Towards positional cloning of the rice submergence tolerance locus Sub1

Submergence stress is one of the primary constraints to the rice production in South and Southeast Asian. It is also common in the United States where rice is seeded directly into standing water. Rice cultivars showing submergence tolerance have been known for more than 40 years. Although extensive studies have been conducted on this trait, genes controlling the tolerance have not been identified until this study. Using molecular markers, a locus conferring submergence tolerance was mapped on rice chromosome 9 in an interval of 11 cM between two RFLP markers, RZ698 and C1232. This locus, designated as Sub1, exerts a major effect on the expression of submergence tolerance. It explained about 70% of the phenotypic variation in the F ₂ mapping population consisting of 169 individuals.;Because of the prevalence of submergence stress and the significant effect of Sub1, it would be desirable to isolate it. In order to accomplish the isolation of Sub1, the positional cloning approach has been employed. This strategy was chosen in this study because the function of Sub1 was not known and rice has the smallest genome in monocotyledonous crops, making it suitable for such an approach. As the first step towards positional cloning of Sub1, a high resolution genetic map in the Sub1 region was constructed using AFLP markers in a large F₂ population comprising 2,950 plants. There are ten AFLP markers closely linked to Sub1, with two cosegregating with the locus and eight within a 0.2-cM interval from Sub1 towards C1232 (or R1164). Flanking markers linked to Sub1 more tightly on the RZ698 side were however not identified. This high resolution map was subsequently enhanced with RAPD and RFLP markers derived from BAC clones. On the basis of the high resolution map enriched with more markers, a BAC contig spanning Sub1 was constructed. The physical location of Sub1 is most likely encompassed in BAC clone TQH17P5 (or TQH9D24) with a size of 75 kb if the Sub1 locus is not surprisingly large.