Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids

Background: Extensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F-1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions. Results: We report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637-3,824 genes from three rice F-1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F-1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F-1 and its parents, and almost all (97.3%) of the genes expressed in F-1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F-1 hybrids of rice. Conclusions: Analysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F-1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F-1 hybrids.