CAPS markers for the analysis of plastid DNA polymorphism in representatives of the subgenus Prunophora (Neck. ex Spach) Focke of the genus Prunus L.

Relevance. Common plum Prunus domestica L., cherry plum Prunus cerasifera Ehrh. and blackthorn Prunus spinosa L. belong to the section Prunus of the subgenus Prunophora (Neck. ex Spach) Focke of the genus Prunus L. It is believed that the species P. domestica originated from hybridization of cherry plum and blackthorn, however, due to the phenotypic heterogeneity of the European plum, the presence of a wide range of variations and transitional forms, as well as a complex hexaploid genome, the question of its origin is still a matter of debate. For in-depth study of phylogenetic relationships, the analysis of polymorphism of plastid genome sites using molecular marking and DNA barcoding technologies is currently widely used. In this study, we aimed to develop a set of CAPS markers for rapid analysis of plastid DNA polymorphism in representatives of the Prunus section. Materials and methods. Based on the analysis of the cpDNA sequence of Prunus cerasifera var. pissardii (Carrière) L.H. Bailey, 21 pairs of plastid-specific primers have been developed. The primers previously applied to cpDNA analysis in other species of the Rosaceae family, namely in representatives of the genus Rubus L., were also used. To test the primers and select restriction enzymes, a subset consisting of seven accessions of P. cerasifera, four cultivars of P. domestica, four accessions of blackthorn P. spinosa and one cultivar of the hybrid species Prunus×rossica Eremin was used. Results. We have developed 10 potential CAPS markers (primer/restriction enzyme combinations) that provide the most visual picture of plastid DNA polymorphism in accessions of European plum, cherry plum and blackthorn. To confirm the diagnostic value of the selected CAPS markers, an analysis was performed on an experimental subset of stone fruit crops from the VIR collection, which included 19 cultivars of P. domestica, 16 accessions of P. spinosa, seven cultivars of P. cerasifera and one hybrid involving Chinese plum Prunus salicina Lindl. The CAPS markers used in the work showed different levels of detectable polymorphism, most of the markers identified from three to five variants of restriction profiles, the most polymorphic was the petN/psbM region (RubPlast9/TaqI marker) with nine different spectra of restriction fragments. Combinations of different restriction profiles for each accession were assessed as a haplotype of cpDNA; in total, 20 haplotypes were identified in a relatively small subset of 43 accessions. Conclusion. The developed CAPS markers allow us to effectively analyze the polymorphism of stone fruit plastomes in the future. They will be used to study broader experimental sets of accessions of European plum, cherry plum, and blackthorn and to investigate the relationships between these species.

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