Agronomic manipulations can enhance the productivity of anaerobic tolerant rice sown in flooded soils in rainfed areas

•The study is conducted in three experiments to determine the effectiveness of germination of IR64–AG cultivars under anoxia.•The different agronomic manipulations in IR64–AG lines with IR64 and IR64–Sub1 were evaluated under submerged condition.•AG cultivars recorded 120.9 and 98.1% higher germination than IR64 and IR64–Sub1, respectively.•Starch concentration under flooded conditions decreased relatively faster and sugar was maintained higher in AG cultivars leading to higher germination.•Higher seed rate and additional P application along with NPK proved its superiority in higher grain yield.