This may be related to poor Oxygen conditions in the root biosphere. leaf yellowing is (chlorophyll damage) the early symptoms of plant stress. However, yellowing is quicker under flooded condition than water stress though ABA regulation can be seen in both situations.
Such condition is called anoxia , the depletion of oxygen from the rhizosphere soil . And , plants will not be able to absorb the nutrients , despite their abundance in soil.
Unlike other crop plants, rice is comparatively well adapted to the anaerobic conditions so it should not be a problem at all. If the plants are completely submerged then it is different.
Kindly check the pH of the soil. Under high pH and in calcareous soils the rice often suffers from micronutrient deficiency including Fe, Zn and Mn. You should also try to look if all leaves or equally yellow or it is interveinal chlorosis and old leaves are comparatively green which could be typical symptom of Fe deficiency. Otherwise it may be due to poor retention of nitrogen.
Under several days of inundation plant suffers from anoxia, as Anoop Kumar Srivastava says. So Alternate wetting and drying (AWD irrigation system) of rice field allows rice plant to use nutrient properly.