Qian Yongqing, Zhou Zuwen, Ouyang Tianmin, Li Dongao, Li Ru, Gan Ping, Qiao Renfei, Tan Yingying, Qian Mingchao, Liu Liezhao, Li Jiana, Lu Kun, Luo Jijing, Chen Ling-Ling, Song Jia-Ming
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, China.
Nat Commun. 2025 Aug 16;16(1):7634. doi: 10.1038/s41467-025-62887-4.
Transposable elements (TEs) introduce genetic and epigenetic variability, contributing to gene expression patterns that drive adaptive evolution in plants. Here, we investigate TE architecture and its effect on cold tolerance in rice. By analyzing a pangenome graph and the resequencing data of 165 rice accessions, we identify 30,316 transposable element insertion polymorphism (TIP) sites, highlighting significant diversity among polymorphic TEs (pTEs). We observe that pTEs exhibit increased H3K27me3 enrichment, suggesting a potential role in epigenetic differentiation under cold stress and in the transcriptional regulation of the cold response. We identify 26,914 TEs responsive to cold stress from transcriptome data, indicating their potential significance in regulatory networks for this response. Our TIP-GWAS analysis reveal two cold tolerance genes OsCACT and OsPTR. The biological functions of these genes are confirmed using knockout and overexpression lines. Our web tool ( https://cbi.gxu.edu.cn/RICEPTEDB/ ) makes all pTEs available to researchers for further analysis. These findings provide valuable targets for breeding cold-tolerant rice varieties, indicating the potential importance of pTEs in crop enhancement.
转座元件（TEs）引入遗传和表观遗传变异，有助于形成驱动植物适应性进化的基因表达模式。在此，我们研究了水稻中转座元件的结构及其对耐寒性的影响。通过分析泛基因组图谱和165份水稻种质的重测序数据，我们鉴定出30316个转座元件插入多态性（TIP）位点，突出了多态性转座元件（pTEs）之间的显著差异。我们观察到pTEs表现出H3K27me3富集增加，表明其在冷胁迫下的表观遗传分化以及冷响应的转录调控中可能发挥作用。我们从转录组数据中鉴定出26914个对冷胁迫有响应的转座元件，表明它们在该响应的调控网络中具有潜在重要性。我们的TIP-GWAS分析揭示了两个耐寒基因OsCACT和OsPTR。使用敲除和过表达株系证实了这些基因的生物学功能。我们的网络工具（https://cbi.gxu.edu.cn/RICEPTEDB/）使所有pTEs可供研究人员进一步分析。这些发现为培育耐寒水稻品种提供了有价值的靶点，表明pTEs在作物改良中的潜在重要性。
