A set of 148 F9 recombinant inbred lines(RILs) was developed from the cross of an indica cultivar 93-11 and japonica cultivar DT713,showing strong F1 heterosis.Subsequently,two backcross F1(BCF1) populations were constructed by backcrossing these 148 RILs to two parents,93-11 and DT713.These three related populations(281BCF1 lines,148 RILs) were phenotyped for six yield-related traits in two locations.Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed in the two BCF1 populations.A total of 42 main-effect quantitative trait loci(M-QTLs) and 109 epistatic effect QTL pairs(E-QTLs) were detected in the three related populations using the mixed model approach.By comparing the genetic effects of these QTLs detected in the RILs,BCF1 performance and mid-parental heterosis(HMP),we found that,in both BCF1 populations,the QTLs detected could be classified into two predominant types:additive and over-dominant loci,which indicated that the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs.Further,we found that the E-QTLs detected collectively explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations.All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice. A set of 148 F9 recombinant in lines (RILs) was developed from the cross of an indica cultivar 93-11 and japonica cultivar DT713, showing strong F1 heterosis. The resulting two backcross F1 (BCF1) populations were constructed by backcrossing these 148 RILs to two parents, 93-11 and DT713.These three related populations (281BCF1 lines, 148 RILs) were phenotyped for six yield-related traits in two locations. Significant inbreeding depression was detected in the population of RILS and a high level of heterosis was observed A total of 42 major-effect quantitative trait loci (M-QTLs) and 109 epistatic effect QTL pairs (E-QTLs) were detected in the three related populations using the mixed model approach. of these QTLs detected in the RILs, BCF1 performance and mid-parental heterosis (HMP), we found that, in both BCF1 populations, the QTLs detected could be classified into two predominant types: additive and over-dominant loci, which indicates tha t the additive and over-dominant effect were more important than complete or partially dominance for M-QTLs and E-QTLs.Further, we found that the E-QTLs gave explained a larger portion of the total phenotypic variation than the M-QTLs in both RILs and BCF1 populations. All of these results suggest that additive and over-dominance resulting from epistatic loci might be the primary genetic basis of heterosis in rice.