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Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield ( qDTY   1.1   , qDTY   1.3  , and  qDTY   8.1  ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits ( qRT   9.1   for root-growth angle and  qRT   5.1   for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus  qDTY   1.1   was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0–22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations  qDTY   1.3  + qDTY   8.1   showed the highest mean grain yield advantage followed by lines having  qDTY   1.1  + qDTY   8.1   and  qDTY   1.1  + qDTY   8.1  + qDTY   1.3  , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.

Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions