FINE-SCALE MAPPING OF THE RICE SUBMERGENCE TOLERANCE GENE

¹ Dep. of Agronomy & Range Science University of California Davis, CA 95616

² Dep. of Plant Pathology University of California Davis, CA 95616

³ USDA-ARS Crops Pathology & Genetics Unit Davis, CA

⁴ Dep. of Soil & Crop Sciences Crop Biotechnology Center Texas A&M University College Station, TX 77843

Rice (Oryza sativa L.) is a crop well suited to growth under submerged conditions. Submergence stress occurs in rainfed areas where water control is limited. Submergence is also a viable strategy for weed control, especially in water-seeded rice. The best source of submergence tolerance in rice is the Indian cultivar FR13A, a selection from a local land race. In 1995, we mapped a gene (Sub1) on chromosome 9 that controls most of this tolerance. This gene was mapped between two RFLP markers RZ698 and C1232, spanning a genetic distance of nearly 10 cM. We generated an F₂ population of 3000 plants to develop a fine-scale map around Sub1. The flanking RFLP markers were applied to the F₂ population and seed of plants with recombination between these markers were selected for submergence screening of the F₃ progeny. The RFLP marker R1164 mapped within 1 cM of Sub1. Several AFLP markers mapped within 0.1 cM of the gene. A microsatellite marker also appears to be closely linked to this gene, and is being used in a marker-assisted selection program to transfer the gene into a japonica rice cultivar. We are currently developing a BAC contig around Sub1 with clones from the Teqing BAC library. Isolation of the Sub1 gene through a positional cloning approach will allow direct transfer of the tolerance allele into intolerant cultivars and other species.