Study of genetic structure and variations in plant germplasm is one of the most important preliminary steps in plant breeding programs. In the present study, genetic diversity in six Iranian cultivated alfalfa (Medicago sativa L.) populations from Yazd, Kerman, Isfahan, Khorasan, Lorestan and Hamadan regions was evaluated using eight microsatellite markers. In Total sixty-eight polymorphic bands were observed in the studied populations. Average intra-population genetic diversity ranged from 0.82 in Kerman to 0.93 in Ghareyonjeh (Hamadan) population, while the level of genetic diversity was the same in either of Khorasan and Lorestan (0.92) populations. Proportion and percentage of genetic diversity among individual plants and populations were analyzed based on analysis of molecular variance (AMOVA). Results revealed a significant difference among populations and plants within populations. Genetic population differentiation was evaluated using fixation index (Fst) as a distance criterion. Pairwise comparison between populations showed highest genetic distance between Ghareyonjeh and the others. As a whole, a higher level of genetic diversity was observed within populations rather than between populations. In conclusion, Iranian alfalfa populations are valuable germplasm sources for plant breeding programs. This study confirmed that microsatellite markers can be used as a powerful tool for assessing inter and intra population genetic diversity as well as genetic differentiation and identification. They can also in be used germplasm management and discrimination of duplicated, as well as synonymous accessions.
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