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

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