Japanese flowering cherry (Prunus subgenus Cerasus; Rosaceae) cultivars, which are characterized by beautiful flowers, have been generated through hybridization among wild Prunus taxa. The analysis of polymorphisms in the maternally inherited chloroplast DNA is an effective complementary approach for tracing the origins of these cultivars. Thus, a set of novel chloroplast simple sequence repeat (cpSSR) markers was developed for the Prunus taxa, and their utility in cross-species amplification was evaluated. Five markers were designed from the partial chloroplast genome sequences of thirteen Prunus taxa. In all, we found 19 haplotypes among the 311 individuals tested. The number of haplotypes, haplotype richness and haplotype diversity in each taxon ranged from 1 to 8, from 1 to 6.613 and from 0 to 0.758, respectively. The major proportion of the total diversity (HT = 0.831) was accounted for by intraspecific diversity (HS = 0.559), and the level of species subdivision, GST, was 0.327. These five cpSSR markers highly polymorphic, and they will be useful not only for tracing the origins of the cultivars but also for studying the population structure, diversity, and phylogeography of Prunus.
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