Mapping additional QTLs from FR13A to increase submergence tolerance in rice beyond SUB1

Submergence is a common naturally occurring disaster in rice production in South and Southeast Asia. The development of mega-varieties with tolerance conferred by the SUB1 gene on chromosome 9 derived from FR13A that can withstand up to 2 weeks of complete submergence has been one of the best solutions. However, the recent severe conditions of flooding because of climate change, which has been predicted to become worse in the near future, calls for the development of an improved variety with superior tolerance of submergence. To search for novel quantitative trait loci (QTLs) that can complement the SUB1 gene, recombinant inbred lines (RILs) derived from an IR42/FR13A mapping population were explored. Five QTLs were detected on chromosomes 1, 4, 8, 9, and 10, four of which were from FR13A and one was from IR42. The study confirms the SUB1 QTL on chromosome 9 with a maximum LOD score of 19.51 and R-2 of 53.60 %. Additional novel QTLs coming from FR13A on chromosomes 1, 8, and 10 were identified with LOD scores of 5.16, 3.56, and 3.85 and R-2 of 23.33, 14.98, and 15.80 %, respectively. Interestingly, lines without SUB1 were still tolerant, with a maximum survival rate up to 95 % because of the presence of these additional QTLs. The non-SUB1 QTLs identified have great potential to enhance tolerance as evidenced by the superior tolerance of FR13A compared with that of the developed Sub1 lines. By transferring selected potential QTLs that are mostly additive to SUB1, it is hoped that crop damage from severe flooding can be significantly decreased.