43. RAPD and RFLP mapping of a submergence tolerance locus in rice
        Kenong Xu and David J. Mackill
        Department of Agronomy and Range Science and USDA-ARS
        University of California, Davis, CA 95616, USA     Submergence tolerance is an important characterisitc to breed into improved rice cultivars for rainfed lowland and deepwater areas. It may also be useful as a strategy for weed management in areas where rice is seeded directly into standing water, and deeper water levels (20cm) can be used for weed suppression. Genetic studies have been conducted (Mohanty et al. 1982; Haque et al. 1989), but the specific genes controlling tolerance have not been identified.
    We studied the inheritance of submergence tolerance in a cross between the highly tolerant indica line IR40931-26-3-3-5 and the susceptible japonica line P1543851. IR40931-26 has a similar level of tolerance to FR13A, from which it derived the trait (Mackill et al. 1993). At 8 DAS, F3 families were subjected to 14-16 d submergence in greenhouse tanks. Individual plants were scored on a scale of 1 (tolerance) to 9 (susceptible) 1 wk after the water was removed.
    Differences among F3 families were highly significant, and means ranged from 1.6 to 8.9, compared to 1.5 and 8.4 for the tolerant and susceptible families. DNA from the F2 plants giving rise to the nine most tolerant and most susceptible F2 families were bulked and assayed with 624 RAPD markers. Five RAPD bands associated with either the tolerant or susceptible families were asseyed on the entire F2 population. These five bands were linked to each other. RFLP markers from Cornell University, USA (McCouch et al. 1988), and from the Rice Genome Program, STAFF Institute, Tsukuba, Japan (Kurata et al. 1994) were used to map these RAPD markers to the end of chromosome 9 (Fig. 1). Analysis by Mapmaker/QTL (Lincoln et al. 1992) identified a locus near the RFLP


Fig. 1. RFLP map of rice chromosome 9 showing RAPD and RFLP markers and putative location of Sub-1(t) (dark bar) based on Mapmaker/QTL analysis. marker C1232 responsible for 69% of the phenotypic variance for this trait. An additional 79 markers distributed on the other rice chromosomes did not detect QTLs. It is not clear whether this locus represents a single gene, or closely linked genes or loci. We have tentatively designated this locus as Sub-l(t). Identification of molecular markers closely linked to Sub-1(t) should greatly facilitate the transfer of submergence tolerance into improved lines.

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