Development of partial inter-specific hybrid (PIH) rice is a promising approach for exploiting inter-specific heterosis between Oryza glaberrima and Oryza sativa. In the present study, the relationship between genetic distance (GD) of parental lines and yield performance of the PIHs was assessed using partial diallel crosses between three indica male sterile lines and 14 introgression lines (ILs) with different fragments of O. glaberrima genes. Twenty two out of the 42 PIHs expressed positive heterobeltiosis (i.e., the F
l hybrid showed superiority over the better parent in the target trait) for panicle number, spikelet number, thousand grain weight and grain yield/plant. The proportion of O. glaberrima genome in the ILs ranged from 0·03 to 0·41, as revealed by 16 informative simple sequence repeat markers. Significant positive correlations were found between the proportion of O. glaberrima genome of the ILs and the GD between the ILs and the three different female parents. Heterosis of spikelet number per panicle in the hybrids was positively proportional with the O. glaberrima genome content of the parental ILs, while that of fertile grain percentage was negatively proportional to the O. glaberrima genome proportion. On average, the PIHs with higher grain yield and highest heterobeltiosis were obtained from the ILs carrying between 0·15 and 0·30 of O. glaberrima genome. The results indicated that a small proportion (<0·15) of the O. glaberrima genome in the ILs might limit heterosis expression of spikelet number per panicle, while a very large proportion (>0·30) of the O. glaberrima genome decreased the grain filling percentage in the PIHs, thus an intermediate range of O. glaberrima genome proportion should be more suitable for breeding heterotic PIHs. The exploitation of inter-specific heterosis between O. glaberrima and O. sativa has potential value for heterotic breeding in rice.