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Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thought to contribute in drought resilience. Selection for root traits is hampered by difficulty in phenotypic measurements. Mapping quantitative trait loci (QTLs) for root traits and their use in marker assisted breeding (MAB) will hasten the development of genotypes with improved root system. Consistent QTLs for root traits have been mapped in rice. Developing and testing near iso-genic lines (NILs) with QTLs for root traits in target populations of environment (TPE) will help to verify the agronomic value of the QTLs. NILs were developed by introgression of three root QTLs from CT9993, an upland japonica into IR20, a lowland indica cultivar through MAB. Considerable variation in drought response and grain yield under rainfed condition in TPE was observed among the NILs. Five out of 41 NILs gave higher yields under rain-fed and irrigated conditions as compared to IR20. Two NILs viz. , 212 and 297, with three and two root QTLs, respectively had thicker and longer nodal roots and higher total and deep nodal root weights than IR20. In addition, NIL 297 had more nodal root volume and surface area, while NIL 212 had more number of nodal roots compared to IR20. Further evaluation of the NILs with farmers for yield and grain quality may help in identification of high-yielding, resilient rice suitable for drought-prone rainfed ecosystems. The NILs may also be useful to study the genes underlying the QTLs and their functions for drought resilience improvement in rice.