Transferability of SSR markers derived from Dendrobium nobile expressed sequence tags (ESTs) and their utilization in Dendrobium phylogeny analysis

Limited availability of genetic marker resources in Dendrobium nobile Lindl. hinders the genetic research on this species for improvement of its horticultural and agricultural traits. As compared to other methods, bioinformatics mining of microsatellite markers from EST datasets is one of the most efficient and economical way. Our study is aimed to generate new EST-SSR markers and to evaluate their potential for cross-species utilization in phylogeny study of genus Dendrobium. A total of 1835 unigene ESTs were assembled by sequencing a normalized cDNA library, in which 500 SSR loci were identified. Of these SSRs, 38.0% (190) were the di-nucleotide repeats, followed by trimer (189, 37.8%), hexamer (81, 16.2%), pentamer (19, 3.8%), and tetramer (21, 4.2%). (AG)n and (AAG)n predominated in dimers and trimers, respectively. One hundred seventy novel D. nobile EST-SSR markers were developed, and 142 of them were successfully transferred to at least one of the other 31 Dendrobium species, with an average transferability of 42% in the genus. SSR markers with high cross-species transferability and high genetic diversity were selected for phylogeny analysis, where the results showed a complex genetic architecture among different sections as well as wide genetic differentiation within section Dendrobium. These microsatellite markers enrich the current resource of molecular markers, which would facilitate further evolution and genetic diversity studies, germplasm appraisal, genetic mapping, and molecular breeding of D. nobile and other congeneric species.