Assessing the suitability of SCoT markers for studying genetic variation and genetic structure of Lepidium species

Lepidium spp. (Brassicaceae) are herbaceous plants grown worldwide and considered as vegetable, phytofood or medicinal plants. The genetic variation and genetic structure of 22 Lepidium (L.) accessions representing 3 species (L. sativum, L. draba and L. latifolium) from Iran were assessed using 14 Start Codon Targeted (SCoT) markers. A high polymorphism (98.4%), polymorphic information content (0.35) and polymorphic bands (4.5) indicated that SCoT markers are reliable for genetic variation analysis in Lepidium spp. Mean values of resolving power (Rp), marker index (MI) and effective multiplex ratio (EMR) were 5.0, 1.6 and 4.4, respectively. The highest percentage of polymorphic loci (92.2%), Nei’s gene diversity (0.35) and Shannon index (0.51) were observed in L. sativum. According to analysis of molecular variance (AMOVA), genetic variation within species was higher than between species. The highest similarity was found between L. draba and L. latifolium (r=0.94). A high level of gene flow was estimated in accessions of Lepidium species (Nm=2.65), which is further confirmed by neighbor-joining (NJ) cluster analysis, principal coordinates analysis (PCoA) and STRUCTURE analysis, that could reveal a poor separation between Lepidium species. NJ cluster analysis divided the Lepidium accessions into three groups, and the grouping of accessions was generally consistent with their origins. This study is the first to explore and prove SCoT markers suitability in genetic diversity of Lepidium spp. The genetic analysis information provided here would be helpful for breeding programs and germplasm conservation in Lepidium species.