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Salinity stress is one of the major soil problems in relation to rice production in Sri Lanka. Development of salinity tolerant rice through rice breeding is a key solution for salinity problem. Saltol is the major Quantitative Trait Loci (QTL) responsible for salt tolerance at the seedling stage of the rice plants which is mapped on chromosome one of the rice genome. To select most salt tolerant rice genotypes for future breeding programmes and test the usefulness of the Microsatellite (SSR) markers associated with Saltol QTL, 18 rice varieties were screened using electrical conductivity 12 dSm-1 nutrient solution for salt tolerance at the seedling stage using a visual score of 1-9 scale. Six polymorphic SSR markers linked to the Saltol QTL were used to determine the impact of these markers associated with salt tolerance in rice. Results of the phenotypic screening of 18 rice genotypes showed different responses for salt stress at the seedling stage. Based on the phenotypic screening rice genotypes were categorized into four groups, and Pokkali accessions were the most tolerant genotypes for salinity stress which can be useful as donor parents for future rice breeding programs. Microsatellite marker RM10843 showed highest allelic number while RM140 and RM10748 showed lowest allelic number. Polymorphism information content (PIC) value varied from 0.1780 for RM10748 to 0.7659 for marker alleles. Based on the six SSR markers, 18 rice genotypes were clustered into two groups and salinity tolerant Pokkali accessions were grouped in a separate cluster. Salinity tolerant and susceptible genotypes were clearly discriminated by RM10852 marker in 3% agarose gel and positively associated with the result of the phenotypic screening. Therefore, the marker will be useful in Marker Assisted Selection (MAS) in rice breeding programmes for salinity tolerance.

Assessment of Marker Based Genotype Diversity of Saltol QTL in Relation to Seedling Stage Salinity Tolerance in Selected Rice Genotypes