Rice is the only crop adaptable for cultivation in the marshy saline coastal agroecosystem. Salinity is the second major abiotic stress that limits rice production. The widely cultivated rice variety Uma in Kerala is the best yielder, but only having moderate tolerance to salinity due to partial introgression of Saltol QTL from Pokkali being the male parent of Uma. In this study, complete introgression of Saltol QTL was effected through a Marker Assisted Precision Breeding using the donor parent FL-478 and confirmed through genotyping and phenotyping. The gene sequence of polymorphic foreground marker SKC-10, the key marker for salinity tolerance, was introgressed into Uma, to tailor it into a saline tolerant variety. The background genome recovery of Saltol introgressed inbred lines of Uma was assessed using genome-wide polymorphic SSR markers between the parents covering all the 12 chromosomes. The aim of the present study was to improve the salinity tolerance level of the most popular elite rice cultivar Uma of Kerala by applying precision molecular breeding techniques.