Classification of interspecific and intraspecific species by genome-wide SSR markers on Dendrobium

Dendrobium is a threatened and valuable genus in orchids. Many of them were common in medicinal and ornamental markets. In this study, a total of 198,990 simple sequence repeats (SSR) were identified from 3814 genomic scaffolds in D. catenatum (180 SSRs/Mb). Dinucleotide, trinucleotide and tetra-nucleotide covered about 0.2428%, 0.0544% and 0.0039% to the whole genome, separately. AT and TA, AAT and TGT, AAAT and TTTA were the corresponded dominant motifs. Total repetition of A and T was significantly greater than that of C and G. Moreover, 100 locus-specific primer pairs were randomly selected. And 73 of them produced polymorphic products in interspecific identification of 37 Dendrobium species. The interspecific effective polymorphic bands (EPBs), polymorphism information content (PIC), genetic diversity (Ht), genetic differentiation (Gst) and gene flow (Nm) of the novel SSR markers were 9.68, 0.528, 0.375, 0.499 and 0.753. The affinity of species and its varietas was confirmed in the phylogenetic tree. Additionally, 23, 25 and 12 SSR markers showed efficacy in intraspecific identification of 32 individuals in D. catenatum, 32 individuals in D. denneanum and 64 individuals in D. nobile, respectively. This confirmed the suitable transferability of SSR markers in cross-species. The intraspecific EPBs, PIC, Ht, Gst and Nm were 3.95, 0.554, 0.626, 0.226 and 2.305. The phylogenetic subgroups were significantly associated with plant height, epidermis and flower color. The electrophoretograms were clear for observation and suitable for auto-genotyping. The releasing of much more genome-wide SSR markers would be valuable for genetic studies and molecular breeding in Dendrobium.