Abstract
Iris kolpakowskiana Regel is a rare wild iris species distributed in southeastern and southern Kazakhstan. To assess its genetic diversity and population structure, 168 individuals from 9 natural populations in the Almaty, Zhambyl, and Turkestan regions were analyzed using expressed sequence tag – simple sequence repeat (EST-SSR) markers. Of the nine primer pairs tested, 6 polymorphic loci were selected for further analysis. The mean number of alleles per locus was 3.1, with an average effective number of alleles of 2.4. Polymorphic information content (PIC = 0.688) indicated moderately high genetic variation and high marker informativeness. The highest genetic diversity was observed in populations from the Zhambyl region. AMOVA revealed that 55% of genetic variation occurred within populations and 45% among populations. High genetic differentiation was detected (FST = 0.481, p < 0.001), accompanied by limited gene flow (Nm = 0.654). Principal Coordinate Analysis, Neighbor-Joining clustering, and STRUCTURE analysis consistently identified two major genetic groups corresponding to southeastern Kazakhstan (Almaty region) and southern Kazakhstan (Zhambyl and Turkestan regions). The Mantel test showed no significant correlation between genetic and geographic distances (R² = 0.0008, p > 0.05). These results revealed geographic structuring and restricted genetic exchange among populations, providing the first genetic assessment of Iris kolpakowskiana and valuable information for its further conservation and management.