Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice
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.
Authors
- Dongao Li (ORCID: https://orcid.org/0000-0001-5412-3741)
- Yong-Qing Qian (ORCID: https://orcid.org/0009-0000-5259-7441)
- Jiana Li (ORCID: https://orcid.org/0000-0002-1605-8528)
- Liezhao Liu (ORCID: https://orcid.org/0000-0001-5781-6121)
- Mingchao Qian
- Zu-Wen Zhou (ORCID: https://orcid.org/0000-0002-1879-5249)
- Tao Ouyang (ORCID: https://orcid.org/0000-0002-1907-3870)
- Jia‐Ming Song (ORCID: https://orcid.org/0000-0002-6636-4152)
- Jijing Luo (ORCID: https://orcid.org/0000-0001-5664-0881)
- Ru Li
- Ping Gan (ORCID: https://orcid.org/0009-0005-6606-5901)
- Ruimin Qiao (ORCID: https://orcid.org/0000-0002-2648-6227)
- Kun Lu (ORCID: https://orcid.org/0000-0003-1370-8633)
- Y. L. Tan
- Ling‐Ling Chen (ORCID: https://orcid.org/0000-0002-3005-526X)
Institutions
- Southwest University (CN)
- Guangxi University (CN)
- Ministry of Education (TH)
- National Hsinchu University of Education (TW)
- Ministry of Education and Child Care (CA)
- State Key Laboratory For Conservation and Utilization of Subtropical Agro-Bioresources (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-16
- DOI
- https://doi.org/10.1038/s41467-025-62887-4
- Citations
- 9
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 15.75
Funders
- National Natural Science Foundation of China
- Natural Science Foundation of Guangxi Province
- Centre Scientifique et Technique du Bâtiment
- Fundamental Research Funds for the Central Universities
- Division of Graduate Education