Genetic diversity and population structure analysis of landrace and improved safflower (Cartamus tinctorious L.) germplasm using arbitrary functional gene-based molecular markers

The genetic diversity and relationships among 48 landrace and improved safflower (Carthamus tinctorius L.) genotypes were analyzed using three gene-targeted markers, start codon-targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP) and CAAT box-derived polymorphism (CBDP). A total of 30 primers (10 primers from each marker) detected genetic polymorphism among the safflower genotypes. Three different marker types showed high level of polymorphism and the CDDP markers produced a higher number of polymorphic bands (74) in comparisons with SCoT and CBDP. The average PIC values for SCoT, CDDP, and CBDP were 0.39, 0.43, and 0.41, respectively. The marker index (MI) in CDDP markers was higher than that in SCoT and CBDP markers. Cluster analysis using SCoT and CDDP markers grouped the safflower genotypes into three distinct groups, whereas the CBDP markers divided the genotypes into two clusters. There were positive correlations between the similarity matrices obtained by each marker type. The results from the cluster analysis and STRUCTURE analysis using combined data grouped the genotypes into two clusters, generally in agreement with their origins. To our knowledge, this is the first detailed report of using gene-targeted molecular markers for genetic diversity analysis in safflower. Our results showed the efficiency of these markers for genetic diversity analysis in safflower and their potential for genome diversity and germplasm conservation.