Sinopodophyllum hexandrum (Royle) Ying is an important medicinal and endangered species. Recently, the size of the wild population of S. hexandrum in western Sichuan Province has been noted to be very low and declining rapidly. Analysis of random amplified polymorphic DNA (RAPD) markers was conducted on seven natural populations of S. hexandrum in western Sichuan Province in order to investigate the genetic diversity and genetic structure of the populations. Leaf samples of 140 individuals from the seven populations were collected. Twelve RAPD primers were designed to generate highly reproducible and stable DNA fragments (the sizes of DNA bands ranged from 200 to 1500 bps). One hundred and eleven discernible DNA fragments were produced depending on these primers, and 32 fragments were polymorphic loci (mean 9.3 bands and 2 .7 polymorphic bands per primer). The percentage of polymorphic bands (PPB) was 28.83% at the species level, and PPB within population ranged from 4. 50% to 16. 22% with an average of 10. 30%. The result of POPGENE analysis indicated that the level of genetic variation of S. hexandrum (He = 0.0622,Ho = 0.0987) was lower than other endangered plants. At the species level, the average effective number of alleles per locus (Ae) was 1. 1011. The average expected heterozygosity was estimated to be 0.0193 within populations (He) and 0.0622 at the species level (Ht) .
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