ASSESSMENT OF GENETIC DIVERSITY AND POPULATION STRUCTURE OF IRIS KOLPAKOWSKIANA REGEL FROM KAZAKHSTAN USING MICROSATELLITE MARKERS
Main Article Content
Authors
M.M. Yermagambetova
Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
S.I. Abugalieva
Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
Y.K. Turuspekov
Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
S.S. Almerekova
Institute of Plant Biology and Biotechnology, 050040, Almaty, Kazakhstan
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.
Keywords
Iris kolpakowskiana, Kazakhstan, EST-SSRs, genetic diversity, AMOVA, genetic structure
Article Details
References
Plants of the World Online (POWO). Facilitated by the Royal Botanic Gardens, Kew [Electronic resource]. URL
Mathew B. The Iris. – London: Batsford Ltd, 1989. – 202 p.
Wang H., Cui Y., Zhao C. Flavonoids of the genus Iris (Iridaceae) // Mini Reviews in Medicinal Chemistry. – 2010. – Vol. 10. – P. 643–661.
Kukula-Koch W., Sieniawska E., Widelski J., Urjin O., Głowniak P., Skalicka-Woźniak K. Major secondary metabolites of Iris spp. // Phytochemistry Reviews. – 2015. – Vol. 14. – P. 51–80.
Khatib S., Faraloni C., Bouissane L. Exploring the use of Iris species: antioxidant properties, phytochemistry, medicinal and industrial applications // Antioxidants. – 2022. – Vol. 11. – 526.
Öztaş F., Türkmen A., Öztaş H., Türkmen M. The medical properties of Iris and its usage in pharmaceutical, perfumery and cosmetic industries // Medical Research and Its Applications. – 2024. – Vol. 4. – P. 114–124.
Almerekova S., Yermagambetova M., Alikhanova A., Yerbolatov D., Osmonali B., Turuspekov Y. Phylogenomics, divergence time estimation, and biogeography of Iris species from Kazakhstan using plastome sequence analysis // Frontiers in Plant Science. – 2026. – Vol. 17. – 1860819.
Baitulin I. O. Red Data Book of Kazakhstan. 2nd ed., rev. and suppl. Vol. 2. Plants. – Astana: ArtPrintXXI, 2014. – 452 p.
Sennikov A., Khassanov F., Ortikov E., Kurbonaliyeva M., Tojibaev K. S. The genus Iris L. s.l. (Iridaceae) in the Mountains of Central Asia biodiversity hotspot // Plant Diversity of Central Asia. – 2023. – Vol. 2, No. 1. – P. 1-104.
Peng J., Xie J., Gu Y., Guo H., Zhang S., Huang X. et al. Assessing population genetic structure and diversity and their driving factors in Phoebe zhennan populations // BMC Plant Biology. – 2024. – Vol. 24. – 1091.
Ding Y., Zhang J., Lu Y., Lin E. P., Lou L., Tong Z. Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis // Biochemical Systematics and Ecology. – 2015. – Vol. 63. – P. 183–189.
Rajarajan K., Sahu S., Handa A. K., Arunachalam A., Priyadarshini E., Bharti A. et al. Genetic diversity and population structure of Azadirachta indica using simple sequence repeat (SSR) markers for genetic resource conservation and utilization // Genetic Resources and Crop Evolution. – 2024. – Vol. 71, No. 7. – P. 3383–3394.
Yermagambetova M., Almerekova S., Turginov O., Sultangaziev O., Abugalieva S., Turuspekov Y. Genetic diversity and population structure of Juniperus seravschanica Kom. collected in Central Asia // Plants. – 2023. – Vol. 12. – 2961.
Ivachenko A., Grudzinskaya L., Gemedzhievo N., Da Silva J. T., Ryabushkina N. Genetic resources of Kazakhstan flora: experience, basic targets and methods for conservation of flowering plants // Floriculture, Ornamental and Plant Biotechnology. – 2006. – Vol. 12. – P. 583–584.
Sedina I. A., Otradnykh I. G. Phenorrhythms of rare ornamental herbaceous plants of the Northern Tien Shan in the Alpine Garden of the Almaty Botanical Garden // Conservation of Plant Diversity in Botanical Gardens: Traditions, Modernity, Prospects: Proceedings of the International Conference Dedicated to the 70th Anniversary of the Central Siberian Botanical Garden (Novosibirsk, August 1–8, 2016). – Novosibirsk, 2016. – P. 288–289.
Alikhanova A., Almerekova S., Turuspekov Y. Complete chloroplast genome sequence data of Iris kuschakewiczii B. Fedtsch., an endemic species of the Northern Tien Shan mountains // Data in Brief. – 2026. – 112563.
Doyle J. J., Doyle J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue // Phytochemical Bulletin. – 1987. – Vol. 19. – P. 11–15.
Tang S., Okashah R. A., Cordonnier-Pratt M. M., Pratt L. H., Johnson V. E., Taylor C. A. et al. EST and EST-SSR marker resources for Iris // BMC Plant Biology. – 2009. – Vol. 9. – P. 1–11.
Sun M. Z., Li M. R., Shi F. X., Li L., Liu Y., Li L. F., Xiao H. X. Genomic and EST-derived microsatellite markers for Iris laevigata (Iridaceae) and other congeneric species // American Journal of Botany. – 2012. – Vol. 99, No. 7. – P. e286–e288.
Zhang G., Han Y., Wang H., Wang Z., Xiao H., Sun M. Phylogeography of Iris loczyi (Iridaceae) in Qinghai–Tibet Plateau revealed by chloroplast DNA and microsatellite markers // AoB Plants. – 2021. – Vol. 13, No. 6. – plab070.
Peakall R., Smouse P. E. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research – an update // Bioinformatics. – 2012. – Vol. 28, No. 19. – P. 2537–2539.
Botstein D., White R. L., Skolnick M., Davis R. W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms // American Journal of Human Genetics. – 1980. – Vol. 32. – P. 314–331.
Mantel N. The detection of disease clustering and a generalized regression approach // Cancer Research. – 1967. – Vol. 27, No. 2. – P. 209–220.
Hammer Ø., Harper D. A. T., Ryan P. D. PAST: Paleontological statistics software package for education and data analysis // Palaeontologia Electronica. – 2001. – Vol. 4, No. 1. – P. 4–9.
Pritchard J. K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data // Genetics. – 2000. – Vol. 155, No. 2. – P. 945–959.
Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study // Molecular Ecology. – 2005. – Vol. 14, No. 8. – P. 2611–2620.
Kopelman N. M., Mayzel J., Jakobsson M., Rosenberg N. A., Mayrose I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K // Molecular Ecology Resources. – 2015. – Vol. 15, No. 5. – P. 1179–1191.
Chesnokov Y. V., Artemyeva A. M. Evaluation of the measure of polymorphism information of genetic diversity // Agricultural biology. – 2015. – № 5. – С. 571–578.
Yermagambetova M., Almerekova S., Ivaschenko A., Abugalieva S. Genetic diversity and population structure of Tulipa buhseana using simple sequence repeat markers // Experimental Biology. – 2024. – Vol. 100, No. 3. – P. 69–82.
Chung M. Y., Merilä J., Li J., Mao K., López-Pujol J., Tsumura Y., Chung M. G. Neutral and adaptive genetic diversity in plants: an overview // Frontiers in Ecology and Evolution. – 2023. – Vol. 11. – 1116814.
Shi W., Yang C.-F., Chen J.-M., Guo Y.-H. Genetic variation among wild and cultivated populations of the Chinese medicinal plant Coptis chinensis (Ranunculaceae) // Plant Biology. – 2008. – Vol. 10, No. 4. – P. 485–491.
Hensen I., Kilian C., Wagner V., Durka W., Pusch J., Wesche K. Low genetic variability and strong differentiation among isolated populations of the rare steppe grass Stipa capillata L. in Central Europe // Plant Biology. – 2010. – Vol. 12, No. 3. – P. 526–536.
Wright S. Evolution and the Genetics of Populations. Vol. 4: Variability Within and Among Natural Populations. – Chicago: University of Chicago Press, 1978. – P. 213–220.
Slatkin M. Gene flow in natural populations // Annual Review of Ecology and Systematics. – 1985. – Vol. 16. – P. 393–430.
Honnay O., Jacquemyn H. Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation // Conservation Biology. – 2007. – Vol. 21, No. 3. – P. 823–831.
Aguilar R., Quesada M., Ashworth L., Herrerias-Diego Y., Lobo J. Genetic consequences of habitat fragmentation in plant populations: susceptible signals in plant traits and methodological approaches // Molecular Ecology. – 2008. – Vol. 17, No. 24. – P. 5177–5188.
Flora of Kazakhstan. Vol. 2 / edited by N. V. Pavlov. – Alma-Ata: Publishing house of the Academy of Sciences of the Kazakh SSR, 1958. – P. 233–246.