The application of heterosis during plant breeding increases rice grain yield. However, there have been limited studies on heterosis during rice grain development during the grain-filling stage; therefore, the genetic basis of heterosis for grain development during the grain-filling stage should be highly valued. In this study, a hybrid combination with the super hybrid rice WFYT025 was used to perform a transcriptomic dynamic analysis in grains at the beginning and middle grain-filling stages. A total of 1556 and 1507 transcripts that were differentially expressed between WFYT025 and its parents (DGHP) were identified at 1-day post-anthesis (DPA) and at 10 DPA, respectively. The analysis of the genetic effects of heterosis showed that the over-dominant effect (66.90% and 55.87%) was the main mode of action during grain development. The KEGG pathway and GO analysis of the DGHP indicated that the gibberellin biosynthetic, starch metabolic, and diterpenoid biosynthetic signaling pathways may be associated with heterosis during grain development. To further explore the candidate genes for grain development heterosis, a recombinant inbred line (RILs) population with a high-density genetic map of 2578 bin markers was constructed by crossing the parents of WFYT025, and nine stable QTLs for grain weight-related traits were identified. By comparing the DGHP with 20 QTLs, LOC_Os02g28820, LOC_Os02g32580, LOC_Os04g25440, and LOC_Os12g04980 were identified as grain development heterosis-related candidate genes. These findings provide resources for the study of heterosis during the grain development of super hybrid rice and provide valuable theoretical references for the cloning and functional analysis of heterosis-related genes.
