In this study, 128 individuals form 14 Epimedium pubescens populations and 1 E. stellulatum population were analyzed by ISSR marker. The data were calculated by POPGENE software and clustered by UPGMA method. Optical microscope was used to observe the main types of the non-glandular hairs and their characteristics in each population. It is found that the following conclusions: Non-glandular hairs can be divided into five morphological categories, long straight pubescent, curly pubescent, appressed curly pubescent, pseudo short appressed hairs and long appressed. Eight primers were screening and a total of 94 bands were detected in ISSR, among which 90 were polymorphic bands. Based on the results of ISSR cluster analysis, 15 populations were divided into 3 clades. E. stellulatum populations should be incorporated into the E. pubescens or as avariety under E. pubescens not be independent and as it has no separate phylogenetic branch for a cluster. The genetic relationship among the populations of E. pubescens was closely related with its geographical distribution and non-glandular hair features. But there were also some inconsistency, which provided a good hint for the further study on the interspecific relationship and natural speciation manner of Epimedium species. Population diversity analysis showed Nm=0.354 4, Nei's=0.585 2. It was showed that E. pubescens has high genetic diversity among populations, for which the main reason was probably the high inbreeding rate and the small range of seed dispersal.
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