Genetic architecture of regulatory variation in Arabidopsis thaliana.
Genetic architecture of regulatory variation in Arabidopsis thaliana.
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DOI：
10.1101/gr.115337.110
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发表时间：
2011-05
期刊：
影响因子：
7
通讯作者：
Xu Zhang;Andrew J Cal;J. Borevitz
中科院分区：
文献类型：
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作者：
Xu Zhang;Andrew J Cal;J. Borevitz
研究基因表达变异的遗传调控是剖析复杂表型性状的重要手段。为了研究拟南芥调控变异的遗传结构，我们在F（1）杂交多样性面板中进行了基因表达的全基因组关联（GWA）定位。在全基因组错误发现率（FDR）为0.2时，相关的单核苷酸多态性（SNP）解释了>38%的性状变异。与远离它们所关联的基因的SNP相比，本地相关的SNP优先发现于具有扩展连锁不平衡（LD）的区域，并且具有不同的衍生等位基因的群体频率（其中琴叶拟南芥具有祖先等位基因），这表明不同的选择力正在起作用。局部关联的SNP倾向于具有加性遗传，而远距离关联的SNP主要是显性的。与连锁研究中表达数量性状基因座（eQTL）定位的结果相反，我们在多样性小组中观察到局部调控基因座的广泛等位基因异质性。通过关联映射的等位基因特异性表达（ASE），我们检测到一个显着富集的顺式作用的变化，在当地的监管变化。除了基因表达变异，剪接变异的关联作图揭示了内含子和外显子水平性状的局部和远距离遗传调控。最后，我们确定了59个不同的表型性状的候选基因被定位到eQTL。
Studying the genetic regulation of expression variation is a key method to dissect complex phenotypic traits. To examine the genetic architecture of regulatory variation in Arabidopsis thaliana, we performed genome-wide association (GWA) mapping of gene expression in an F(1) hybrid diversity panel. At a genome-wide false discovery rate (FDR) of 0.2, an associated single nucleotide polymorphism (SNP) explains >38% of trait variation. In comparison with SNPs that are distant from the genes to which they were associated, locally associated SNPs are preferentially found in regions with extended linkage disequilibrium (LD) and have distinct population frequencies of the derived alleles (where Arabidopsis lyrata has the ancestral allele), suggesting that different selective forces are acting. Locally associated SNPs tend to have additive inheritance, whereas distantly associated SNPs are primarily dominant. In contrast to results from mapping of expression quantitative trait loci (eQTL) in linkage studies, we observe extensive allelic heterogeneity for local regulatory loci in our diversity panel. By association mapping of allele-specific expression (ASE), we detect a significant enrichment for cis-acting variation in local regulatory variation. In addition to gene expression variation, association mapping of splicing variation reveals both local and distant genetic regulation for intron and exon level traits. Finally, we identify candidate genes for 59 diverse phenotypic traits that were mapped to eQTL.