The developmental behavior of gene expression for transparency of rice (TR) was analyzed from two-year experimental data at different filling stages by using both conditional and unconditional analysis methods for quantitative traits of seeds in cereal crops. It was revealed that the gene expression was most active for the performance of TR at the middle and late filling stages (8-21 d after flowering). The differences of expression at different environments for triploid endosperm nuclear genes, cytoplasmic genes and diploid maternal plant nuclear genes were found for the performance of TR. The phenomena of which some genetic effects were spasmodically expressible were detected among filling stages of rice. Because of the higher additive and cytoplasmic effects along with their interaction effects for TR at the filling stages, the better improving effects for this trait could be expected by selection in rice breeding. Some parents such as Zhenan 3 and 1391 were better than others for improving TR.