Different geographical plant populations within a single species can exhibit variation, in the production of secondary metabolites. Genetic and environmental variations both contribute to differences between populations; however, the relative importance of these factors is unclear. Here, the extent of variation in the production of four flavonoid glycosides (epimedin A, B, C and icariin) were investigated in eleven wild populations of Epimedium sagittatum used in traditional Chinese medicine. Secondary metabolite profiles were classified into five chemotypes. A common garden experiment indicated this chemotype variation has a significant genetic basis. Extensive genetic variation among intraspecific populations was shown using a retrotransposon-based molecular marker system. These results will assist in development of strategies for conservation, utilization and domestication of E. sagittatum.
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