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Identifying the genomic regions (quantitative trait loci (QTL)) significantly linked to grain yield under drought stress could expedite the development of novel rice cultivars suited for rainfed areas through marker‐assisted breeding. This study identified QTL regions linked to plant phenology and production traits by evaluating 122 recombinant inbred lines (RILs) of Danteshwari × Daggaddeshi under different environmental conditions. A consistent QTL region associated with grain yield under water stress (60.4 Mbp) was mapped on chromosome 1 between RM428 and RM24 with an LOD score of 4.0. Another QTL region (9.4 Mbp) linked to plant height under all environmental conditions was mapped on chromosome 1 between RM1‐HvSSR1‐87 with a LOD score of 7.5 and phenotypic variance of 25%. A core set of 402 diverse rice accessions was also evaluated under water stress conditions and subjected to genome‐wide association analysis. Twelve markers linked to grain yield under drought were identified, out of which five were significantly associated with grain yield and days to flowering under drought. The markers linked to grain yield were compared between the bi‐parental population and germplasm accessions to identify the common markers. Three markers (RM1, RM259 and RM201) were found to be consistently linked to drought stress across the seasons in both bi‐parental population and germplasm accessions studied and could be potential candidates for application in marker‐assisted selection for improving grain yield under drought stress in rice. [ABSTRACT FROM AUTHOR]