Genetic diversity and relationships of medicinal Chrysanthemum morifolium revealed by start codon targeted (SCoT) markers

Abstract Chrysanthemum morifolium plants are important commercial herbs in China, widely used in ornamental horticulture and traditional medicine. In this study, start codon targeted (SCoT) polymorphic markers were applied to assess genetic relationships among 32 populations of C. morifolium . Thirty-two SCoT primers produced 872 loci, 90% (785) of which showed polymorphism. Average polymorphism information content of the SCoT primers was 0.987 (0.950–0.993), showing that plenty of genetic diversity exists among Chinese C. morifolium cultivars. Cluster analysis of SCoT markers (based on UPGMA and PCoA method) grouped all the cultivars of C. morifolium into two clusters. The partition of clusters in the dendrogram and PCoA plot was similar and large degree of grouping according to their origin and ecological distribution. Our results will provide much more useful information for C. morifolium germplasm resource protection and will also useful to improve the current plant breeding programs. Our results also indicated that SCoT markers are informative and could be used to evaluate genetic diversity of Chinese medicinal C. morifolium cultivars.