Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice
Abstract 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...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62887-4 |
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| author | Yongqing Qian Zuwen Zhou Tianmin Ouyang Dongao Li Ru Li Ping Gan Renfei Qiao Yingying Tan Mingchao Qian Liezhao Liu Jiana Li Kun Lu Jijing Luo Ling-Ling Chen Jia-Ming Song |
| author_facet | Yongqing Qian Zuwen Zhou Tianmin Ouyang Dongao Li Ru Li Ping Gan Renfei Qiao Yingying Tan Mingchao Qian Liezhao Liu Jiana Li Kun Lu Jijing Luo Ling-Ling Chen Jia-Ming Song |
| author_sort | Yongqing Qian |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-8471d2426f644eb3af3247bbcdce8b48 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-8471d2426f644eb3af3247bbcdce8b482025-08-20T03:47:12ZengNature PortfolioNature Communications2041-17232025-08-0116111610.1038/s41467-025-62887-4Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in riceYongqing Qian0Zuwen Zhou1Tianmin Ouyang2Dongao Li3Ru Li4Ping Gan5Renfei Qiao6Yingying Tan7Mingchao Qian8Liezhao Liu9Jiana Li10Kun Lu11Jijing Luo12Ling-Ling Chen13Jia-Ming Song14Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityState Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi UniversityIntegrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest UniversityAbstract 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.https://doi.org/10.1038/s41467-025-62887-4 |
| spellingShingle | Yongqing Qian Zuwen Zhou Tianmin Ouyang Dongao Li Ru Li Ping Gan Renfei Qiao Yingying Tan Mingchao Qian Liezhao Liu Jiana Li Kun Lu Jijing Luo Ling-Ling Chen Jia-Ming Song Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice Nature Communications |
| title | Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| title_full | Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| title_fullStr | Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| title_full_unstemmed | Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| title_short | Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| title_sort | pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice |
| url | https://doi.org/10.1038/s41467-025-62887-4 |
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