Population Structure Analysis Reveals the Rich Genetic Diversity of Honeybee (Apis mellifera L.) Populations in Kazakhstan

Honeybee (<i>Apis mellifera</i> L.) populations are a vital resource for pollination and honey production, yet their genetic diversity in Central Asia remains poorly understood. This study provides a comprehensive genetic assessment of 16 honeybee populations from Kazakhstan, with comparative samples from Russia, Georgia and Kyrgyzstan, utilizing mitochondrial <i>COI</i>-<i>COII</i> intergenic region and 12 highly polymorphic nuclear STR markers. Mitochondrial DNA analysis revealed the predominance of the Eastern European C lineage (<i>A. m. carnica</i>), while a few populations from East Kazakhstan and Russia attributed the M lineage (<i>A. m. mellifera</i>), indicating local introgression and the persistence of relict lineages. STR analyses showed high levels of polymorphism and genetic diversity, with variation in heterozygosity and inbreeding across populations. Analyses of population genetic structure delineated four principal genetic clusters shaped by regional differentiation, historical gene flow, and sporadic admixture. Concordance between mitochondrial and nuclear markers confirms the robustness of these findings. Overall, this study highlights the rich genetic diversity of honeybees from Kazakhstan and emphasizes the importance of conserving local populations and implementing selective breeding programs to sustain adaptive potential and long-term apiculture.