Predicting hybrid fertility from maker-based genetic divergence index of parental varieties: implications for utilizing inter-subspecies heterosis in hybrid rice breeding

Utilizing inter-subspecies heterosis of indica-japonica rice hybrids is a potential solution to break the yield ceiling for hybrid rice breeding. However, the reduced panicle fertility (PF) of the inter-subspecies hybrids caused by reproductive isolation due to genetic divergence between parental varieties has hampered the effective utilization of the inter-subspecies heterosis. This is because significantly reduced fertility always leads to low yield of the F1 hybrids. To study the association between genetic divergence of indica-japonica parental varieties and panicle fertility of their inter-subspecies hybrids, we developed a method to determine the genetic divergence index (GDI) of the two parents, assisted by the insertion/deletion (InDel) molecular genotyping. Based on parents’ GDI, we produced 103 combinations of F1 hybrids whose parental varieties showed a wide range of indica-japonica genetic divergence. PF of all the F1 hybrids in different combinations was measured to analyze its association with GDI of their corresponding parents. A negative correlation between GDI of indica-japonica parental varieties and PF of their corresponding F1 hybrids was detected based on field experiments conducted in three independent locations. The results suggested that GDI of parental varieties can be used to predict PF of their indica-japonica hybrids before a hybridization experiment is conducted. The molecular-maker-based GDI provides a useful tool to assist in selecting indica and japonica parental varieties for hybrid rice breeding in a more designed manner to achieve reasonable heterosis and panicle fertilities in F1 hybrids.