AbstractRice (Oryza sativaL.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between theindicaandjaponicarice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes atSb,Sc,SdandSeloci for F1male sterility and the gene atS5locus for F1female sterility. Theindica-compatiblejaponicalines (ICJLs) developed by pyramiding theindicaallele (S-i) atSb,Sc,SdandSeloci and the neutral allele (S-n) atS5locus injaponicagenetic background through marker-assisted selection are compatible withindicarice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.