Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice

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 () and Jia-Ming Song ()
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Yongqing Qian: Southwest University
Zuwen Zhou: Guangxi University
Tianmin Ouyang: Guangxi University
Dongao Li: Guangxi University
Ru Li: Guangxi University
Ping Gan: Guangxi University
Renfei Qiao: Guangxi University
Yingying Tan: Southwest University
Mingchao Qian: Southwest University
Liezhao Liu: Southwest University
Jiana Li: Southwest University
Kun Lu: Southwest University
Jijing Luo: Guangxi University
Ling-Ling Chen: Guangxi University
Jia-Ming Song: Southwest University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-62887-4

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