Identification of salt tolerant rice genotypes and their genetic diversity analysis using SSR markers

Twenty six rice germplasms were used to evaluate salinity tolerance at the seedling stage. Salinity and nonsalinized setup were maintained at seedling stage. Phenotyping for salinity screening of the rice genotypes was done using salinized (EC level 12 dS /m) nutrient solution in hydroponic system following IRRI standard protocol. Genotypes were evaluated individually for salinity tolerance on 1-9 scale on the basis of seedling growth parameters following modified SES of IRRI. At the seedling stage, sixteen moderately tolerant and ten susceptible genotypes were identified using Standard Evaluation Score (SES).On the basis of SES score and phenotypic performance, out of 26 rice germplasms two (BINAdhan-8 and AYT SL-3)were selected as compare to other germplasms. For genotypic salt tolerance of 26 rice germplasms, DNA was extracted from leaf samples using CTAB mini-prep method. Then six selected SSR markers viz., RM10701, RM304, RM11757, RM336, RM7075, and RM152 were used for identification of salt tolerant genotypes. The band obtain from reaction with different markers were compared to the selected genotypes (BINAdhan-8 and AYT SL-3). Assessment of genetic diversity is an essential component in germplasm characterization and conservation. In DNA profiling, a total of 60 alleles were detected with an average number of alleles of 10 per locus (range 8 to 12 per locus) and the PIC values ranged from a low of the 0.7459 (RM152) to a high of 0.8908 (RM10701) and averaged 0.857. Positive correlations were found between gene diversity, PIC value and number of allele. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from (Nei’s, 1972) genetic distance produced two main clusters of 26 rice germplasms. The lowest genetic distance (0.200) was found in CSR-28 vs. CSR90IR-2 genotype pair indicating that they are genetically much closer among the genotypes. A cluster was consisted with a moderate salt tolerant due to higher similarity, while the mostly susceptible germplasms in the second cluster due to lower genetic distance between germplasms.