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Background  Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F 3:4  mapping populations derived from crosses of N22, a drought-tolerant  aus  cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.    Results  A major QTL for GY under RS,  qDTY 1.1  , was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years,  qDTY   1.1   showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS.  qDTY   1.1   also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.    Conclusions  This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.

qDTY 1.1 , a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds