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Not AvailablePoor seedling emergence and establishment are a major restraint for adopting direct seeding in rice.This is especially critical in rainfed lowlands where floods can occur immediately after sowing, creat-ing anaerobic conditions during germination and early seedling growth. Developing rice cultivars thatcan germinate in flooded soils will ensure good crop establishment. Several major quantitative trait loci(QTLs) for tolerance of anaerobic conditions during germination (anaerobic germination; AG) were iden-tified from different landraces; and near isogenic lines (NILs) containing one of these QTLs (qAG-9-2, AG1)in the background of IR64 were developed. This study is an attempt to determine the effectiveness ofAG1 QTL in improving germination of two IR64-AG NILs; IR 93312-30-101-20-3-66-6 (IR64–AG131) andIR93312-30-101-20-13-64-21 (IR64-AG132) sown under flooded conditions. The study also evaluatedselected agronomic practices anticipated to further enhance crop establishment in flooded soils. IR64-AG NILs showed 81% and 217% higher plant populations over IR64-Sub1 and IR64, respectively, and thiswas also reflected as significantly higher grain yields. IR64-AG NILs mobilized relatively more starch intosoluble sugars while submerged and maintained higher soluble sugar supply to the developing embryoresulting in faster and higher germination rates than the non-AG genotypes. Agronomic manipulationslike higher seed rate (60 kg ha−1), better seeding methods and nutrient application improved seedlinggrowth after germination and emergence, increasing plant height, leaf area, number of tillers and biomassaccumulation. These improvements were reflected as higher grain yield even in the intolerant cultivarIR64. Application of 20% more phosphorus with the recommended N-P-K resulted in 21%, 16% and 19%higher grain yield in IR64-AG, IR64-Sub1 and IR64, respectively, over the control. The results establishedthat combining proper crop establishment practices with tolerant genotype could enhance crop estab-lishment in flooded soils using direct seeding methods, with consequent reduction in production costsand water use and subsequent increase in farmers’ income.ICA