Genetic Diversity and Population Structure of a Cucumber (Cucumis sativus L.) Breeding Collection from Kazakhstan Revealed by SSR Markers

Efficient exploitation of genetic diversity is essential for broadening the genetic base of cucumber (Cucumis sativus L.) breeding. This study evaluated the genetic diversity and population structure of a cucumber breeding collection comprising 60 accessions representing four breeding-origin groups: Eastern Europe (n = 34), Western Europe (n = 14), East Asia (n = 5), and locally developed breeding materials from Kazakhstan (n = 7). Fifteen chromosome-specific SSR markers were screened, of which 10 polymorphic loci were retained for downstream analyses. The marker panel showed moderate informativeness, with a mean polymorphism information content (PIC) of 0.438 ± 0.032, while CS-SSR05723 (PIC = 0.587) and CS-SSR23370 (PIC = 0.528) were the most informative loci. Bayesian clustering and complementary multivariate and network-based analyses revealed extensive intermixing among breeding-origin groups, indicating that geographic origin was only weakly associated with genetic relatedness in the analyzed collection. Eastern European germplasm exhibited the highest genetic diversity (Na = 2.9, Ne = 2.198, He = 0.516, I = 0.856) and was the only group to carry three private alleles. AMOVA revealed that 96.30% of the total molecular variation occurred within geographic groups and 3.70% among groups (Fst = 0.037, p = 0.043). These findings identify informative SSR markers for cucumber DNA fingerprinting and suggest that Eastern European germplasm constitutes an important source of genetic diversity within the analyzed breeding collection. The study provides a baseline molecular characterization of the cucumber breeding collection currently maintained in Kazakhstan and supports its future utilization in breeding and germplasm management.