An investigation was carried out to distinguish genotypes and to assess the genetic relatedness among 30 selected chrysanthemum (Dendranthema grandiflora Tzvelev) genotypes using ISSR and SSR markers. Ten ISSR primers were used to generate polymorphism which resulted in 175 amplicons with 100% polymorphism showing significant differences among the 30 chrysanthemum genotypes. Molecular analysis of 50 loci using 17 SSR primer pairs resulted in 80.4% mean polymorphism. Using dendrogram, three distinct groups were found based on SSR and ISSR indicating significant differences among the genotypes. The results showed that, there was a large genetic diversity exists among the chrysanthemum genotypes which helps in the selection of suitable genotypes for breeding. The results suggested that both ISSR and SSR were found to be effective for characterization studies in chrysanthemum.

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