Genetic diversity and population structure of cultivated Dendrobium nobile Lindl. in southwest of China based on genotyping-by-sequencing

Dendrobium nobile Lindl. is one of the most important Orchid plants worldwide. The genotype-by-sequencing (GBS) method has now been widely used to access genetic diversity because of its high-throughput and cost-effective in molecular markers. The goal of this study was to employ the GBS technique for diversity evaluation of D. nobile and determine genetic differences between populations. A total of 129 accessions of D. nobile collected from 10 imitation-wild cultivated populations growing in Sichuan, Guizhou and Yunnan of southwestern China were sequenced, a total of 135 G clean reads and a total of 836,786 high quality SNPs were yielded and used for analysis of genetic diversity and population structure. The accessions of D. nobile were classified into three groups, excepts for 14 accessions belonging to admixed group. Genetic variation was greater within populations (87.80%) than among populations (12.20%). There was gene exchange between different populations. The 10 populations were classified into three groups, and group III could be further divided into two subgroups. The results will not only provide valuable information for the level of genetic diversity of D.nobile growing in southwestern of China, but also help for formulation of strategies for genetic resource protection and utilization. The accessions used in this study could be applied to the scientific research, breeding and production of D. nobile.