Genetic diversity of Prunus sibirica L. superior accessions based on the SSR markers developed using restriction-site associated DNA sequencing

Prunus sibirica (Siberian apricot) has ecological, economic, and social benefits that makes it an important fruit-bearing tree in China. However, current fruit yields are low and unstable, thus restricting development of Prunus sibirica industry. To provide a scientific basis for successful breeding research aimed at developing superior cultivars, 98 screened SSR markers were first used in our study, developed by restriction-site associated DNA sequencing, to assess the genetic diversity of 66 Prunus sibirica accessions collected from four populations. The average number of alleles per locus (9.910) and the number of effective alleles (5.445) showed high polymorphism in the entire population, and the polymorphism information content (0.675) indicated that these markers were highly polymorphic. There was gene flow among the Prunus sibirica accessions, however the genetic differentiation coefficient showed 15.4% gene frequency differentiation among the provenances. Meanwhile, extensive linkage disequilibrium (D′ > 0.5, P < 0.01) was found, however the overall level was low (r2 < 0.5, p < 0.01). Additionally, the 66 accessions clustered into four groups, and these groups were extremely significantly correlated with the provenances classification. The clustering results showed that geographical distribution and genetic diversity changed from high to low as the geographic separation between provenances increased. Furthermore, population structure analysis supported these findings as genetic structure and provenances were extremely significantly correlated (p < 0.01). Additionally, the relationships between the geographical and genetic distances of the provenances and of the individuals were significantly correlated, indicating that geographical isolation importantly influenced Prunus sibirica evolution. The geographic and genetic effects underlying the superior accessions which we selected provide a reference for future molecular marker assisted breeding of Prunus sibirica.