Harun KARCI, Servet ARAS, Salih KAFKAS, Aysen KOÇ, Murat GÜNEY, Hakan KELEŞ

Characterization of quince (Cydonia oblonga Mill.) accessions by simple sequence repeat markers

In Turkey, quince (Cydonia oblonga Mill.) is found as both a wild and a cultivated tree species. The Karanlıkdere Valley is a pitarea between Şefaatli and Yerköy districts in Yozgat Province that originates from the River Delice. Members of the Yozgat KaranlıkdereValley quince population, containing 17 quince accessions and 15 commercial quince cultivars, were DNA fingerprinted using 30 simplesequence repeat (SSR) primers to identify the genetic relationships among them. A total of 111 alleles were detected for all 32 accessions,and the number of alleles revealed by SSR analysis ranged from 2 to 10 alleles per locus with a mean value of 3.70 alleles per locus.The Ms06g03 primer gave the highest number of alleles (Na = 10). Polymorphism information content (PIC) values ranged from 0.20(CH05e04) to 0.78 (Ms06g03) with a mean PIC value of 0.45. Structure analysis and unweighted pair group method with arithmeticaverage (UPGMA) clustering of the accessions depicted three major clusters, where several pairs of accessions could not be separated.This study indicated that the SSR markers could be utilized as a reliable tool for the determination of genetic variations and relationshipsof quince accessions. Furthermore, the results of this study will be useful for starting a cross-breeding cultivar program for quince.

PDF

___

Azad MK, Nasiri J, Abdollahi H (2013). Genetic diversity of selected Iranian quinces using SSRs from apples and pears. Bioch Genet 5: 426-442.
Bayazit S, Imrak B, Küden A, Güngör MK (2011). RAPD analysis of genetic relatedness among selected quince (Cydonia oblonga Mill.) accessions from different parts of Turkey. Hort Sci 38: 134-141.
Bouhadida M, Casas AM, Moreno MA, Gogorcena Y (2007). Molecular characterization of Miraflores peach variety and relatives using SSRs. Sci Hortic 111: 140-145.
Bucheyeki TL, Gwanama C, Mgonja M, Chisi M, Folkertsma R, Mutegi R (2009). Genetic variability characterisation of Tanzania sorghum landraces based on simple sequence repeats (SSRs) molecular and morphological markers. Afr Crop Sci J 17: 71-86.
Bucsek MJ, Nyeki J, Szabo Z, Kadar A (1996). Quantitation of mineral elements of different fruit pollen grains. Mikrochim Acta 13: 333-338.
Cadee N (2000). Genetic and environmental effects on morphology and fluctuating asymmetry in nestling barn swallows. J Evol Biol 13: 359-370.
Cantini C, Cimato A, Sani G (1999). Morphological evaluation of olive germplasm present in Tuscany region. Euphytica 109: 173-181.
Doyle JJ, Doyle JL (1987). A rapid isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
Dumanoğlu H, Güneş NT, Aygün A, San B, Akpınar AE, Bakır M (2009). Analysis of clonal variations in cultivated quince (Cydonia oblonga ‘Kalecik’) based on fruit characteristics and SSR markers. New Zeal J Crop Hort 37: 113-120.
Fan L, Zhang M, Liu Q, Li L, Song Y, Wang L, Zhang S, Wu J (2013). Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol Biol Rep 31: 1271-1282.
Faostat (2016). Agriculture data [online]. Accessed October 2017. http://faostat.fao.org. Fernandez-Fernandez F, Harvey NG, James CM (2006). Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L). Mol Ecol Notes 6: 1039-1041.
Gasi F, Kanlic K, Stroil BK, Pojskic N, Asdal A, Rasmussen M, Kaiser C, Meland M (2016). Redundancies and genetic structure among ex situ apple collections in Norway examined with microsatellite markers. HortScience 51: 1458-1462.
Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni AF, Stover EW, Bell RL, Wisniewski ME, Korban SS (2009). Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed. 23: 397-411.
Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R (1997). Microsatellites in Malus × domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94: 249-254.
Han Y, Chagne D, Gasic K, Rikkerink EHA, Beever JE, Gardiner SE, Korban SS (2009). BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple. Genomics 93: 282-288.
Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever JE, Korban SS (2011). Integration of physical and genetic maps in apple confirms whole-genome and segmental duplications in the apple genome. J Exp Bot 62: 5117-5130.
Hemmat M, Weeden NF, Brown SK (2003). Mapping and evaluation of Malus × domestica microsatellites in apple and pear. J Am Soc Hortic Sci 128: 515-520.
Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JK (1998). Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus × domestica Borkh. core subset collection. Theor Appl Genet 97: 671-683.
Hormaza JI (2002). Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theor Appl Genet 104: 321-328.
Inoue E, Matsuki Y, Anzai H, Evans K (2007). Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 7: 445-447.
Kacem NS, Muhovski Y, Djekoun A, Watillon B (2017). Molecular characterization of genetic variation in somaclones of durum wheat (Triticum durum Desf) using SSR markers. Eur Sci J 13: 426-437.
Kafkas S, Ozkan H, Ak BE, Acar I, Atli HS, Koyuncu S (2006). Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm: comparison of AFLP, ISSR and RAPD markers. J Am Soc Hortic Sci 131: 522-529.
Keles H, Akca Y, Ercisli S (2014). Selection of promising walnut genotypes (Juglans regia L.) from inner Anatolia. Acta Sci Pol Hortorum Cultus 13: 167-173.
Khan MA, Durel CE, Duffy B, Drouet D, Kellerhals M, Gessler C, Patocchi A (2007). Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker assisted selection. Genome 50: 568-577.
Lacis G, Rashal I, Ruisa S, Trajkovski V, Iezzoni AF (2009). Assessment of genetic diversity of Latvian and Swedish sweet cherry (Prunus avium L.) genetic resources collections by using SSR (microsatellite) markers. Sci Hortic 121: 451-457.
Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg E, Gessler C (2002). Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10: 217-241.
Liu K, Muse SV (2005). PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21: 2128- 2129.
Moriya S, Iwanami H, Kotoda N, Haji T, Okada K, Terakami S, Mimida N, Yamamoto T, Abe K (2012). Aligned genetic linkage maps of apple rootstock cultivar ‘JM7’ and Malus sieboldii ‘Sanashi 63’ constructed with novel EST-SSRs. Tree Genet Genomes 8: 709-723.
Oddou-Muratorio S, Aligon, C, Decroocq S, Plomion C, Lamant T, Mush-Demesure B (2001). Microsatellite primers for Sorbus torminalis and related species. Mol Ecol Notes 1: 297-299.
Özbek S (1978). Özel Meyvecilik. Çukurova Üniversitesi, Ziraat Fakültesi Yayın No: 128, 485 s.
Peakall R, Smouse PE (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics 28: 2537-2539.
Pınar H, Kaymak S, Özogun S, Uzun A, Unlu M, Bircan M, Ercişli S, Orhan E (2016). Morphological and molecular characterization of major quince cultivars from Turkey. Not Bot Horti Agrobo 44: 72-76.
Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945- 59.
Rakonjac V, Akšić MF, Nikolić D, Milatović D, Čolić S (2010). Morphological characterization of ‘Oblačinska’sour cherry by multivariate analysis. Sci Hortic 125: 679-684.
Rohlf FJ (2009). NTSYSpc: Numerical Taxonomy System, ver.2.21c. Setauket, NY, USA: Exeter Publishing.
Sanchez EE, Menendez RA, Daley LS, Boone RB, Jahn OL, Lombard PB (1988). Characterization of quince (Cydonia) cultivars using polyacrylamide gel electrophoresis. J Environ Hortic 6: 53-59.
Scheulke M (2000). An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234.
Schlotterer C, Tautz D (1992). Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20: 211-215.
Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F et al. (2006). Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2: 202-224.
Silva BM, Andrade PB, Ferreres F, Domingues AL, Seabra RM (2002). Phenolic profile of quince fruit (Cydonia oblonga Mill.) pulp and peel. J Agric Food Chem 50: 4615-4618.
Silva BM, Andrade PB, Martins RC, Valentao P, Ferreres F, Seabra RM, Ferreira MA (2005). Quince (Cydonia oblonga Mill.) fruit characterization using principal component analysis. J Agric Food Chem 53: 111-122.
Topçu H, Kafkas S, Doğan A, Akcay ME, Ercişli S (2015). Turkey genetic relatedness among quince (Cydonia oblonga Miller) accessions from Turkey using amplified fragment length polymorphisms. J Appl Bot Food Qual 88: 197-201.
Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002a). Simple sequence repeats for genetic analysis in pear. Euphytica 124: 129-137.
Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002b). Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2: 14-16.
Yamamoto T, Kimura TJ, Soejima T, Sanada T, Ban Y, Hayashi T (2004). Identification of quince varieties using SSR marker developed from pear and apple. Breed Sci 54: 239-244.
Yüksel C, Mutaf F, Demirtaş I, Öztürk G, Ergül A (2013). Characterization of Anatolian traditional quince cultivars, based on microsatellite markers. Genet Mol Res 12: 5880-5888.
Zaloğlu S, Kafkas S, Doğan Y, Güney M (2015). Development and characterization of SSR markers from pistachio (Pistacia vera L.) and their transferability to eight Pistacia species. Sci Hortic 189: 94-103.