华中农业大学杨庆勇等研究人员合作发现，结构变异重塑2105个油菜品种的群体基因表达和性状变异。该研究于2024年11月5日在线发表于国际一流学术期刊《自然—遗传学》。

研究人员构建了一个包含334461个结构变异（SV）的参考库，该库来源于16个代表性形态类型的新多倍体油菜（Brassica napus）品种的基因组组装，并在2105个重测序基因组中检测到了258865个SV。结合5种组织的群体转录组数据，研究人员揭示了285976个与基因表达变化相关的SV-表达定量性状位点（eQTL）。

这些位点与73580个基因的表达变化相关。研究人员开发了一个高通量联合分析的管线，用于分析SV-全基因组关联研究（SV-GWAS）、转录组全基因组关联研究、表型数据的eQTLs和eQTL-GWAS的共定位。研究人员识别了726个SV–基因表达–性状变异的关联，其中一些已经通过转基因验证。

通过葡萄糖苷酸合成和转运途径，研究人员证明了SV对性状变异重塑的普遍影响。该研究突显了全基因组和物种规模SV的影响，并提供了一个强有力的方法策略和宝贵的资源，用于研究物种演化、基因发现和育种。

据了解，尽管已知个体基因组SV会影响基因表达和性状变异，但SV在物种范围内的影响程度和规模仍然不清楚。

附：英文原文

Title: Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

Author: Zhang, Yuanyuan, Yang, Zhiquan, He, Yizhou, Liu, Dongxu, Liu, Yueying, Liang, Congyuan, Xie, Meili, Jia, Yupeng, Ke, Qinglin, Zhou, Yongming, Cheng, Xiaohui, Huang, Junyan, Liu, Lijiang, Xiang, Yang, Raman, Harsh, Kliebenstein, Daniel J., Liu, Shengyi, Yang, Qing-Yong

Issue&Volume: 2024-11-05

Abstract: 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.

DOI: 10.1038/s41588-024-01957-7

Source: https://www.nature.com/articles/s41588-024-01957-7