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A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

文献类型： 外文期刊

作者： Li, Xiaoxia 1 ; Dai, Xiaofan 1 ; He, Huiying 1 ; Lv, Yang 1 ; Yang, Longbo 1 ; He, Wenchuang 1 ; Liu, Congcong 1 ; Wei, Hua 1 ; Liu, Xiangpei 1 ; Yuan, Qiaoling 1 ; Wang, Xianmeng 1 ; Wang, Tianyi 1 ; Zhang, Bintao 1 ; Zhang, Hong 1 ; Chen, Wu 1 ; Leng, Yue 1 ; Yu, Xiaoman 1 ; Qian, Hongge 1 ; Zhang, Bin 1 ; Guo, Mingliang 1 ; Zhang, Zhipeng 1 ; Shi, Chuanlin 1 ; Zhang, Qianqian 1 ; Cui, Yan 1 ; Xu, Qiang 1 ; Cao, Xinglan 1 ; Chen, Dandan 1 ; Zhou, Yongfeng 1 ; Qian, Qian 1 ; Shang, Lianguang 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Shenzhen, Shenzhen Branch, Lab Lingnan, Shenzhen 518120, Guangdong, Peoples R China

2.Shenyang Agr Univ, Rice Res Inst, Shenyang 110866, Peoples R China

3.Yazhouwan Natl Lab, Sanya 572024, Peoples R China

4.China Natl Rice Res Inst, State Key Lab Rice Biol, Hangzhou 310006, Peoples R China

5.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Inst, Natl Key Lab Trop Crop Breeding, Haikou 571101, Peoples R China

关键词： transposable element; super pan-genome; pan-TE; rice

期刊名称：NATIONAL SCIENCE REVIEW （ 影响因子：16.3； 五年影响因子：18.6 ）

ISSN： 2095-5138

年卷期： 2024 年 11 卷 6 期

页码：

收录情况： SCI

摘要： Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

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