Characterization of Wild Apricot (Prunus armeniaca L.) Genotypes Selected from Cappadocia Region (Nevşehir-Turkey) by SSR Markers

Tarım Bilimleri Dergisi Journal of Agricultural Sciences Dergi web sayfası: www.agri.ankara.edu.tr/dergi Journal homepage: www.agri.ankara.edu.tr/journal TARIM BİLİMLERİ DERGİSİ — JOURNAL OF AGRICULTURAL SCIENCES 25 (2019) 498-507 Tar. Bil. Der. Characterization of Wild Apricot (Prunus armeniaca L.) Genotypes Selected from Cappadocia Region (Nevşehir-Turkey) by SSR Markers Melike BAKIRa, Hatice DUMANOĞLUb, Veli ERDOĞANb, Cemil ERNİMc, Tahir MACİTd a Erciyes University, Seyrani Faculty of Agriculture, Department of Agricultural Biotechnology, Kayseri, TURKEY b Ankara University, Faculty of Agriculture, Department of Horticulture, Ankara, 06110, TURKEY c Apricot Research Institute, Aşağıbağlar Mah. İsmetpaşa Caddesi, No: 163, Yeşilyurt, Malatya, TURKEY d Malatya Directorate of Provincial Agriculture and Forestry, Karakavak Mahallesi, Ankara Asfaltı, 7. km, Malatya, TURKEY ARTICLE INFO Research Article Corresponding Author: Veli ERDOĞAN, E-mail: , Tel: +90 (312) 596 12 56 Received: 06 September 2018, Received in Revised Form: 05 October 2018, Accepted: 31 October 2018 ABSTRACT Cappadocia region of Anatolia hosts the third largest wild apricot population in Turkey. The objective of the study was to characterize 44 wild apricot genotypes selected from Cappadocia Region (Nevşehir-Turkey) as prominent with their late flowering, resistance to spring late frosts, large fruit sizes and/or late fruit ripening characteristics and 5 reference apricot cultivars (‘Hacıhaliloğlu’, ‘Kabaaşı’, ‘Hasanbey’, ‘Aprikoz’ and ‘Levent’) with SSR (simple sequence repeats) markers. A total of 16 SSR primers were used and 13 of them were successfully amplified. Total number of alleles was 107, average number of alleles was 8.23; average He and Ho values were 0.722 and 0.669, respectively. Polymorphism information content (PIC) values varied between 0.471 and 0.845. There was a quite high genetic diversity among wild apricot genotypes that genetic similarity values varied between 12 and 96%. Homonymous and synonymous genotypes were not encountered. Keywords: Wild apricot; Prunus armeniaca; Genetic diversity; Genetic relationship; Molecular characterization; SSRs © Ankara Üniversitesi Ziraat Fakültesi 1. Introduction Vavilov (1951) indicated the origin centers of culture apricots (Prunus armeniaca L.) as China, Central Asia and defined Near-East centers extending from Northeastern Iran to Caucasus and Central Anatolia as the secondary origin center of cultured forms. Kostina (1969) divided P. armeniaca species into 4 large eco-geographical groups and 13 regional subgroups and placed Turkey into Iran-Caucasus ecogeographic group (Layne et al 1996; Zhebentyayeva et al 2012). Anatolia (Turkey) is located within the DOI: 10.15832/ankutbd.457850 secondary origin center of apricots, thus has a great genetic diversity (Ercisli 2004). Nevşehir province is located right at the center of Cappadocia region of Anatolia, and the province hosts the 3rd largest wild apricot population with about 145000 trees (TUIK 2017). This population is characterized with late flowering, resistance to spring late frosts, large fruits and late ripening. Thus the population exhibits a large variation in fruit physical and quality attributes. Such a diverse population was evaluated for the first time by Dumanoğlu et al (2018) within Characterization of Wild Apricot (Prunus armeniaca L.) Genotypes Selected from Cappadocia Region..., Bakır et al the scope of a scientific research project, and superior genotypes were identified. These genotypes were then put under protection in a collection orchard. The genotypes constitute significant materials for apricot breeding studies and genetic relationships among these genotypes should be identified with further molecular techniques. Microsatellites or simple sequence repeats (SSRs) are short repeat sequences (1-6 base length) and have co-dominant characteristics, greater polymorphism ratios, are abundant in genome and have quite high repeatability. Therefore, they have a significant place among DNA markers (Litt & Luty 1989; Gupta et al 1996). These markers are commonly used in identification of species, preservation of genetic materials, population genetics, quantitative trait loci mapping, marker assisted selection and similar studies. SSR markers are also used in genetic characterization of Prunus species, including apricots. However, SSR markers were not developed at the same rates for each one of the significant species (apricot, peach, plum, and almond), thus potential use of SSR markers of a species in other Prunus species (crosstransferability) have become a significant issue (Hormaza 2002; Romero et al 2003; Zhebentyayeva et al 2003; Hagen et al 2004; Messina et al 2004; Mnejja et al 2005; Sanchez-Perez et al 2005; Ruthner et al 2006; Bouhadida et al 2009; Wünsch 2009; Akpınar et al 2010; Bourguiba et al 2010; Liu et al 2013; Wang et al 2014; Eroglu & Cakir 2015; Gürcan et al 2015; Murathan et al 2017). In this study, genetic relationships between wild apricot genotypes selected from the wild apricot gene sources of Nevşehir province with regard to late flowering, resistance to spring late frosts, large fruits and or late fruit ripening characteristics were identified with SSR markers developed from P. armeniaca and P. persica. 2. Material and Methods 2.1. Plant material and DNA isolation In this study, 44 wild apricot genotypes selected from Nevşehir (Cappadocia Region-Turkey) locality and the reference apricot cultivars of ‘Aprikoz’, ‘Kabaaşı’, ‘Hasanbey’, ‘Hacıhaliloğlu’ and ‘Levent’ were used as the plant material. DNA isolations were performed from fresh shoot tips and young leaf samples collected from the genotypes (Lefort et al 1998). DNA purity and concentrations were determined in ND-1000 spectrophotometer and isolated DNA was visually controlled in 1% agarose gel. 2.2. SSR reactions A total of 16 SSR loci were selected as of 10 P. armeniaca (apricot), 4 P. persica (peach) and 2 P. armeniaca EST-SSR loci (Table 1). Selected SSR loci were tested and the polymorphic ones were used in genetic identifications. PCR amplifications were performed by using M13-tailed primer according to the methods described by Schuelke (2000) in Prunus genotypes. A tail (M13 universal sequence (-21), TGTAAAACGACGGCCAGT) was added to the 5’ end of each forward primers. PCR amplifications were performed in 15 µL reaction mixture containing 90 ng genomic DNA, 0.1 µM of each SSR primer, 0.1 µM labelled M13 (-21) universal primer, 0.2 mM of each dNTPs, 1X DreamTaq Green Buffer (includes MgCl2 at a concentration of 2 mM) (Thermo Scientific) and 0.5 U DreamTaq DNA Polymerase (Thermo Scientific). The amplification program consisted of an initial step of 3 min at 94 °C, followed by 35 cycles of 1 min at 94 °C, 1 min at 50-66 °C, 2 min at 72 °C, followed by 8 cycles of 1 min at 94 °C, 1 min at 53 °C, 2 min at 72 °C, and a final extension at 72 °C for 10 min. The M13 (-21) primer was 5 (...truncated)