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Background  Combining ability is a measure for selecting elite parents that make the highest contributions to hybrid performance. However, the genetic bases of combining ability and how they contributed to heterosis is seldomly known.    Results  We constructed a both NCII and NCIII population derived from an  indica-japonica  cross to study the relationship among parental performance, combining ability and hybrid performance of 11 agronomic traits. Among them, specific combining ability is more important to grain yield than parental performance and general combining ability. We performed linkage analyses to phenotypic values and combining ability of all 11 traits in Doubled haploid lines and its two backcross populations and identified 108 QTLs in total. Among these QTLs, four known loci,  Sd1 ,  Ghd7 ,  Ghd8  and  DEP1  contribute a lot to GCA effects of agronomic traits except grain yield and seed setting rate. Three QTLs,  Ghd8 ,  S5  and  qS12 , contribute a lot to SCA effects of grain yield and present overdominace.    Conclusions  Our study provides insights into the genetic bases of combining ability and heterosis and will promote the improvements of  indica-japonica  hybrid breeding.    Electronic supplementary material  The online version of this article (10.1186/s12284-017-0179-9) contains supplementary material, which is available to authorized users.

Dissecting combining ability effect in a rice NCII-III population provides insights into heterosis in indica-japonica cross