Submergence Gene Sub1A Transfer into Drought-Tolerant japonica Rice DT3 Using Marker-Assisted Selection

Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress tolerance and can be selected using the marker-assisted backcross (MAB) breeding method. For foreground selection, Sub1A and SubAB1 were utilized as markers on the BC(2)F(1), BC(3)F(1), and BC(3)F(2) generations to select the submergence-tolerant gene, Sub1A. Background selection was performed in the Sub1A-BC(3)F(2) genotypes, and the percentages of recurrent parent recovery within individuals ranged from 84.7–99.55%. BC(3)F(3) genotypes (N = 100) were evaluated for agronomic traits, yield, and eating quality. Four of the eleven BC(3)F(4) lines showed good yield, yield component, grain, and eating quality. Four BC(3)F(4) lines, SU39, SU40, SU89, and SU92, exhibited desirable agronomic traits, including grain quality and palatability, consistent with those of DT3. These genotypes displayed a high survival rate between 92 and 96%, much better compared with DT3 with 64%, and demonstrated better drought tolerance compared to IR64 and IR96321-345-240. This study provides an efficient and precise MAB strategy for developing climate-resilient rice varieties with good grain quality for flood-prone regions.