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

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

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
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.

transposable elementsuper pan-genomepan-TErice

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

展开 >

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

Rice Research Institute,Shenyang Agricultural University,Shenyang 110866,China

Yazhouwan National Laboratory,Sanya 572024,China

State Key Laboratory of Rice Biology,China National Rice Research Institute,Hangzhou 310006,China

National Key Laboratory of Tropical Crop Breeding,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou 571101,China

展开 >

National Natural Science Foundation of ChinaNational Natural Science Foundation of ChinaGuangdong Basic and Applied Basic Research FoundationInnovation Program of Chinese Academy of Agricultural sciencesYouth Innovation of the Chinese Academy of Agricultural Sciences

32188102321017182023B1515020053CAAS-CSIAF-202303Y2023QC36

2024

10.1093/nsr/nwae188

国家科学评论(英文版)

国家科学评论(英文版)

CSTPCD
ISSN：
年,卷(期)：2024.11(6)
  • 1