| DUS criteria are used world-wide for the granting of Plant Breeders' Rights (PBR) and variety registration. The tests are mainly based on morphological and physiological markers. Many of the characters are multi-genic, quantitative or continuous characters and their expression can be altered by environmental factors. Furthermore, because the number of registered varieties increases over time, the traditional method of DUS testing is time-consuming and expensive, and it is impossible to check efficiently each new variety against all varieties of common knowledge. To circumvent these problems, microsatellite markers, which are currently identified as the most widely used marker system for plant variety characterization, are selected to analysis the uniformity, genetic diversity, genetic relationship of major rice varieties in China, and a microsatellite-based database of these varieties has been constructed. The primary results were summarized as following:1. A set of five well-chosen microsatellite markers were presented to detect clear and effectively within-cultivar variation in rice. 18 (43.90%) of 41 rice varieties with 2-7 sources show within-cultivar heterogeneity among different sources with the same name, therefore it should be noted that the sources of the materials were selected carefully as used in constructing a microsatellite database. To assess accurately intra-cultivar uniformity of the major rice varieties in China at 5 microsatellite loci, 11 typical varieties were selected and analyzed with larger samples containing 50 individuals per variety. The degrees of non-uniformity of selected varieties varied from 0-10.0%, with the percentage of heterogeneity ranged from 0.36 to 5.45%, and an overall average of 1.67% at 5 SSR loci. The results show that 6 of 11 typical rice varieties in China are completely uniform, and the degrees of non-uniformity within varieties across all loci are in general lower than 5%.2. A set of 24 SSR primer pairs located on 12 chromosomes in rice were used to construct a microsatellite database, evaluate the genetic diversity and analysis the genetic relationship of sixty-three major conventional varieties and parental lines of major hybrid combinations, which were widely used in the commercial rice production in China. A total of 135 alleles were detected, and the number of alleles per marker ranged from 2 to 9, with an average of 5.6. FP (Frequency of polymorphism) values ranged from 0.486-0.840, with an average of 0.682. All the varieties can be clearly discriminated from each other based on the information obtained from the 24 markers. Cluster analysis of the 63 cultivars based on the genetic similarity showed three major groups and eight subgroups. Group III corresponded to the japonica subspecies, whereas group I and II belonged to the indica subspecies. The result from cluster analysis still showed a significant feature of geographical distribution. The indica varieties (group I) were divided into two subgroups (G I -1 and G I -2), which separately distributed in South China and the Changjiang River area. The japonica varieties(group III) were divided into two subgroups (GIII-1 and GIII-2) , which separately distributed in North China and Jiangsu, Zhejiang provinces. The average genetic similarity of indica materials (0.388) was significantly lower than that of japonica materials (0.638), which showed that indica materials had a higher level of genetic diversity. Both Male sterile lines and restorer lines of hybridcombinations showed vulnerable genetic background. Compared to male sterile lines, restorer lines showed higher level of genetic variation. The results indicated that the genetic relationship constructed by SSR markers was identical with pedigree analysis.
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