Climate change causes increasing the salinity crisis of arable land in the world. It is crucial to develop salt tolerant genotypes that can maintain optimum yield levels. Therefore, the aim of this study was to discover prospective genotypes tolerant to salinity by using Microsatellites/ Simple Sequence Repeats (SSR) primers. Selection for salinity tolerant genotypes of rice based on phenotypic performance alone is less reliable and will delay progress in breeding. Recent advents of molecular markers have been used in selecting salt tolerant rice genotypes. A total of 13 Simple Sequence Repeats (SSR) primers were used to identify salinity tolerance in 30 rice genotypes. A total number of 39 alleles were detected. The number of alleles per locus ranged from 3 to 6 with an average of 4.3. The Polymorphism Information Content (PIC) values ranged from 0.17 to 0.70 with an average of 0.51. The average gene diversity over all SSR loci for the 30 genotypes was 0.56, ranging from 0.18 to 0.74. The “Unweighted Pair Group Method of Arithmetic Means (UPGMA)” dendrogram constructed from Nei’s (1983) genetic distance produced three main distinct clusters among the 30 rice genotypes. Clusters are formed based on lower genetic distance between the genotypes. Cluster I consisted of only the salt tolerant check Pokkali, cluster II was made up of susceptible genotypes, while cluster III comprises of mostly moderately tolerant and tolerant genotypes. Molecular characterization and genetic diversity assessment is an important component in order to guide breeders in the choice of parents for a breeding programme.
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