The genus Prunus comprises five subgenera: Prunus, Amygdalus, Cerasus, Padus, and Laurocerasus and includes ≈200 species, which are economically important as sources of fruits, nuts, oil, timber, and ornamentals (Reynders and Salesses, 1990). The subgenus Prunus includes section Prunophora comprising plums and section Armeniaca containing apricots. Each of these sections is considered to be a single gene pool (Watkins, 1976). Plums are adapted to the cooler temperate regions, whereas apricots are grown in warmer temperature regions of the world. Plums belonging to subgenus Prunophora are considered to be important for Prunus evolution because they include more than 20 species with abundant variation in their morphology. Differences in genetic diversity between plums and apricots are much influenced by the self-(in)compatibility phenotype of these species (Halasz et al., 2007a, 2007b; Milatovic and Nikolic, 2007). Although the basic chromosome number of Prunus species is x = 8, some species within subgenus Prunophora are triploid, tetraploid, and hexaploid. According to the derivative systems of these polyploids, Prunus domestica L. (6x), one of the European plums, is considered to be derived from a natural cross between Prunus spinosa L. (4x) and Prunus cerasifera Ehrh. (2x) (Crane and Lawrance, 1952). However, Zohary (1992) hypothesized that the origin of Prunus domestica is an autopolyploid derived from Prunus cerasifera. In addition, regarding the origin of European plums, Eryomine (1991) stated that it is originated of mixed descent from many other species, including Prunus microcarpa, Prunus salicina, Prunus armeniaca, and Prunus persica. The term Japanese plum was applied originally Prunus salicina Lindl. (2x) (Okie and Weinberger, 1996).
Under the generic term “apricot,” four different species and one naturally occurring interspecific hybrid are usually included (Mehlenbacher et al., 1990). Prunus armeniaca L. is a diploid species with eight pairs of chromosomes. Most cultivated apricots belong to the species P. armeniaca that originated in Central Asia where it has been cultivated for millennia and from where it was later disseminated both eastward and westward (Hormaza, 2002; Maghuly et al., 2005). The subgenus Cerasus comprising diploid sweet cherry and tetraploid tart cherry constitutes a distinct group distantly related to the other two subgenera, Amygdalus and Prunus (Reynders and Salesses, 1990).
Breeding barriers exist among subgenera possessing different ploidy levels, even within the same subgenus, but artificial or natural hybrids are generally successful, in particular between Prunophora (plums) and Armeniaca (apricots), when both parents have the same ploidy level (Okie and Weinberger, 1996). The subgenera Padus and Laurocerasus are more isolated within the genus Prunus.
The traditional taxonomic classification within the genus Prunus is mainly based on fruit morphology and has been controversial (Aradhya et al., 2004). This approach is also subject to environmental influences, mainly as a result of the long generation time and large size of the trees. Trees are also influenced by agricultural factors like rootstocks or pruning. Therefore, precise characterization and identification of species within the Prunus subgenus are important to recognize gene pools, to identify pitfalls in germplasm collections, and to develop effective conservation and management strategies. New methods based on molecular evaluations may provide further insight into the genetic structure and differentiation within Prunus (Aradhya et al., 2004). Genetic characterization of diversity and relationships at both inter- and intraspecific levels in the genus, Prunus, is limited to a few molecular phylogenetic studies using ITS and chloroplast trnL-trnF spacer sequence variation (Bortiri et al., 2001) and amplified fragment length polymorphism (Aradhya et al., 2004).
Choice of the marker system to use for a particular application depends on its ease of use and the particular objectives of the investigation (Rafalski et al., 1996). Recently, inter-simple sequence repeat (ISSR) markers have emerged as an alternative system with the reliability and several advantages over random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR). ISSR is a simple and quick method that combines most of the advantages of SSRs and AFLPs to the universality of RAPDs. The major limitations of RAPD, AFLP, and SSR methods are low reproducibility of RAPD and high cost of AFLP while flanking sequences have to be known to develop species-specific primers for SSR polymorphism. ISSR overcomes most of these limitations (Reddy et al., 2002). The main disadvantages of ISSR are the dominant nature and lower multiplex ratio. This method has been used in several fruit crops such as olive (Terzopoulos et al., 2005), pistachio (Kafkas et al., 2006), plum (Lisek et al., 2007), citrus (Shahsavar et al., 2007), and mulberry (Vijayan and Chatterjee, 2003; Vijayan et al., 2006a, 2006b) for the purposes of cultivar identification, germplasm characterization, natural population diversity evaluation, phylogenetic relationship analysis, genetic linkage mapping, and marker-assisted selection. The ISSR was also applied in genus Prunus (Goulao et al., 2001; Liu et al., 2007) and showed higher reproducibility and percentage of polymorphism than AFLP (Goulao et al., 2001). In addition, Turkish Prunus genotypes have only been characterized by morphological data so far and, in other words, no comparative studies on the molecular diversity among subgenera and sections in Turkish Prunus had been done. Therefore, in the present study, we used ISSR markers for fingerprinting a set of Prunus and Cerasus genotypes within genus Prunus.
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