‘Napoleon’. Molecular Ecology Notes 3: 578580.CrossRefGoogle Scholar
Clarke, JB, Sargent, DJ, Boskovic, RI, Belaj, A and Tobutt, KR (2009) A cherry map from the inter-specific cross Prunus avium ’Napoleon’ × P. nipponica based on microsatellite, gene-specific and isoenzyme markers. Tree Genetics and Genomes 5: 4151.CrossRefGoogle Scholar
DeNise, S, Johnston, E, Halverson, J, Marshall, K, Rosenfeld, D, McKenna, S, Sharp, T and Edwards, J (2004) Power of exclusion for parentage verification and probability of match for identity in American kennel club breeds using 17 canine microsatellite markers. Animal Genetics 35: 1417.CrossRefGoogle ScholarPubMed
Dirlewanger, E, Cosson, P, Tavaud, M, Aranzana, J, Poizat, C, Zanetto, A, Arus, P and Laigret, F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theoretical and Applied Genetics 105: 127138.CrossRefGoogle ScholarPubMed
Doyle, JJ and Doyle, JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemistry Bulletin 19: 1115.Google Scholar
Gerlach, HK and Stosser, R (1997) Patterns of random amplified polymorphic DNAs for sweet cherry (Prunus avium L.) cultivar identification. Journal of Applied Botany – Angew Botany 71: 212218.Google Scholar
Granger, AR (2004) Gene flow in cherry orchards. Theoretical and Applied Genetics 108: 497500.CrossRefGoogle ScholarPubMed
Guarino, C, Santoro, S, De Simone, L and Cipriani, G (2009) Prunus avium: nuclear DNA study in wild populations and sweet cherry cultivars. Genome 52: 320337.CrossRefGoogle ScholarPubMed
Hampl, V, Pavlicek, A and Flegr, J (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. International Journal of Systematic and Evolutionary Microbiology 51: 731735.CrossRefGoogle ScholarPubMed
IPGRI (1985) Cherry Descriptors. Rome: International Plant Genetic Resources Institute.Google Scholar
Jeffreys, AJ, Macleod, A, Tamaki, K, Neil, DL and Monckton, DG (1991) Minisatellite repeat coding as a digital approach to DNA typing. Nature 354: 204209.Google Scholar
Koukouroyiannis, V (1996) Trends in sweet cherry production and marketing. Agriculture Husbandry (in Greek) 2: 2431.Google Scholar
Lacis, G, Rashal, I, Ruisa, S, Trajkovski, V and Iezzoni, AF (2009) Assessment of genetic diversity of Latvian and Swedish sweet cherry (Prunus avium L.) genetic resources collections by using SSR (microsatellite) markers. Scientia Horticulturae 121: 451457.CrossRefGoogle Scholar
Marchese, A, Tobutt, KR, Raimondo, A, Motisi, A, Boskovic, RI, Clarke, J and Caruso, T (2007) Morphological characteristics, microsatellite fingerprinting and determination of incompatibility genotypes of Sicilian sweet cherry cultivars. Journal of Horticultural Science and Biotechnology 82: 4148.CrossRefGoogle Scholar
Marshall, RE (1954) Cherries and cherry products. In: Economic Crops. vol. 5. New York: Interscience.Google Scholar
Marshall, TC, Slate, J, Kruuk, LEB and Pemberton, JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639655.Google Scholar
Milbourne, D, Meyer, R, Bradshaw, JE, Baird, E, Bonar, N, Provan, J, Powell, W and Waugh, R (1997) Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Molecular Breeding 3: 127136.CrossRefGoogle Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences 70: 33213323.Google Scholar
Paetkau, D, Calvert, W, Stirling, I and Strobeck, C (1995) Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4: 347354.CrossRefGoogle ScholarPubMed
Pasqualone, A, Lotti, C and Blanco, A (1999) Identification of durum wheat cultivars and monovarietal semolinas by analysis of DNA microsatellites. European Food Research and Technology 210: 144147.Google Scholar
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288295.Google Scholar
Pinto, LR, Vieira, MLC, de Souza, CL and de Souza, AP (2003) Genetic-diversity assessed by microsatellites in tropical maize populations submitted to a high-intensity reciprocal recurrent selection. Euphytica 134: 277286.Google Scholar
Powell, W, Morgante, M, Andre, C, Hanafey, M, Vogel, J, Tingey, S and Rafalski, A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2: 225238.CrossRefGoogle Scholar
Prasad, M, Varshney, KR, Roy, KJ, Balyan, SH and Gupta, KP (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theoretical and Applied Genetics 100: 584592.Google Scholar
Schueler, S, Tusch, A, Schuster, M and Ziegenhagen, B (2003) Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) – markers for individual identification and reproductive processes. Genome 46: 95102.CrossRefGoogle ScholarPubMed
Song, YE, Zhai, H, Yao, YX, Li, M and Du, YP (2006) Analysis of genetic diversity of processing apple varieties. Agricultural Sciences in China 5: 745750.CrossRefGoogle Scholar
Sosinski, B, Gannavarapu, M, Hager, LD, Beck, LE, King, GJ, Ryder, CD, Rajapakse, S, Baird, WV, Ballard, RE and Abbott, AG (2000) Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theoretical and Applied Genetics 101: 421428.CrossRefGoogle Scholar
Stockinger, EJ, Mulinix, CA, Long, CM, Brettin, TS and Iezzoni, AF (1996) A linkage map of sweet cherry based on RAPD analysis of a microspore-derived callus culture population. Journal of Heredity 87: 214218.CrossRefGoogle ScholarPubMed
Tamura, K, Dudley, J, Nei, M and Kumar, S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 15961599.CrossRefGoogle ScholarPubMed
UPOV (1976) Guidelines for the conduct of test for distinctness, homogeneity and stability of the cherry. International Union for the Protection of New Varieties of Plants. Genova, Italy, p. 15.Google Scholar
Vaughan, SP and Russell, K (2004) Characterization of novel microsatellites and development of multiplex PCR for large-scale population studies in wild cherry, Prunus avium. Molecular Ecology Notes 4: 429431.Google Scholar
Webster, AD (1996) The taxonomic classification of sweet and sour cherries and a brief history of their cultivation. In: Webster, AD and Looney, NE (eds) Cherries. Wallingford OX 10 8DE, UK: Cab International, pp. 325.Google Scholar
Wunsch, A (2009) Cross-transferable polymorphic SSR loci in Prunus species. Scientia Horticulturae 120: 348352.CrossRefGoogle Scholar
Wunsch, A and Hormaza, JI (2002) Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach [Prunus persica (L.) Batsch] SSR sequences. Heredity 89: 5663.CrossRefGoogle ScholarPubMed
Yoon, J, Liu, D, Song, W, Liu, W, Zhang, A and Li, S (2006) Genetic diversity and ecogeographical phylogenetic relationships among peach and nectarine cultivars based on simple sequence repeat (SSR) markers. Journal of the American Society for Horticultural Science 131: 513521.CrossRefGoogle Scholar