Abstract
This study aimed to evaluate the genetic diversity of five natural populations of Allium atrosanguineum collected in the Almaty region of Kazakhstan using 17 SSR markers. The selected markers revealed notable polymorphism, with an average polymorphic information content (PIC) value of 0.496, indicating high marker informativeness. Genetic diversity was unevenly distributed among populations, with Population 1 exhibiting the highest overall diversity, as reflected by higher allelic richness and a more even distribution of allele frequencies, whereas the remaining populations showed predominantly moderate variation. Analysis of Molecular Variance (AMOVA) revealed that 76% of the total genetic variation was attributable to differences within populations, confirming moderate gene flow (Nm = 1.541) among A. atrosanguineum populations. Classical hierarchical cluster analysis, Principal Coordinate Analysis (PCoA), and STRUCTURE analysis consistently grouped the five populations by geographic origin, yielding three distinct clusters. Populations in close geographic proximity tended to cluster, reflecting greater genetic similarity, whereas populations separated by greater distances formed independent groups, highlighting the influence of spatial isolation on population structure. These results highlight the effectiveness of SSR markers in revealing genetic structure and confirm the applicability of cross-species SSR markers for population genetic studies in wild Allium species.