Psathyrostachys huashanica Keng., a species endemic to China, is only distributed in Huashan Mountain in Shaanxi Province. It has been listed as "national first-class protected rare species." In this study, the microsatellites of barley were used to analyze genetic diversity of P. huashanica populations sampled from three valleys (Huangpu, Xian and Huashan Valleys) in Mt. Huashan. A total of 33 alleles of 11 loci were detected from 266 individuals. The observed average number of alleles (A) is 2.75; the effective number of alleles (Ae) is 1.67. The percentage of polymorphic loci (PPB) is 58.33% in Huangpu Valley, 75% in Xian Valley, 83.33% in Huashan Valley, and the total PPB is 83.33%. About 77.6% of (FST= 0.324) genetic diversity was observed within the subpopulations. Genetic differentiation within each subpopulations was higher than that among the subpopulations. Mean genetic distance is 0.17 (range: 0.010-0.401). Correlation analysis detected significant correlation between genetic distance and vertical distance of altitude in Huashan Valley. Differentiation mainly occurred between the higher altitude subpopulations and the lower altitude subpopulations, suggesting that altitude might be the major factor that restricted the gene flow between different altitude subpopulations and resulted in differentiation of subpopulations. © 2006 Elsevier Ltd. All rights reserved.
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