Predicting the relationship between molecular marker heterozygosity and hybrid performance using RAPD markers in rice (Oryza sativa L.)

Successful prediction of heterosis and performance of F-1-hybrids from genetic similarity of their parents based on molecular markers has been reported in various crops. Estimation of genetic diversity and distance among various rice (Oryza sativa L.) genotypes and the correlation between genetic distance (GD) and hybrid performance would determine breeding strategies, define heterotic groups and predict future hybrid performance. In the present study, we surveyed genetic divergence among 26 rice genotypes using DNA markers and assessed the relationship between genetic distance and hybrid performance of 64 hybrids in a Line x Tester (4 lines x 16 testers) mating design. The 64 F-1 hybrids together with the 20 parents were evaluated for nine traits of agronomic importance, including yield, in a replicated field trial. The 20 parents along with the other six rice varieties were examined for DNA polymorphism using 53 random decamer oligonucleotide primers of which 36 primers generated clear banding profiles. A total of 245 polymorphic variants were generated and based on the polymorphism data, genetic distances (GDs) ranged from 0.23 to 0.53. Heterosis was observed in hybrids for most of the traits and yield exhibited the highest heterosis among the nine traits examined. The correlation values of GDs with F1 performance were mostly non-significant, except for days to 50% flowering and test weight. The correlations of GDs with mid parent, better-parent heterosis and standard heterosis were not significant enough to be of predictive value. However, when specific combining ability (SCA) value was correlated with GD values of a group of hybrid (BPT 5204), there was high significance pertaining to a particular hybrid with relatively higher yield. These results indicated that GDs based on the random amplified polymorphic DNA (RAPD) markers may be useful for predicting heterotic combinations in rice and support the idea that the level of correlation between hybrid performance and genetic divergence is dependent on the germplasm used.