Genetic diversity and methylation polymorphism analysis of Chrysanthemum nankingense

The diploid species Chrysanthemum nankingense (Anthemideae, Asteraceae) is closely related to the commercially important hexaploid ornamental species Chrysanthemum morifolium and is well adapted to poor environments. In this study, phenotypic variants of C. nankingense were first identified by morphological traits. Using EST-SSR (simple sequence repeat) analysis, we detected some absent EST-SSRs. The percentage of AFLP (amplified fragment length polymorphism) polymorphic fragments was 78.2%, indicating high genetic diversity. To evaluate the genome methylation level and methylation polymorphism, we used the MSAP (methylation-sensitive amplification polymorphism) technique to analyze the 30 C. nankingense lines. The total DNA methylation level ranged from 54.6% to 62.6%. Most of the MSAP-methylated fragments (97%) were polymorphic in the lines. The U-values associated with hemi-methylation were larger than those associated with full methylation in four of the 30 lines, and six individual values were statistically significant (U > 1.96). The high genomic diversity as well as the high methylation polymorphism may be responsible for the morphological polymorphism. There was no significant correlation between the phenotypic and genetic diversity among the lines.