1. Department of Plant Pathology, University of California, Davis, California 95616, USA
2. Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124, USA
3. International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines

Correspondence to: Pamela C. Ronald¹David J. Mackill³ Correspondence and requests for materials should be addressed to P.C.R. (Email: pcronald@ucdavis.edu) or D.J.M. (Email: d.mackill@cgiar.org). Sequences were submitted to GenBank/EMBL/DDJB under accession numbers DQ011597–DQ011607 and DQ453964–DQ453966.

Most Oryza sativa cultivars die within a week of complete submergence—a major constraint to rice production in south and southeast Asia that causes annual losses of over US$1 billion and affects disproportionately the poorest farmers in the world^{1, 2}. A few cultivars, such as the O. sativa ssp. indica cultivar FR13A, are highly tolerant and survive up to two weeks of complete submergence owing to a major quantitative trait locus designated Submergence 1 (Sub1) near the centromere of chromosome 9 (refs 3 , 4 , 5 –6). Here we describe the identification of 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 analysed. 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.

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