Application of simple sequence repeat (SSR) markers to the genetic diversity of a chrysanthemum germplasm collection

Chrysanthemum (Chrysanthemum morifolium), one of the most popular ornamentals throughout the world, has approximately 1600 years of cultivation history in China. In this study, 10 simple sequence repeat (SSR) markers were used to identify a collection of 88 chrysanthemum and its related genera accessions. In total, 42 effective alleles across 88 accessions were detected; 3429 bands were obtained by PCR amplification, including 2630 polymorphic bands. The similarity coefficient ranged from 0.53 to 0.88. Cluster analysis based on UPGMA illustrated that the wild species and large-flower cultivars were first divided into two clusters, then the large-flower cultivars formed five distinct groups according to petal type, indicating that petal type can be a classification criterion. In the wild species cluster, C. vestitum and C. zawadskii grouped with A. trilobata, suggesting that the Ajania genus was closely related to the Chrysanthemum genera. 'Hang-baiju', 'Gong-ju' and 'Chu-ju' were grouped together, and 'Bo-ju', O. longilobus and C. mongolicum constituted another branch, showed a correlation with geographic region of origin. Population structure analysis was subsequently performed with K values ranging from 2 to 10, and the most likely estimate for the population structure is five subpopulations, which is nearly consistent with the clustering results. Principle component analysis was further performed to verify the classification results. The results showed that these SSR markers are very powerful for studying genetic relationships and will be useful tools in the identification and classification of chrysanthemum.