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Background  Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of  qDTY   1.1  ,  qDTY   2.1  ,  qDTY   3.1   and  Sub1.  Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal.    Results  Grain yield advantage of the NILs with  qDTY   1.1    + qDTY   2.1   +  qDTY   3.1   +  Sub1  and  qDTY   2.1   +  qDTY   3.1   +  Sub1  ranged from 76 to 2479 kg ha − 1  and 396 to 2376 kg ha − 1  under non-stress (NS) respectively and 292 to 1118 kg ha − 1  and 284 to 2086 kg ha − 1  under reproductive drought stress (RS), respectively. The NIL, IR96322–34-223-B-1-1-1-1 having  qDTY   1.1    + qDTY   2.1   +  qDTY   3.1   +  Sub1  has been released as variety CR dhan 801 in India. IR 96321–1447-651-B-1-1-2 having  qDTY   1.1   +  qDTY   3.1   +  Sub 1  and IR 94391–131–358-19-B-1-1-1 having  qDTY   3.1   +  Sub1  have been released as varieties Bahuguni dhan-1′ and ‘Bahuguni dhan-2’ respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322–34-223-B-1-1-1-1, IR 96321–1447-651-B-1-1-2 and IR 94391–131–358-19-B-1-1-1 respectively on 6 K SNP Infinium chip.    Conclusion  The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha − 1  under reproductive stage drought stress and 0.1 to 1.0 t ha − 1  under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.    Electronic supplementary material  The online version of this article (10.1186/s12284-019-0269-y) contains supplementary material, which is available to authorized users.

Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas