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Extensively Current Activity of Transposable Elements in Natural Rice Accessions Revealed by Singleton Insertions

文献类型： 外文期刊

作者： Liu, Zhen 1 ; Zhao, Han 3 ; Yan, Yan 2 ; Wei, Ming-Xiao 2 ; Zheng, Yun-Chao 2 ; Yue, Er-Kui 2 ; Alam, Mohammad Shah 2 ; Smartt, Kwesi Odel 2 ; Duan, Ming-Hua 4 ; Xu, Jian-Hong 1 ;

作者机构： 1.Zhejiang Univ, Hainan Inst, Sanya, Peoples R China

2.Zhejiang Univ, Inst Crop Sci, Zhejiang Key Lab Crop Germplasm, Hangzhou, Peoples R China

3.Jiangsu Acad Agr Sci, Inst Biotechnol, Jiangsu Prov Key Lab Agrobiol, Nanjing, Peoples R China

4.Zhejiang Zhengjingyuan Pharm Chain Co Ltd, Hangzhou, Peoples R China

5.Hangzhou Zhengcaiyuan Pharmaceut Co Ltd, Hangzhou, Peoples R China

关键词： transposable element (TE); transposition activity; singleton insertion; unique insertion site; rice (Oryza sativa)

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）

ISSN： 1664-462X

年卷期： 2021 年 12 卷

页码：

收录情况： SCI

摘要： Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.

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