A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions
A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions
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DOI：
10.1093/molbev/msx234
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发表时间：
2017-12
影响因子：
10.7
通讯作者：
Kazumasa Shirai;Fumio Matsuda;Ryo Nakabayashi;Masanori Okamoto;Maho Tanaka;Akihiro Fujimoto;Minami Shimizu;K. Shinozaki;M. Seki;K. Saito;Kousuke Hanada
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作者：
Kazumasa Shirai;Fumio Matsuda;Ryo Nakabayashi;Masanori Okamoto;Maho Tanaka;Akihiro Fujimoto;Minami Shimizu;K. Shinozaki;M. Seki;K. Saito;Kousuke Hanada
谱系特异性基因重复导致不同植物物种之间专门代谢物的巨大差异。单一植物物种内的专门代谢物也存在相当大的变异性。然而，尚不清楚源自基因重复事件的拷贝数变异（CNV）是否有助于物种内专门代谢物的多样性。我们鉴定了与定量代谢变异相关的代谢组数量性状基因 (mQTG)，并检查了 mQTG 和 CNV 之间的关系。我们使用液相色谱-四极杆飞行时间质谱法从全球 53 个拟南芥种质中获得了 1,335 个专门代谢物信号。在这项研究中，与专门代谢物相关的基因是通过普遍授权的全基因组关联研究（GWAS）方法或对基因表达与代谢物积累之间关联的新颖分析来推断的。通过这两种分析合格的基因被定义为 mQTG。集成方法使我们能够以较低的误报率 (=5.71 × 10-4) 检测 mQTG。我们还鉴定了与 1,335 种专门代谢物相关的 5,654 个基因。其中，4.4%的基因受到CNV的影响，超出预期（χ2检验：P < 0.01）。这一结果表明，CNV 会导致物种内特定代谢物的变化。为了评估 CNV 对拟南芥适应性进化的贡献，我们检查了 mQTG 周围的选择性扫描。我们观察到带有 CNV 的 mQTG 倾向于进行选择性扫描。这些观察结果表明，CNV 引起的专门代谢物的变化有助于拟南芥的适应性进化。
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (=5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.