A total of 94 polymorphic SSR markers were used for genotyping of 90 F₄ plants. Among these, 56 markers fitted for the expected Mendelian ratio of segregation whereas, 38 significantly deviated from it (P<0.01). Only 63 SSR markers could be assigned to 12 linkage groups (LGs) covering a total of 1652.3 cM of the rice genome at an average marker density of 26.22 cM. The number of markers on each linkage group ranged from 3 (LG 10) to 7 (LG2 and LG 8). A total of 26 QTLs were identified for yield and physiological traits with the phenotypic variation ranging from 0.14% to 26.17%. Among these, 18 QTLs were identified under drought stress and remaining 8 QTLs were detected under irrigated conditions. The QTLs for days to 50% flowering remained consistent in the marker intervals of RM519-RM3331 on chromosome 12 under both hydrological conditions. Four QTLs were localized on the long arm of chromosome 1 between the marker intervals of RM3825-RM243. Thus, with further fine mapping of this region may identify some novel genes associated with drought tolerance which can be used in marker-assisted breeding (MAB) for the development of drought tolerant rice variety.