To study the genetic diversity and structure of lily (Lilium L.), we collected 35 samples from Vytautas Magnus University Kaunas Botanical Garden, and analyzed their mutual Simple Sequence Repeat (ISSR) molecular markers. For genetic analysis of lily we chose the lily 6 markers. ISSR data revealed a relatively high level of genetic diversity at the different levels of the group, with 95% of polymorphic loci, effective number of alleles of 1.21, the average expected heterozygosis of 0.15 and Shannon’s information index of 0.26. ANOVA analysis and UPGMA-dendrogram suggested a hierarchical structure between species.
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