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Development of rice varieties with sodicity tolerance would help to boost the rice productivity in salt affected areas of Tamil Nadu. A major QTL ‘Saltol’ has been reported to be responsible for conferring salt tolerance at seedling stage in rice. The present study was conducted to validate the ‘Saltol’ QTL under sodicity and to identify the reliable SSR marker tightly linked to this QTL. The results confirmed that ‘Saltol’ QTL worked under sodicity. The SSR markers viz., RM 3412, RM 10748 and SKC 2a especially in a combined manner is suggested to be used for discriminating sodicity tolerance and sensitivity. Possibilities of role of newer QTLs of Pokkali origin in conferring sodicity tolerance at seedling stage was also indicated