Peng Xin, Wu Yahui, Gan Yuli, Tan Jiantao, Qian Qian, Shen MengYuan, Sun Kangli, Huo Xing, Zhou Degui, Liu Qi
Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Rice Science and Technology, Guangdong Rice Engineering Laboratory, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
Institute of Grain and Oil Crops, Meizhou Academy of Agricultural and Forestry Sciences, Meizhou, China.
Plant J. 2025 Sep;123(5):e70471. doi: 10.1111/tpj.70471.
Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the Oryza genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific Oryza hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using Oryza sativa L. ssp. japonica cv. Nipponbare (NIP), Oryza rufipogon Griff. acc. CWR, and their resulting F hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.
杂种优势，即杂交活力，是指杂种与其亲本相比具有更优越的表型，在农业中得到广泛应用。稻属种间杂种在水稻品种的系统改良方面显示出巨大潜力。然而，稻属种间杂种杂种优势的分子机制仍不清楚。在这里，我们利用粳稻品种日本晴（NIP）、野生稻（CWR）及其杂交F1代（命名为NC），系统地进行了表型鉴定、全基因组亚硫酸氢盐测序、RNA测序和小RNA分析。NIP和CWR表现出明显的表型和分子差异。种间杂种NC表现出显著的产量杂种优势。在杂种中，大多数表观遗传和转录特征相对于亲本表现出加性遗传模式。分析表明，驯化选择基因在杂种和亲本系中均保持相对较低的DNA甲基化水平和较高的表达水平。此外，我们发现非加性miRNA可能参与调控杂种的育性、细胞生长和细胞分裂过程。DNA甲基化水平与基因表达之间存在显著的负相关。功能富集分析表明，杂种中差异表达基因（DEGs）与开花时间调控、碳水化合物代谢、光合作用、蛋白质磷酸化、种子发育和防御反应显著相关。通过加权基因共表达网络分析，我们鉴定了102个功能基因模块，其中6个与产量相关杂种优势显著相关。总之，我们的研究结果为理解优良品种与野生稻亲缘种间杂交提供了一个多组学框架，突出了野生稻作为水稻改良未开发遗传资源的重要性。
