Determination of the genetic variability of asian rice (Oryza sativa L.) varieties using microsatellite markers

The microsatellite or simple sequence repeat (SSR) marker analysis was done to determine the allelic diversity and relationship among thirty five Asian cultivars of rice including 19 aromatic, 13 non-aromatic and 3 japonica type cultivars. A total of 144 alleles were detected at the 32 SSR loci, of which 141 (98%) were polymorphic. The number of alleles generated by each marker ranged from 2 to 13 with an anverage of 4.5 alleles per marker The size of smallest and largest allele ranged from 8(RM122) to as high as 71 (RM302). Polymorphism information content (PIC) values ranged between 0.157 (RM19, RM55) and 0.897 (RM70), with an average of 0.603 per marker. Basmati rice varieties amplified different alleles at 15 of the SSR loci than those in the japonica and/ or indica rice varieties. A number of SSRs were identified that could be utilized to differentiate between basmati and other non-basmati rice varieties. The RM252 and RM310 showed a clear differentiation of japonica cultivars from other ones. Pair-wise Nei and Lis similarity coefficients ranged from 0.19 to 0.90. The dendrogram based on the cluster analysis by microsatellite polymorphism, grouped 35 rice cultivars into two major groups effectively differentiating the tall, late maturing and slender aromatic cultivars from the short statured, early, short bold and long bold non-aromatic cultivars. These results could be useful for monitoring purity, genotype identification and for plant variety protection