Estimation of genetic diversity in rice (Oryza sativa L.) genotypes using SSR markers under salinity stress

In order to study the genetic diversity in rice (Oryza sativa L.), 29 genotypes consis􀀓ng land races, pure and improved lines were evaluated using simple sequence repeat (SSR) markers. A total of 30 SSR primers were used to amplify some part of rice genome in germplasms, the PIC values ranged from 0.07 (RM 340) to 0.71 (RM 7426) with an average of 0.45. The results showed a total number of 106 amplified bands. Among them, the primer RM7426 showed the highest number alleles while the lowest was observed for RM340 primer. Average number of observed alleles in total genotypes was 3.53. The lowest PIC value was observed in RM445, RM466, RM3345, and RM7424 primers and the highest PIC value was observed in RM7426, RM1337, RM47, and RM5430 primers. PCA components explained 84.40% of variation. The clustering patterns of the genotypes were assigned into three clusters based on their response to salinity and morpho-physiological characteristics. Cluster analysis grouped the genotypes in salt tolerant, intermediate tolerant and sensitive classes. The results showed that information from SSR data can complement information obtained from quantitative methods.