Genetic variability and relationships among Salvia ecotypes/species revealed by TRAP-CoRAP markers

Abstract

In this study, target region amplification polymorphism (TRAP) and conserved region amplification polymorphism (CoRAP) markers were used for genetic diversity and relationship analysis of 25 Salvia ecotypes/species. Twelve TRAP and CoRAP primer combinations (four arbitrary primers and three fixed primers from Salvia miltiorrhiza expressed sequence tag sequences) amplified 180 loci, of which all were polymorphic. The obtained high average PIC and MI values revealed high capacity of TRAP and CoRAP primers to detect polymorphic loci among Salvia species. TRAPs and CoRAPs had similar efficiency in detecting polymorphisms with excellent ability to differentiate the closely related Salvia ecotypes. Based on both TRAP and CoRAP data, tetraploid Salvia virgata (2n = 4x = 32) showed the highest values for Na (1.17, 1.29), Ne (1.29, 1.35), Shannon index (0.26, 0.32) and heterozygosity (0.172, 0.212) in all 11 studied species. The Nei’s genetic distances with TRAPs and CoRAPs ranged from 0.23 to 0.69 and 0.19 to 0.64, respectively. The tree pattern based on combined CoRAP + TRAP data with the neighbour joining method clustered 25 Salvia species/ecotypes into five major groups that showed good alignment with the population structure analysis results. In both TRAPs and CoRAPs data analysis of molecular variance (AMOVA), the estimated variance within Salvia species was greater than that among Salvia species.