Characterization of polymorphic SSRs among Prunus chloroplast genomes

Authors: Chen, Chunxian

Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/18/2016
Publication Date: 1/14/2017
Citation: Chen, C. 2017. Characterization of polymorphic SSRs among Prunus chloroplast genomes. International Plant and Animal Genome IX Conference. 25:P0123.

Interpretive Summary: Peach conventional breeding is hindered by limited knowledge of pedigrees of elite peach cultivars and breeding lines. Peach chloroplast genome markers can be explored and utilized to categorize the maternal origin of peach materials, which may facilitate optimal parental selection and breeding efficiency improvement. Molecular markers in peach chloroplast genome are discovered, characterized, and used in all peach cultivars and breeding lines maintained in the USDA peach breeding program at Byron, GA. The genotyping results have provided new insights into the maternal relation among the peach cultivars.

Technical Abstract: 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.