Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Researchers identified a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analyzed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers. Submergence of plants inhibits aerobic respiration and photosynthesis, and stimulates a variety of responses that can enhance survival, such as a switch from aerobic to anaerobic respiration. In contrast to deep-water rice cultivars that avoid submergence stress by growing above the water surface and thereby restoring gas exchange, submergence-tolerant rice can survive 10–14 days of complete submergence and renew growth when the water subsides. The Sub1 locus was mapped to an interval of 0.06 centimorgans on chromosome 9 using a mapping population. The Sub1 region, bordered by the markers CR25K and SSR1A, physically spans over 182 kilobases. This interval encodes three genes containing ethylene-response-factor (ERF) domains and designated Sub1A, Sub1B and Sub1C, ten non-ERF genes, and over 50% retrotransposon-related sequences. Plant proteins that contain ERF domains are known regulators of abiotic and biotic stress responses. The accumulation of Sub1A and Sub1C messenger RNAs was strongly but transiently promoted by submergence and further reduced on de-submergence in seedling leaves of tolerant FR13A. Sub1C mRNA induction was earlier and more pronounced in intolerant Nipponbare compared with FR13A, suggesting that the rapid induction of Sub1A limits expression of Sub1C. Adh1 gene transcript levels were more strongly induced in the tolerant line, indicating that Sub1A may positively regulate certain acclimation responses. The three SUB1Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Researchers identified a cluster of three genes at the Sub1 locus, encoding putative ethylene response factors. Two of these genes, Sub1B and Sub1C, are invariably present in the Sub1 region of all rice accessions analyzed. In contrast, the presence of Sub1A is variable. A survey identified two alleles within those indica varieties that possess this gene: a tolerance-specific allele named Sub1A-1 and an intolerance-specific allele named Sub1A-2. Overexpression of Sub1A-1 in a submergence-intolerant O. sativa ssp. japonica conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of Alcohol dehydrogenase 1 (Adh1), indicating that Sub1A-1 is a primary determinant of submergence tolerance. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers. Submergence of plants inhibits aerobic respiration and photosynthesis, and stimulates a variety of responses that can enhance survival, such as a switch from aerobic to anaerobic respiration. In contrast to deep-water rice cultivars that avoid submergence stress by growing above the water surface and thereby restoring gas exchange, submergence-tolerant rice can survive 10–14 days of complete submergence and renew growth when the water subsides. The Sub1 locus was mapped to an interval of 0.06 centimorgans on chromosome 9 using a mapping population. The Sub1 region, bordered by the markers CR25K and SSR1A, physically spans over 182 kilobases. This interval encodes three genes containing ethylene-response-factor (ERF) domains and designated Sub1A, Sub1B and Sub1C, ten non-ERF genes, and over 50% retrotransposon-related sequences. Plant proteins that contain ERF domains are known regulators of abiotic and biotic stress responses. The accumulation of Sub1A and Sub1C messenger RNAs was strongly but transiently promoted by submergence and further reduced on de-submergence in seedling leaves of tolerant FR13A. Sub1C mRNA induction was earlier and more pronounced in intolerant Nipponbare compared with FR13A, suggesting that the rapid induction of Sub1A limits expression of Sub1C. Adh1 gene transcript levels were more strongly induced in the tolerant line, indicating that Sub1A may positively regulate certain acclimation responses. The three SUB1