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Understanding genetic diversity in target populations is of great importance in breeding and a prerequisite for association mapping of traits. In this study, 57 cross species simple sequence repeat (SSR) markers were screened for amplification in China aster. Twenty six polymorphic markers were used to estimate the genetic diversity in forty two China aster genotypes. The observed and expected heterozygosities within the genotypes were ranged from 0.00 to 0.80 and 0.17 to 0.50, respectively. Weighted Neighbor Joining method, grouped China aster genotypes into five major clusters which coincided for morphological traits mostly flower color and form, but not correlated for their geographical locations. The results suggested that, population may be useful for the genome-wide marker–trait association mapping. These set of cross species transferable SSR markers would enable the application of the SSR technique in China aster crop improvement.

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