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Rice line 1892S is an elite thermo-sensitive genic male sterile (TGMS) line for two-line hybrid rice production. However, 1892S is susceptible to rice blast, bacterial blight and submergence. Here we reported the introduction of blast resistance (R) gene Pi9, bacterial blight R gene Xa21 and submergence tolerance gene Sub1A into 1892S genetic background through backcrossing and marker-assisted selection. The improved TGMS line 31892S and its hybrids conferred disease resistance to rice blast and bacterial blight, and showed submergence tolerance for over 14 d without significant loss of viability. The sterility-fertility conversion of 31892S was similar to that of 1892S. 31892S and its derived hybrid rice had similar agronomic traits and grain quality with 1892S and the control hybrid rice, respectively. The newly developed 31892S provided an improved TGMS line for two-line hybrid rice production with disease resistance to rice blast and bacterial blight, and submergence tolerance with no yield penalty or change in grain quality.