| New hybrid rice cultivars, as a basis for the development of seed industry, either in quality or quantity, have been raised significantly. However, there have been all kinds of industrial infringement in reality due to technical limitations. In this study, hybrid rice DNA fingerprinting system was constructed to detect the distinctness of hybrid rice. These combinations ranged from the major 43 hybrid rice cultivars in Hunan of 2001-2008,140 cultivars in Hunan of 2009-2011 and 130 cultivars in other provinces. As was concluded,48 pairs of SSR had been confirmed according to their band clarity, high polymorphism and comprehensive distribution. A hybrid rice DNA fingerprint database, comprising 313 rice cultivars×48 SSR, had been successfully constructed to further standardize and improve the Hunan Hybrid Rice Area Test and provide technical support to cultivar validation and management.48 pairs of SSR were used to analyze 140 cultivars in Hunan of 2009-2010 and the cluster (pedigree) analysis could be used to broaden the basis of the genetic breeding of hybrid rice and judge sub-species genetic relationships based on similarity coefficient. The average genetic similarity coefficient of 2009,2010,2011 was respectively 0.725,0.69,0.695. Their amplitude was 0.47-0.98,0.53-0.85 and 0.56-0.83, respectively. Cluster analysis showed that genetic diversity of rice cultivars in this study was relatively narrow.The database included a.wide range of variety presentation and the unlimited capacity for the newly admitted. It had been published to the Internet in order that it could be fully shared.
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