Heterosis refers to the phenomenon of the superior performance of a hybrid over its parents in terms of biomass development rates, yield, stress tolerance, and other agronomic traits , which is very important for agriculture production. Rice (Oryza sativa L.) is a staple food crop for more than half of the world's population. The ability to increase yield potential would be a critical factor in achieving the global rice requirement of 810 million tons by 2025 . Rice is also one of the most important crops which showed the greatest success on heterosis application. Hybrid rice that has a yield advantage of 10%-20% over the conventional varieties was developed and released commercially in the 1970s. The success of hybrid rice has made a great contribution to the self-sufficiency of the food supply in China and world food security. However, the molecular mechanism governing yield heterosis has not been elucidated to date .
Since George H. Shull rediscovered heterosis in 1908 , three major genetic models have been proposed to explain the mechanisms of heterosis [5, 6]. The first proposed hypothetical genetic mechanism was dominance , which states the heterosis caused by the complementation of deleterious recessive alleles . The over-dominance hypothesis attributes heterosis to the superior fitness of heterozygous genotypes over homozygous genotypes at a single locus . Epistasis hypothesis refers to the interaction between alleles from different loci . The current majority of genetic studies on heterosis mainly start from these three hypotheses. The heterosis phenomenon varied with species, traits, and parents . Thus, it is probable that no single genetic mechanism can adequately explain all aspects of that [9, 10]. In rice, dominance , over-dominance, and epistasis model  have been proposed underlying the heterosis mechanisms.
High-throughput sequencing technologies have enabled detailed investigations of the molecular basis of heterosis at the whole genome level [13–15]. With high-throughput sequencing and record the phenotypes of 10,074 F2 lines from 17 representative hybrid rice crosses, heterosis-associated loci were identified by GWAS analysis, revealing the genetic mechanisms of heterosis of three different hybrid rice systems [16, 17]. The advent of RNA-Seq has provided an opportunity for transcriptional profiling in heterosis studies [1, 18, 19]. At present, a series of phased progress results have been made in studying the molecular genetic mechanisms of heterosis through transcriptomics. In rice, Wei et al.  conducted a comparative analysis of gene expression in seven tissues, including leaves and spikes of super rice Liang-You-Pei-Jiu and its parents. A large number of differentially expressed genes in the F1 progeny were significantly higher than that of the parents. The differential gene expression between hybrid and parents can help to clarify the molecular mechanism underlying hybrid heterosis.
Allele-specific expression (ASE) is the phenomenon that only one of the parental alleles was transcribed in the hybrid, also played an important role in hybrid vigor [21–23]. A total of 3,270 ASE genes were identified in the F1 from the cross between ZS97 and MH63 in three tissues under four conditions and be further classified into two categories: 1) ASE genes biased toward one parental allele in all tissues/conditions, and 2) ASE genes biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The first type is associated with partial or complete dominance, while the second may lead to over-dominance .
Two elite hybrid varieties, Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ) with high yield heterosis, were certificated as super rice with high yielding ability by the Ministry of Agriculture and Rural Affairs of the People's Republic of China in 2017 and 2018, respectively. JLYHZ and LLYHZ all showed wide adaptability and got through all of the four state regional trials (the middle and lower reaches of Yangtze River, upper reaches of Yangtze River, South China, and Wuling Mountainous area) with an average increased yield of 6.7% and 7.3%, respectively, and certificated by the national new variety examination and approval committee (NNVEAC). Since getting the first new variety certification in 2015, JLYHZ and LLYHZ had become the top three widely cultivated hybrid rice varieties in China, with annual promotion areas of more than 313,111 and 258,667 hectares, respectively, during 2018–2020. In 2020, JLYHZ and LLYHZ promoted 326,000 and 215,333 hectares, and ranked the first and third most widely cultivated hybrid rice varieties in China, respectively. JLYHZ and LLYHZ were derived from the cross of two thermo-sensitive genic male sterile (TGMS) lines Jing4155S (J4155S), Longke638S (LK638S) with the common restorer line Hua-Zhan (HZ), respectively. J4155S and LK638S were two elite TGMS lines developed by Yuan Longping High-Tech Agriculture Co., Ltd. in 2014. By 2021, a total of 40 and 76 hybrid varieties derived from J4155S and LK638S have been developed and certificated by NNVEAC, respectively. The annual promotion area of hybrids of J4155S and LK638S has reached more than 2.5 million hectares in 2020. Female HZ is an elite two and three-line hybrid restorer line developed in the 2000s with high combining ability, high diseases resistance, high productive tiller number, moderate plant height, and high adaptability for different cultivation regions. At least a total of 158 hybrid varieties had been developed so far using HZ as the restorer line. To reveal the underlying mechanism of super hybrid rice, we performed transcriptome sequencing of leaves and panicles of two widely promoted super hybrid rice and their parental lines. Additionally, whole-genome resequencing was also performed on the parents to identify allele-specific expression. We identified actively and differentially expressed genes between two hybrids and their parental lines, and analyzed GO enrichment and KEGG enrichment for differential expressed genes. The transcriptome data and resequencing data were used to analyze the genome-wide allele-specific expression genes (ASEGs) of the two hybrids.