Yan Tao, Kuang Liuhui, Gao Fei, Chen Jian, Li Lin, Wu Dezhi
College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
Yuelushan Laboratory, Changsha, 410128, China.
Plant J. 2025 Jan;121(2):e17218. doi: 10.1111/tpj.17218.
Rice (Oryza sativa L.) subspecies japonica and indica show distinct morphological and genetic differentiation. However, the differences in the genome-wide DNA methylation and its effects on gene expression and metabolic levels between japonica and indica rice remain unclear. In this study, we investigated the genome-wide DNA methylation, transcriptomes and metabolomes of 12 representative japonica and indica rice accessions, to reveal the differentiation between rice subspecies. We detected 83 327 differentially methylated regions (DMRs) and 14 903 DMR-associated genes between two subspecies. Indica rice showed significantly lower levels of the CG, CHG, and CHH methylation compared with japonica rice. Subsequently, we identified 5596 differentially expressed genes between the two subspecies, predominantly enriched in pathways related to carbohydrate and amino acid metabolism. By integrating DNA methylation with transcriptomic data, a significant correlation was established between methylation patterns and the expression level of key agronomic genes in rice. Furthermore, multi-omics analyses reveal that carbohydrate metabolism pathways, especially the tricarboxylic acid (TCA) cycle metabolites, are remarkable differentiation between rice subspecies. These results provide a foundation for future studies in rice domestication and genetic improvement.
水稻（Oryza sativa L.）的粳稻和籼稻亚种表现出明显的形态和遗传分化。然而，粳稻和籼稻在全基因组DNA甲基化及其对基因表达和代谢水平的影响方面的差异仍不清楚。在本研究中，我们调查了12个有代表性的粳稻和籼稻品种的全基因组DNA甲基化、转录组和代谢组，以揭示水稻亚种之间的分化。我们在两个亚种之间检测到83327个差异甲基化区域（DMR）和14903个与DMR相关的基因。与粳稻相比，籼稻的CG、CHG和CHH甲基化水平显著较低。随后，我们在两个亚种之间鉴定出5596个差异表达基因，主要富集在与碳水化合物和氨基酸代谢相关的途径中。通过将DNA甲基化与转录组数据整合，在水稻甲基化模式与关键农艺基因表达水平之间建立了显著的相关性。此外，多组学分析表明，碳水化合物代谢途径，尤其是三羧酸（TCA）循环代谢物，是水稻亚种之间的显著分化特征。这些结果为未来水稻驯化和遗传改良的研究奠定了基础。
