Epistasis plays an important role as genetic basis of heterosis in rice.

The genetic basis of heterosis in rice was studied in a cross between Zhenshan 97 and Minghui 63, the parents of the best hybrid widely used in rice production in China. Field data for yield and yield components traits were collected over two years from 240 F(2:3) families of this cross planted in replicated field trials. These families were assayed with 151 marker loci that were polymorphic between the parents and a linkage map was constructed with Mapmaker analysis. A total of 32 quantitative trait loci (QTLs) were identified for yield and the three component traits: 12 QTLs were detected in both years and the remaining 20 QTLs were observed in only one year. A search for the entire genome by using two-way analyses of variance with all possible two-locus combinations detected a very large number of significant digenic interactions involving both the QTLs resolved by single-locus analysis and loci that did not show significant effects by single-locus analysis. Many of the interactions were simultaneously detected in both years. Partitioning of the epistatic interactions recovered all three types of interactions, i. e. additive by additive, additive by dominance and dominance by dominance, for all the traits. Some of the epistatic interactions even showed pleiotropic effects by simultaneously affecting two or more traits. The results clearly indicate that epistasis plays a significant role in the inheritance of yield traits as well as in the genetic basis of heterosis.