Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Molecular Basis Of Submergence Tolerance In Rice

Kenong Xu¹ , Xia Xu¹ , Takeshi Fukao² , Patrick Canlas¹ , Reycel Maghirang-Rodriguez³ , Sigrid Heuer³ , Abdelbagi M. Ismail³ , Julia Bailey-Serres² , Pamela C. Ronald¹ , David J. Mackill³

¹  Department of Plant Pathology, University of California, Davis, CA 95616

²  Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521

³  International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines

Although rice is well known for its ability to grow in flooded soil, most rice cultivars die within a week of complete submergence. Short-term submergence frequently damages rice production in south and southeast Asia and causes annual losses of over US $1 billion in the world. A few cultivars, such as FR13A, are highly tolerant and survive up to two weeks of complete submergence. Our initial effort demonstrated that submergence tolerance inherited from FR13A is largely attributed to a major QTL Sub1 on chromosome 9. Using an F₂ population of 4,022 individuals, we delimited the Sub1 locus within an interval of 0.06 cM. The Sub1 locus physically spans over 182 kb and harbors a cluster of three genes encoding putative ethylene response factors (ERF). 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 Sub1A-1 (tolerant) and Sub1A-2 (intolerant) within those indica varieties that possess this gene. Overexpression of Sub1A-1 in a submergence-intolerant japonica rice conferred enhanced tolerance to the plants, downregulation of Sub1C and upregulation of alcohol dehydrogenase 1, indicating that Sub1A-1 is a primary determinant of submergence tolerance. Physiological experiments showed that Sub1 haplotype dictates positive and negative regulation of cellular and hormonal responses to submergence. The FR13A Sub1 locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. Cultivation of this new variety is expected to provide protection against damaging floods.