Target Region Amplification Polymorphism (TRAP) for Assessing Genetic Diversity and Relationships Among Cultivated Populations of Dendrobium officinale

Dendrobium officinale (Orchidacesae) is one of the rare and endangered species of herbs in China. Therefore, it will be beneficial to investigate the genetic diversity and relationships of cultivated populations of D. officinale for quality improvement. In this study, eight target region amplification polymorphism (TRAP) primer combinations were selected from fifty-four combinations, which were designed based on the related genes of the polysaccharides and alkaloids. A total of 148 fragments were scored in nine cultivated populations of D. officinale, including 130 (87.84%) polymorphic fragments. The analysis of genetic diversity revealed high level of genetic diversity in cultivated populations of D. officinale (H = 0.4125, I = 0.5985). Based on analysis of genetic structure, there was a moderate variation (Gst = 0.4706) and lower gene flow (Nm = 0.5625) among the cultivated populations due to some isolated measures, and domestication of excellent cultivars. Moreover, UPGMA dendrogram and Principal Coordinate Analysis (PCoA) indicated that nine cultivated populations were divided into four major groups. The results suggested that genetic relationships were associated with geographical germplasm sources instead of cultivation locations. Therefore, TRAP markers can be effectively employed to analyze genetic diversity and relationships among cultivated populations of D. officinale.

Genetic Diversity Analysis ofHypsizygus marmoreuswith Target Region Amplification Polymorphism

Hypsizygus marmoreusis an industrialized edible mushroom. In the present paper, the genetic diversity among 20 strains collected from different places of China was evaluated by target region amplification polymorphism (TRAP) analysis; the common fragment of TRAPs was sequenced and analyzed. Six fixed primers were designed based on the analysis ofH. marmoreussequences from GenBank database. The genomic DNA extracted fromH. marmoreuswas amplified with 28 TRAP primer combinations, which generated 287 bands. The average of amplified bands per primer was 10.27 (mean polymorphism is 69.73%). The polymorphism information content (PIC) value for TRAPs ranged from 0.32 to 0.50 (mean PIC value per TRAP primer combination is 0.48), which indicated a medium level of polymorphism among the strains. A total of 36 sequences were obtained from TRAP amplification. Half of these sequences could encode the known or unknown proteins. According to the phylogenetic analysis based on TRAP result, the 20 strains ofH. marmoreuswere classified into two main groups.