Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations

Xiyu Tan; Wanyong Zeng; Yujian Yang; Zhansheng Lin; Fuquan Li; Jianhong Liu; Shaotong Chen; Yao-Guang Liu; Weibo Xie; Xianrong Xie

doi:10.1016/j.jgg.2025.03.005

Volume 52 Issue 6

Jun. 2025

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Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations

doi: 10.1016/j.jgg.2025.03.005

a. Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China;
b. National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, China

Funds:

This work was supported by the National Natural Science Foundation of China (32172010) and the Major Program of Guangdong Basic and Applied Basic Research (2019B030302006).

Received Date: 2025-03-03
Accepted Date: 2025-03-10
Rev Recd Date: 2025-03-10

Available Online: 2025-07-11

Publish Date: 2025-03-14

Abstract

Abstract

Short tandem repeats (STRs) modulate gene expression and contribute to trait variation. However, a systematic evaluation of the genomic characteristics of STRs has not been conducted, and their influence on gene expression in rice remains unclear. Here, we construct a map of 137,629 polymorphic STRs in the rice (Oryza sativa L.) genome using a population-scale resequencing dataset. A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency, mutational patterns, chromosomal distribution, and functional properties of STRs are correlated with the sequences and lengths of repeat motifs. Leveraging a transcriptome dataset from 127 rice accessions, we identify 44,672 expression STRs (eSTRs) by modeling gene expression in response to the length variation of STRs. These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures. Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits. By editing the (ACT)₇ STR in OsFD1 promoter, we further experimentally validate its role in regulating gene expression and phenotype. Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
- Gene expression,
- Genomic variation,
- Rice,
- Short tandem repeat,
- STR,
- Transcriptional regulation

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References

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