Genetic diversity and SSR marker assisted salt screening of rice (Oryza sativa L.)

Assessment of genetic diversity of rice (Oryza sativa L.) is an important tool for rice breeding and an essential component in germplasm characterization and conservation. Phenotypic and genotypic evaluation for salinity tolerance was done at the seedling stage. Phenotyping was done in hydroponic system using salinized (EC 12 dS/m) nutrient solution following International Rice Research Institute (IRRI) standard protocol. Among them, 7 germplasms were found to be saline tolerant viz. Horkuch, STL20, PBSAL730, PBSAL655, FL378, FL478 and PBRC37. According to SES scoring, 24 rice germplasms were selected to identify the level of salt tolerance and fingerprinted by using nine simple sequence repeat (SSR) primers. In DNA profiling, a total number of 76 alleles were detected. The number of allele per locus ranged from 6 to 15, with an average of 8.44 and the Polymorphism Information Content (PIC) value ranged from 0.5956 to 0.7725 with an average of 0.6847. The average gene diversity over all SSR loci for the 24 genotypes was 0.7140, ranging from 0.6188 to 0.7908. 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 (1983) genetic distance produced two main distinct clusters of the 24 rice genotypes. A cluster was consisted with a highly susceptible germplasms, while the second cluster comprises of mostly salt tolerant and moderately tolerant germplasms because of lower genetic distance between the varieties. These findings can have the potential role for further improvement of salinity tolerance rice genotypes through marker assisted breeding.