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Analysis of Genetic Diversity Among ‘Misket’ Apple Clones Using AFLP, SSR and RAPD Markers

  • Berna Doğru Çokran
  • Turan Karadeniz
  • Hatice İktenEmail author
Original Article
  • 26 Downloads

Abstract

Knowledge of genetic relationship among genotypes is an important concern for utilization of germplasm resources in breeding. The need for knowledge in local apple cultivars is increasing and molecular marker analysis has contributed to understanding of the apple genetic diversity and phylogenetic relationship between genotypes. Three different DNA-based techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) were used for detecting genetic variation among the 30 local ‘Misket’ apple genotypes. A total of 423 bands amplified and 205 polymorphic band were obtained with three marker techniques. Thirty RAPD primers amplified 207 bands, of which 91 were polymorphic (40.1%), 10 SSR primers produced 33 bands and 26 of them were polymorphic (78.78%) and 5 AFLP combinations amplified 183 bands of which 88 were polymorphic (48.08%). The average numbers of polymorphic marker per primer combination were 17.6, 3.03 and 2.6 for AFLP, RAPD and SSR respectively. Our results indicate that SSR was less informative in characterizing closely related ‘Misket’ apple genotypes, compared with RAPD and AFLP markers. AFLP seemed to best suited for evaluating the genetic relationship among the apple genotypes. Closely related genotypes may require more than one marker technique. The findings will be useful to identify and evaluate the local growing apple genetic resources.

Keywords

Apple Molecular markers Local genotypes Genetic relationship 

Analyse der genetischen Diversität zwischen Apfelklonen der Sorte ‘Misket’ mithilfe von AFLP-, SSR- und RAPD-Markern

Schlüsselwörter

Apfel Molekulare Marker Lokale Genotypen Genetische Verwandtschaft 

Notes

Conflict of interest

B. Doğru Çokran, T. Karadeniz and H. İkten declare that they have no competing interests.

Supplementary material

10341_2019_430_MOESM1_ESM.docx (15 kb)
Supplementary Tables 1, 2, 3 and 4

References

  1. Cervera MT, Cabezas JA, Sanchez-Escribano E, Cenis JL, Martinez-Zapter JM (2000) Characterization of genetic variation within table grape varieties based on AFLP markers. Vitis 39:109–114Google Scholar
  2. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus (Madison) 12:13–15Google Scholar
  3. Duneman F, Kahnau R, Schmidt H (1994) Genetic relationships in Malus evaluated by RAPD fingerprinting of cultivars and wild species. Plant Breed 113:150–159CrossRefGoogle Scholar
  4. Ercisli S (2004) A short review of the fruit germplasm resources of Turkey. Genet Resour Crop Evol 51:419–435CrossRefGoogle Scholar
  5. Erturk U, Akçay ME (2010) Genetic variability in accessions of ‘Amasya’ apple cultivar using RAPD markers. Not Bot Hortic Agrobot Cluj Napoca 38(3):239–245Google Scholar
  6. Galli Z, Halász G, Kiss E, Heszky E, Dobránszki J (2005) Molecular identification of commercial apple cultivars with microsatellite markers. HortScience 40:1974–1977CrossRefGoogle Scholar
  7. Garkava-Gustavsson L, KolodinskaBrantestam A, Sehic J, Nybom H (2008) Molecular characterization of indigenous Swedish apple cultivars based on SSR and S‑allele analysis. Hereditas 145:99–112CrossRefGoogle Scholar
  8. Goulão L, Oliveira CM (2001) Molecular characterization of cultivars of apple (Malus x domestica Borkh.) using microsatellite (SSR and ISSR) markers. Euphytica 122:81–89CrossRefGoogle Scholar
  9. Guasmi F, Belhaj K, Triki T, Drine S, Ali BS, Mohamed BM, Bousorra F, Nagaz K (2016) Molecular comparison of some variety of apple (Malus domestica L.) “DouceDjerba” by ISSR and RAPD markers. Int J Biol Res 1(4):36–40Google Scholar
  10. Gupta R, Modgil M, Chakrabarti SK (2009) Assessment of genetic fidelity of micropropagated apple rootstock plants, EMLA 111, using RAPD markers. Indian J Exp Biol 47(11):925–928Google Scholar
  11. Hokanson SC, Lamboy WF, Szewc-McFadden AK, McFerson JR (2001) Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids. Euphytica 118:281–294CrossRefGoogle Scholar
  12. Juniper BE, Watkins R, Harris SA (1998) The origin of the apple. Eucarpia Symposium on Fruit Breeding and Genetics. Acta Hortic 484:27–34CrossRefGoogle Scholar
  13. Koc A, Akbulut M, Orhan E, Celik Z, Bilgener S, Ercisli S (2009) Identification of Turkish and standard apple rootstocks by morphological and molecular markers. Genet Mol Res 8(2):420–425CrossRefGoogle Scholar
  14. Larsen AS, Asmussen CB, Coart E, Olrik DC, Kjær ED (2006) Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris). Tree Genet Genomes 2(2):86–97CrossRefGoogle Scholar
  15. Li L, Wanapu C, Huang X, Huang T, Li Q, Peng Y, Huang G (2011) Comparison of AFLP and SSR for Genetic Diversity Analysis of Brassica napus Hybrids. J Agric Sci 3(3):101–110Google Scholar
  16. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van De Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed 10:217–241CrossRefGoogle Scholar
  17. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220Google Scholar
  18. Modgil M, Mahajan K, Chakrabartı SK, Sharma DR, Sobtı RC (2005) Molecular analysis of genetic stability in micropropagated apple rootstock MM106. Sci Hortic 104(2):151–160CrossRefGoogle Scholar
  19. Muzher BM, Younis RAA, El-Halabi O, Ismail O (2007) Genetic identification of some Syrian Local Apple (Malus sp.) cultivars using molecular markers. Res J Agric Biol Sci 3(6):704–713Google Scholar
  20. Roldán-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134CrossRefGoogle Scholar
  21. Rus-Kortekaas W, Smulders MJ, Arens P, Vosman B (1994) Direct comparison of levels of genetic variation in tomato detected by a GACA-containing microsatellite probe and by random amplified polymorphic DNA. Genome 37(3):375–381CrossRefGoogle Scholar
  22. Saker MM, Youssef SS, Abdallah NA, Bashandy HS, El Sharkawy AM (2005) Genetic analysis of some Egyptian rice genotypes using RAPD, SSR and AFLP. Afr J Biotechnol 4(9):882–890Google Scholar
  23. Schnitzler A, Arnold C, Cornille A, Bachmann O, Schnitzler C (2014) Wild European apple (Malus sylvestris (L.) Mill.) population dynamics: Insight from genetics and ecology in the Rhine Valley. Priorities for a Future Conservation Programme. PLoS ONE 9(5):e96596CrossRefGoogle Scholar
  24. Sivaci A (2006) Seasonal changes of total carbohydrate contents in three varieties of apple (Malus sylvestris Miller) stem cuttings. Sci Hortic 109(2006):234–237CrossRefGoogle Scholar
  25. Vos P, Hogers R, Bleeker M, Reijans M, Van De Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414CrossRefGoogle Scholar
  26. Zhou ZQ, Li YN (2000) The RAPD evidence for the phylogenetic relationship of the closely related species of cultivated apple. Genet Resour Crop Evol 47:353–357CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Deutschland, ein Teil von Springer Nature 2019

Authors and Affiliations

  1. 1.Faculty of Agriculture, Department of HorticultureIgdır UniversityIgdırTurkey
  2. 2.Faculty of Agriculture and Natural SciencesAbant İzzet Baysal UniversityBoluTurkey
  3. 3.Faculty of Agriculture, Department of Agricultural BiotechnologyAkdeniz UniversityAntalyaTurkey

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