Development and characterization of chloroplast simple sequence repeat markers for Prunus taxa (eleven Japanese native taxa and two foreign taxa)

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 (H_T = 0.831) was accounted for by intraspecific diversity (H_S = 0.559), and the level of species subdivision, G_ST, 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.