Characterization of Polymorphic SSRs among Prunus Chloroplast Genomes

There is little information on peach chloroplast microsatellites. An in silico mining process yielded 80, 75, and 78 microsatellites in the chloroplast genome of Prunus persica, P. kansuensis, and P. mume. A and T repeats were predominant in the three genomes, accounting for 67.8% on average and most of them were successful in primer design. For the 80 P. persica microsatellites, 49 are in non-coding sequences, 15 in exons, and 16 in introns. In another categorization, 69 of them are in the long single copy (LSC) region, 1 in the inverted repeat A (IRA) region, 7 in the small single copy (SSC) region, and 3 in the IRB region. Considering one set of three adjacent microsatellites and four sets of two adjacent microsatellites sharing the same forward and reverse primers as one locus, respectively, there are 68 P. persica microsatellite loci that are given primer names and can be used for genotyping in peach and other Prunus species. 57 of them were found polymorphic among two or three of the three chloroplast genomes, in terms of their motif and/or amplicon lengths. Based on the genotyping data of selected in silico polymorphic primers, all genotyped peach materials are categorized into nine unique maternal lineages. These amplicons from the representative material for each lineage were confirmed by Sanger sequencing, revealing addition single nucleotide polymorphisms within the amplicons.