IntroductionDrought and submergence are contrasting abiotic stresses that often occur in the same rice crop season and cause complete crop failure in many rain-fed lowland areas of Asia.MethodsTo develop rice varieties with good tolerances to drought and submergence, 260 introgression lines (ILs) selected for drought tolerance (DT) from nine BC2populations were screened for submergence tolerance (ST), resulting in 124 ILs with significantly improved ST.ResultsGenetic characterization of the 260 ILs with DNA markers identified 59 DT quantitative trait loci (QTLs) and 68 ST QTLs with an average 55% of the identified QTLs associated with both DT and ST. Approximately 50% of the DT QTLs showed ‘epigenetic’ segregation with very high donor introgression and/or loss of heterozygosity (LOH). Detailed comparison of the ST QTLs identified in ILs selected only for ST with ST QTLs detected in the DT-ST selected ILs of the same populations revealed three groups of QTLs underlying the relationship between DT and ST in rice: a) QTLs with pleiotropic effects on both DT and ST; b) QTLs with opposite effects on DT and ST; and c) QTLs with independent effects on DT and ST. Combined evidence identified most likely candidate genes for eight major QTLs affecting both DT and ST. Moreover, group b QTLs were involved in theSub1regulated pathway that were negatively associated with most group aQTLs.DiscussionThese results were consistent with the current knowledge that DT and ST in rice are controlled by complex cross-talks between or among different phytohormone-mediated signaling pathways. Again, the results demonstrated that the strategy of selective introgression was powerful and efficient for simultaneous improvement and genetic dissection of multiple complex traits, including DT and ST.