IntroductionThe cultivated apple (Malus × domestica Borkh.) is one of the most economically important temperate fruit crops, with 76.3 × 10 6 t produced on approximately 4.8 × 10 6 ha in 2012. Turkey is the fourth largest apple-producing country in the world with a production of 2.89 × 10 6 t in 2012 (http://faostat.fao.org/). Although apple is functionally diploid (2n = 2x = 34), the Maloideae are believed to be of allopolyploid origin (Chevreau et al., 1985).Although apples are grown in many regions of Turkey, approximately 60% of commercial apple production occurs in 5 provinces: Isparta, Karaman, Niğde, Denizli, and Antalya. These provinces are located in the southern part of Central Anatolia and in the northern Mediterranean region. Apples are also commercially grown in the provinces of Kayseri, Çanakkale, Mersin, Konya, and Bursa (http://www.turkstat.gov.tr/).Most apple cultivars in Turkish commercial orchards are exotic, with local cultivars having very limited production because of their low yields. Nevertheless, local cultivars have various characteristics that make them attractive for breeding purposes. One such example is Amasya, which has a pleasing taste and flavor and other superior fruit quality characteristics. Although fruit size and alternate-bearing characteristics of Amasya limit its commercialization, this cultivar is a very good genetic resource for breeding and genetic studies.Genetic improvement of apple by marker-assisted selection requires development of transferable molecular markers, construction of genetic maps, and association of molecular markers with quantitative trait loci (QTLs) and major genes of economic and horticultural importance (Wang et al., 2012). Linkage maps are usually constructed using dominant markers, such as random-amplified polymorphic DNA (RAPD), amplified fragment length polymorphism, and codominant simple sequence repeat (SSR, or microsatellite) markers. Because of their reproducibility, transferability, and multiallelic nature,
