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ARS Home » Southeast Area » Byron, Georgia » Fruit and Tree Nut Research » Research » Publications at this Location » Publication #342882

Research Project: Breeding Stone Fruit Adapted to the Production Environment of the Southeastern United States

Location: Fruit and Tree Nut Research

Title: Characterization of polymorphic chloroplast microsatellites in Prunus species and maternal lineages in peach genotypes

Author
item Chen, Chunxian
item OKIE, WILLIAM - Retired ARS Employee

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2017
Publication Date: 5/30/2017
Citation: Chen, C., Okie, W.R. 2017. Characterization of polymorphic chloroplast microsatellites in Prunus species and maternal lineages in peach genotypes. Journal of the American Society for Horticultural Science. 142(3):217-224.

Interpretive Summary: There is little knowledge of marker-based phylogenetic relation among all peach collections maintained in the USDA peach breeding program at Byron, GA. Genotyping these materials using molecular markers can facilitate parental choices and conventional hybridization breeding. Peach chloroplast microsatellite markers are exploited to determine and categorize maternal origins of all peach materials. Eight maternal lineage groups of peach materials were classified. Some unique peach materials, along with those inconsistent with their expected maternal groups, were determined. The grouping results have provided new insights into the maternal relation among the peach materials and helpful guidance for parental choices and combinations. The knowledge of the maternal relations may be helpful for optimization of parents and improvement of breeding efficiency.

Technical Abstract: Several available Prunus chloroplast genomes have not been exploited to develop polymorphic chloroplast microsatellites that could be useful in Prunus maternal lineage and phylogenetic analysis. In this study, using available bioinformatics tools, 80, 75, and 78 microsatellites were identified from the chloroplast genome of P. persica (CPpe), P. kansuensis (CPka), and P. mume (CPmu), respectively. The genome features and polymorphism status of these microsatellites were characterized. The genomic locations and motif types of most chloroplast microsatellites were conserved in CPpe, CPka, and CPmu. Of the 67 microsatellites with primer sequences and names, 57 were polymorphic for their in silico motif and/or amplicon lengths among the three genomes. Based on the genotyping data of eight most polymorphic microsatellites, eight unique maternal lineage groups (MLGs) were found among the 736 peach materials in a breeding program. A majority of peach cultivars (89 of 138 genotyped) belong to MLG-1, the Chinese Cling derived group reflecting the heavy use of this germplasm in early peach development. Thirty-five cultivars belong to MLG-2, the European derived group of peaches. MLG-3 consists of only a few ornamental accessions. MLG-4 to 6 consist of selections derived from P. tangutica, P. davidiana, and P. mira, respectively. MLG-7 and 8 contain only ‘Flordaking’ and ‘Reliance’, respectively. These amplicons from the representative material for each MLG were sequenced, revealing additional single nucleotide polymorphisms within the amplicons. With the polymorphism status and amplification reliability validated, these new polymorphic chloroplast microsatellite markers may be useful in Prunus phylogenetic analysis.