Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions
文献类型： 外文期刊
作者： Zhang, Yuanyuan 1 ; Yang, Zhiquan 2 ; He, Yizhou 1 ; Liu, Dongxu 2 ; Liu, Yueying 1 ; Liang, Congyuan 2 ; Xie, Meili 1 ; Jia, Yupeng 2 ; Ke, Qinglin 1 ; Zhou, Yongming 2 ; Cheng, Xiaohui 1 ; Huang, Junyan 1 ; Liu, Lijiang 1 ; Xiang, Yang 4 ; Raman, Harsh 5 ; Kliebenstein, Daniel J. 6 ; Liu, Shengyi 1 ; Yang, Qing-Yong 2 ;
作者机构： 1.Chinese Acad Agr Sci, Oil Crops Res Inst, Key Lab Biol & Genet Improvement Oil Crops, Minist Agr PRC, Wuhan, Peoples R China
2.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Hubei Hongshan Lab, Wuhan, Peoples R China
3.Guangzhou Univ, Sch Life Sci, Innovat Ctr Mol Genet & Evolut, Guangzhou, Peoples R China
4.Guizhou Acad Agr Sci, Guizhou Rapeseed Inst, Guiyang, Peoples R China
5.Wagga Wagga Agr Inst, NSW Dept Primary Ind, Wagga WaggaNew South Wales, Wagga Wagga, NSW, Australia
6.Univ Calif Davis, Dept Plant Sci, Davis, CA USA
期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）
ISSN： 1061-4036
年卷期： 2024 年 56 卷 11 期
页码：
收录情况： SCI
摘要： Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV-gene expression-trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.
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