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Background The exploitation of useful genes through interspecific and intersubspecific crosses has been an important strategy for the genetic improvement of rice. Postzygotic reproductive isolation routinely occurs to hinder the growth of pollen or embryo sacs during the reproductive development of the wide crosses. Result In this study, we investigated the genetic relationship between the hybrid breakdown of the population and transferred resistance genes derived from wide crosses using a near-isogenic population composed of 225 lines. Five loci ( qSS12 ,  qSS8 ,  qSS11 ,  ePS6 -1, and  ePS6 -2) associated with spikelet fertility (SF) were identified by QTL and epistatic analysis, and two out of five epistasis interactions were found between the three QTLs ( qSS12 ,  qSS8  and  qSS11 ) and background marker loci ( ePS6 -1 and  ePS6 -2) on chromosome 6. The results of the QTL combinations suggested a genetic model that explains most of the interactions between spikelet fertility and the detected loci with positive or negative effects. Moreover, the major-effect QTLs,  qSS12  and  qSS8 , which exhibited additive gene effects, were narrowed down to 82- and 200-kb regions on chromosomes 12 and 8, respectively. Of the 13 ORFs present in the target regions, Os12g0589400 and Os12g0589898 for  qSS12  and OS8g0298700 for  qSS8  induced significantly different expression levels of the candidate genes in rice at the young panicle stage. Conclusion The results will be useful for obtaining a further understanding of the mechanism causing the hybrid breakdown of a wide cross and will provide new information for developing rice cultivars with wide compatibility.

Identification of QTL Combinations that Cause Spikelet Sterility in Rice Derived from Interspecific Crosses