Tolerance of longer-term partial stagnant flooding is independent of the SUB1 locus in rice

► Stagnant flooding (SF) badly damage rice varieties especially when it occurs after submergence. ► Contrasting genotypes were evaluated under SF in field and greenhouse trials. ► SF is more severe when it follows complete submergence and shorter genotypes are most affected. ► SF tolerance is independent of SUB1, but both can be combined in high yielding varieties.