evaluating allele frequency and polymorphism of microsatellite markers linked to gene loci controlling rice grain quality

in this research, allele frequency and polymorphism of 27 microsatellite markers linked to gene loci controlling grain quality were determined between 47 rice varieties from four different groups including 21 iranian local, 16 improved, 7 irri and 3 upland rice varieties. average number of polymorphic information content (pic) and shannon’s diversity index were 0.54 and 1.14, respectively. maximum number of polymorphic alleles, pic and shannon’s diversity index were observed in rm276 (on chromosome 6). calculated allele frequencies were significantly different between four different studied groups in all studied markers. the allele frequency was not correlated to allele size values. cluster analysis with upgma method based on simple matching coefficient divided the studied cultivars into four groups and separated cultivars with same quality and genetic similarity from others. in conclusion, the result of this research showed that there was high genetic diversity between all studied genotypes especially between landrace rice genotypes for microsatellite regions, so this diversity can use to improved grain quality characteristics especially in high yielded rice lines. furthermore, microsatellite markers linked to gene loci controlling rice grain quality could distinguish genotypes with high grain quality from others, therefore, using these markers especially markers which were more informative recommended for marker-assisted selection (mas).