Rice is a staple food crop globally, and increasing its yield while maintaining or improving grain quality is a major challenge for food security. Hybrid rice, due to its heterosis (hybrid vigor), offers a significant advantage in yield. However, sometimes the quality of hybrid rice is compromised. Therefore, developing hybrid rice varieties that combine high yield with superior grain quality is a high priority in rice breeding research. Despite significant progress in hybrid rice breeding, the underlying molecular mechanisms responsible for yield heterosis and high-quality grain remain elusive. Understanding these mechanisms is essential for guiding future breeding efforts towards the development of even more productive and superior rice varieties. This study focuses on the hybrid rice variety Chuanyou6203 (CY6203), known for its high yield and exceptional grain quality, to investigate the molecular basis of these traits through an integrated approach of comparative transcriptomics and genomics. By comparing the transcriptome and genome of CY6203 with its parents, this research aims to identify key genes and pathways responsible for the observed heterosis and superior quality, providing valuable insights into the complex interplay of genetic and molecular factors governing rice yield and quality.

Previous research has explored the molecular mechanisms of heterosis in various crops, including rice. Several hypotheses, such as dominance, over-dominance, and epistasis, have been proposed to explain heterosis. Studies using serial analysis of gene expression (SAGE) and transcriptome analysis have identified differentially expressed genes (DEGs) between hybrid lines and their parents, suggesting that these DEGs play a significant role in heterosis. For instance, Bao et al. (2005) identified 3,926 DEGs in a hybrid rice strain (LYP9) and its parents. Similarly, Wei et al. (2009) conducted a transcriptomic analysis of superhybrid rice LYP9 and its parents, highlighting the importance of DEGs in heterosis. Other studies have focused on the role of polymorphic promoter cis-regulatory elements in regulating gene expression and contributing to both additive and non-additive gene action (Zhang et al., 2008). Huang et al. (2015) reported that numerous superior alleles contribute to heterosis, with a small number of loci exhibiting strong overdominance significantly affecting hybrid performance. The contribution of overdominant effects to grain number heterosis has also been reported (Chen et al., 2018). However, a comprehensive understanding of the molecular mechanisms underlying both high yield and superior grain quality in hybrid rice remains limited, underscoring the need for further investigation.

This study utilized a combination of genomic resequencing and RNA sequencing to analyze the hybrid rice variety Chuanyou6203 (CY6203) and its parents, Chuan 106B (C106B) and Chenghui 3203 (CH3203). The rice lines were grown under field conditions, and phenotypic data including yield and quality traits were collected. Genomic DNA was extracted from the parents (C106B and CH3203), and total RNA was extracted from panicles and flag leaves of CY6203 and its parents at three developmental stages: seven days before heading, three days after heading, and fifteen days after heading. Illumina sequencing was performed to generate genomic and transcriptomic data. The genomic data allowed for the identification of SNPs and InDels between the parents, revealing a total of 66,319 variations affecting 7473 genes. The transcriptomic data were mapped to the Nipponbare reference genome, and differentially expressed genes (DEGs) were identified using edgeR. The quality of RNA-Seq data was validated by qRT-PCR. A total of 39,503 DEGs were identified across all samples. Common DEGs between CY6203 and both parents were further analyzed. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify co-expressed gene modules. KEGG pathway and GO enrichment analysis were performed to annotate the functions of these modules. The expression levels of cloned genes previously associated with yield, quality, and KEGG pathways were compared between CY6203 and its parents. RNA editing events were also analyzed to assess the contribution of post-transcriptional modifications to heterosis. The analysis of variations and gene expression profiles provided a comprehensive understanding of the genetic and molecular basis of yield heterosis and quality in CY6203.

The study identified 66,319 SNPs and InDels between the two parents of CY6203, affecting 7,473 genes. A significant number of common DEGs (differentially expressed genes) were found between CY6203 and both parents across different developmental stages and tissues. The number of upregulated DEGs between CY6203 and CH3203 was consistently higher than those between CY6203 and C106B. Analysis of mRNA editing revealed that approximately 40.61% of editing ratios fell between 0.4 and 0.6, indicating balanced expression from both parents. A small percentage (1.68%) exhibited editing ratios ≥ 0.8, favoring one parent, suggesting the involvement of dominance or epistasis in the heterosis mechanism. WGCNA identified 19 modules of co-expressed genes. The green-yellow module was significantly enriched in pathways related to photosynthesis, nitrogen metabolism, and carbon fixation, suggesting a major contribution to yield heterosis. The balanced expression of major high-quality alleles from both parents in CY6203 was determined to contribute to its superior grain quality. Specifically, the balanced expression of genes related to amylose content (AC), gel consistency (GC), and alkali spreading value (ASV) in CY6203 likely resulted in its superior quality.

The findings indicate that the high yield and quality of CY6203 are the result of a complex interplay of genetic and epigenetic factors. The significant enrichment of the green-yellow module in pathways related to photosynthesis and nitrogen metabolism suggests that enhanced photosynthetic efficiency and nitrogen utilization contribute significantly to the increased yield observed in CY6203. The balanced expression of alleles from both parents for genes controlling grain quality traits such as AC, GC, and ASV explains its superior quality compared to the parents. The observation of mRNA editing events favoring one parent in a small subset of genes supports the involvement of dominance or epistasis in the heterosis mechanism. The results highlight the importance of both additive and non-additive genetic effects in determining the phenotype of hybrid rice. This integrated approach of transcriptomics and genomics is effective in elucidating the molecular basis of hybrid rice traits.

This study provides a comprehensive analysis of the transcriptome and genome of the high-yielding, high-quality hybrid rice variety CY6203 and its parents. The findings reveal a complex interplay of genetic and epigenetic mechanisms contributing to its superior performance. Key genes and pathways associated with yield heterosis (photosynthesis, nitrogen metabolism) and quality traits (amylose content, gel consistency, alkali spreading value) have been identified. This research offers valuable insights into the molecular basis of hybrid rice improvement and can guide future breeding strategies towards developing superior rice varieties. Future studies could focus on further dissecting the regulatory networks governing the identified genes and pathways, as well as exploring the potential for manipulating these networks to enhance yield and quality in rice.

The study is limited to a single hybrid rice variety and its parents, thus generalizability might be limited. Environmental factors during the growth period could have influenced the results. While RNA editing was analyzed, it remains incompletely understood and further investigation of its full contribution to the phenotype is needed. The study focused mainly on transcriptional changes, and post-transcriptional and translational regulations were not fully explored.