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

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

机构地区：[1]Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518120,China [2]Rice Research Institute,Shenyang Agricultural University,Shenyang 110866,China [3]Yazhouwan National Laboratory,Sanya 572024,China [4]State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China [5]National Key Laboratory of Tropical Crop Breeding,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China

出　　处：《National Science Review》2024年第6期98-111,共14页国家科学评论（英文版）

基　　金：supported by the National Natural Science Foundation of China(32188102 and 32101718);the Guangdong Basic andApplied BasicResearch Foundation(2023B1515020053);the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSIAF-202303);the Youth Innovation of the Chinese Academy of Agricultural Sciences(Y2023QC36)。

摘　　要：Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highlyrepetitive. 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 bothcultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derivedstate using outgroups. We found TEs were one source of phenotypic variation during rice domesticationand differentiation. We identified 1246 genes whose expression variation was associated with TEs but notsingle-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB’s relative expressionactivity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detectmultiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions ofTEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for genecloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关 键 词：transposable element super pan-genome pan-TE RICE 

分 类 号：Q948[生物学—植物学]