Plant Materials and Growth Conditions

Rice RILs from a cross between Taichung 65 (O. sativa L. ssp. japonica), and Bhadua (O. sativa L. ssp. indica; Bangladesh) were used in this study. Seed stocks for the RILs were provided by the National Bio-Resource Project (NBRP) in Japan. We used 85 RILs described by Nagai et al. (2014). The rice seeds were sterilized by boiling at 60°C for 10 min, allowed to germinate in water (30°C for 72 h), and then sown in June 2011 in perforated plastic pots (diameter 10 cm, height 12 cm) filled with soil. They were grown in the greenhouse under a natural light environment. During growth, the water level was beneath the soil surface (air conditions). One month after germination, eight-leaf-stage plants were put into the tank of 160 cm height and completely submerged in water for phenotypic evaluation or microarray analysis.