To access, purchase, authenticate, or subscribe to the full-text of this article, please visit this link: http://dx.doi.org/10.1186/s12284-018-0229-y Byline: Liang Chen (1,2), Jianmin Bian (1,2,3), Shilai Shi (1,2), Jianfeng Yu (1,2), Hira Khanzada (1,2), Ghulam Mustafa Wassan (1,2), Changlan Zhu (1,2,3), Xin Luo (1,2), Shan Tong (1,2), Xiaorong Yang (1,2), Xiaosong Peng (1,2,3), Shuang Yong (1), Qiuying Yu (1), Xiaopeng He (1,2), Junru Fu (1,2), Xiaorong Chen (1,2), Lifang Hu (1,2,3), Linjuan Ouyang (1,2), Haohua He (1,2,3) Keywords: Rice; Super-hybrid Rice; Heterosis; Grain number; RNA-seq Abstract: Background Despite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy. Results Here, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DG.sub.HP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DG.sub.HP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DG.sub.HP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DG.sub.HP enriched in the KEGG pathway with QTLs associated with grain number, several DG.sub.HP were located on the same chromosomal segment with some of these grain number QTLs. Conclusion Through young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DG.sub.HP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs. Author Affiliation: (1) 0000 0004 1808 3238, grid.411859.0, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China (2) 0000 0004 1808 3238, grid.411859.0, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China (3) Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Changsha, China Article History: Registration Date: 06/06/2018 Received Date: 17/01/2018 Accepted Date: 06/06/2018 Online Date: 15/06/2018 Article note: Liang Chen, Jianmin Bian and Shilai Shi contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1186/s12284-018-0229-y) contains supplementary material, which is available to authorized users.