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A total of 52 rice SSR markers well distributed on 12 chromosomes were used   to characterize and assess the genetic diversity among ninety four rice   genotypes. The total number of polymorphic alleles was 361 alleles with the   average of 5.86 alleles per SSR locus. The study revealed that some markers   such as RM276 and RM5642 on chromosome 6 and RM14 and RM1 on chromosome 1   have more than 9 observed alleles compared to other primers like RM16, RM207,   RM208 and RM317 with 3-4 alleles. The highest and lowest PIC values were   observed for primers RM276 (0.892 and RM208 (0.423) respectively. Using   Shannon´s diversity index, a mean genetic diversity of 1.641 was obtained   from the analysis, indicating a high level of genetic variation among these   cultivars. Cluster analysis using the complete linkage method based on   jaccard similarity coefficient revealed that all genotypes were classified to   nine clusters at genetic similarity level of 0.010.75, which contained 12,   16, 2, 18, 3, 6, 16, 10 and 11 varieties, respectively. Results of   discriminant analysis showed that the nine cluster groups were confirmed at   high levels of correct percent (96.8) and revealed true differences among   these clusters. As a final result from this study, we selected eight   cultivars from different cluster including Daylamani, Tarom mohali (landrace   rice cultivars), RI1843046, Back cross line, RI184472, RI184421 (promising   cultivars), Line 23 and IR50 (IRRI lines) as parents. All of the selected   cultivars will be arranged in complete diallel design to obtain combining   abilities, gene effects and heterosis for each important morphology and   physico-chemical characters

Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers