Zhao Yiyong, Li Tao, Liu Daliang, Yin Hao, Wang Liang, Lu Song, Yu Houlin, Sun Xinhao, Zhang Taikui, Zhao Quanzhi
Institute of Rice Industry Technology Research, College of Agriculture, Guizhou University, Guiyang, 550025, China.
State Key Laboratory of Public Big Data, College of Computer Science and Technology, Guizhou University, Guiyang, 550025, China.
BMC Biol. 2025 Jun 4;23(1):153. doi: 10.1186/s12915-025-02255-2.
Understanding the evolutionary history of cultivated rice (Oryza sativa) and the genomic basis of heterosis is crucial for advancing rice productivity and ensuring global food security. The origins of the two main subspecies, indica and japonica, remain contentious, with debates over single versus multiple domestication events. Additionally, the genetic mechanisms underlying heterosis in elite super-hybrid rice varieties are not fully elucidated.
We performed a comprehensive genome-scale phylogenomic analysis using 33 high-quality Oryzeae genomes, integrating 39,984 gene trees. Our findings support the independent origins of indica and japonica subspecies, with molecular dating and synonymous substitution rates indicating nearly synchronous evolutionary trajectories. Analysis of 1383 gene duplications in the common ancestor of O. sativa revealed their involvement in vital biological processes and environmental adaptability. Phylogenomic analyses revealed no significant genomic signatures indicative of extensive hybridization events between the progenitors of indica and japonica. Newly generated 71.67 Gb of whole-genome sequencing data of five elite super-hybrid rice varieties and their progenitors uncovered differential positive selection and genetic exchanges between subspecies, contributing to heterosis formation. Transcriptome analyses highlighted the predominance of non-additive gene expression in heterosis, especially in genes related to DNA repair and recombination. Furthermore, expression quantitative trait locus (eQTL) and de novo mutation analyses identified key developmental and stress response genes, offering potential targets for enhancing heterosis.
Our study provides robust evidence for the independent domestication of indica and japonica rice subspecies and elucidates the genomic features associated with heterosis in super-hybrid rice. By identifying key genes linked to adaptability and heterosis, we offer valuable insights and genetic resources for breeding programs aimed at improving rice yield and resilience. These findings enhance our understanding of rice evolution and the complex genetic factors driving heterosis, contributing to future strategies for agricultural productivity enhancement.
了解栽培稻（亚洲栽培稻）的进化历史以及杂种优势的基因组基础对于提高水稻产量和确保全球粮食安全至关重要。两个主要亚种籼稻和粳稻的起源仍存在争议，围绕是单次还是多次驯化事件存在争论。此外，优良超级杂交水稻品种中杂种优势的遗传机制尚未完全阐明。
我们使用33个高质量稻族基因组进行了全面的全基因组系统发育分析，整合了39984个基因树。我们的研究结果支持籼稻和粳稻亚种的独立起源，分子年代测定和同义替换率表明它们的进化轨迹几乎同步。对亚洲栽培稻共同祖先中1383个基因重复的分析表明，它们参与了重要的生物学过程和环境适应性。系统发育分析未发现表明籼稻和粳稻祖先之间存在广泛杂交事件的显著基因组特征。新生成的五个优良超级杂交水稻品种及其亲本的71.67Gb全基因组测序数据揭示了亚种间不同的正选择和基因交换，这有助于杂种优势的形成。转录组分析突出了杂种优势中非加性基因表达的主导地位，特别是与DNA修复和重组相关的基因。此外，表达数量性状位点（eQTL）和从头突变分析确定了关键的发育和应激反应基因，为增强杂种优势提供了潜在靶点。
我们的研究为籼稻和粳稻亚种的独立驯化提供了有力证据，并阐明了超级杂交水稻中与杂种优势相关的基因组特征。通过鉴定与适应性和杂种优势相关的关键基因，我们为旨在提高水稻产量和抗逆性的育种计划提供了有价值的见解和遗传资源。这些发现加深了我们对水稻进化以及驱动杂种优势的复杂遗传因素的理解，有助于未来提高农业生产力的策略制定。
