Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale

Abstract

Dendrobium officinale is a critically endangered and valuable medicinal herb. In this study, two transcriptome libraries were constructed from 2-year-old stems of two cultivated varieties and sequenced with the Ion Torrent PGM™ platform. A total of 51,683 all-transcripts with average length of 505 bp, and 40,405 all-unigenes with N50 of 644 bp were achieved. Totally, 8527 potential genic simple sequence repeats (SSRs) were identified from 7332 (18.15%) unigene sequences, of which 1023 (2.53%) unigenes contained more than one SSR. Finally, 68 locus-specific primer pairs were designed, and 17 of them produced polymorphic products in D. officinale individuals. The number of alleles per locus ranged from 2 to 15, the observed and expected heterozygosity estimates ranged from 0.194 to 0.903 and from 0.360 to 0.893, respectively. These loci were further tested for cross-species transferability to D. huoshanense. All the 17 primer pairs were successfully amplified to yield locus-specific PCR products in D. huoshanense. Due to their high level of polymorphism and transferability, these genic SSR markers are valuable tools not only for germplasm conservation of this species but also for phylogenetic studies of Dendrobium.