A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima

doi:10.16819/j.1001-7216.2026.250213

Abstract

Abstract: 【Objective】Transposable elements (TEs) are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice. However, due to the highly repetitive nature of TE sequences, their identification typically requires high-quality genome sequences. Currently, the limited genomic resources for African cultivated rice (Oryza glaberrima, Og) hinder systematic investigations into TE diversity and its contributions to the Og domestication process.【Method】We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions (11 Og and 10 Oryza barthii [Ob]). We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.【Result】The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb, with 61.7% of the TE variations larger than 1 kb. The total number of TE variations in the Ob accessions was greater than that in the Og accessions. A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process, which were significantly enriched in biological processes related to basic metabolism. Notably, 30 genes with known functions were involved in the independent domestication of Og.【Conclusion】This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process. The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.

Key words: Oryza glaberrima, Oryza barthii, transposable element, pan-genome, domestication

摘要： 【目的】转座子(TE)是水稻遗传多样性的重要来源，在亚洲栽培稻(Oryza sativa)的驯化过程中发挥了关键作用。然而，由于TE序列的高度重复性，其鉴定通常依赖于高质量的基因组序列。目前，非洲栽培稻(Oryza glaberrima，Og)的基因组资源有限，导致对其TE的多样性及其在驯化过程中的贡献仍然缺乏系统性研究。【方法】本研究基于11份Og和10份短舌野生稻(Oryza barthii，Ob)的染色体级别的基因组序列，构建了Og和Ob群体的高精度泛TE变异图谱。通过对该图谱进行选择性分析，鉴定了854个在Og驯化过程中受到选择的TE变异。【结果】该泛TE图谱共包含17,097个高质量的TE变异，覆盖基因组总长度39.1 Mb，其中61.7%的TE变异长度超过1 kb。Ob群体的TE变异总数高于Og群体。在Og驯化过程中，共鉴定出658个含受选择TE变异的基因，这些基因显著富集于基础代谢相关的生物过程，其中包括30个在Og独立驯化过程中发挥作用的已知功能基因。【结论】本研究揭示了TE变异是Og驯化过程中表型变异的重要来源，构建的高质量泛TE变异图谱不仅丰富了水稻育种的可用变异库，也为Og种质资源的遗传改良提供了重要的理论依据和资源支持。

关键词: 非洲栽培稻, 短舌野生稻, 转座子, 泛基因组, 驯化

LI Xiaoxia, ZHANG Tianchi, HE Wenchuang, HE Huiying, PAN Nan, LIU Yifan, QIAN Qian, SHANG Lianguang. A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima[J]. Chinese Journal OF Rice Science, 2026, 40(5): 598-606.

李笑霞, 张天驰, 贺文闯, 贺慧英, 盘楠, 刘祎凡, 钱前, 商连光. 泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用[J]. 中国水稻科学, 2026, 40(5): 598-606.

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