Plantegenet Stephanie, Weber Johann, Goldstein Darlene R, Zeller Georg, Nussbaumer Cindy, Thomas Jérôme, Weigel Detlef, Harshman Keith, Hardtke Christian S
Department of Plant Molecular Biology, University of Lausanne, Biophore Building, Lausanne, Switzerland.
Mol Syst Biol. 2009;5:242. doi: 10.1038/msb.2008.79. Epub 2009 Feb 17.
In Arabidopsis thaliana, gene expression level polymorphisms (ELPs) between natural accessions that exhibit simple, single locus inheritance are promising quantitative trait locus (QTL) candidates to explain phenotypic variability. It is assumed that such ELPs overwhelmingly represent regulatory element polymorphisms. However, comprehensive genome-wide analyses linking expression level, regulatory sequence and gene structure variation are missing, preventing definite verification of this assumption. Here, we analyzed ELPs observed between the Eil-0 and Lc-0 accessions. Compared with non-variable controls, 5' regulatory sequence variation in the corresponding genes is indeed increased. However, approximately 42% of all the ELP genes also carry major transcription unit deletions in one parent as revealed by genome tiling arrays, representing a >4-fold enrichment over controls. Within the subset of ELPs with simple inheritance, this proportion is even higher and deletions are generally more severe. Similar results were obtained from analyses of the Bay-0 and Sha accessions, using alternative technical approaches. Collectively, our results suggest that drastic structural changes are a major cause for ELPs with simple inheritance, corroborating experimentally observed indel preponderance in cloned Arabidopsis QTL.
在拟南芥中，表现出简单单基因座遗传的自然生态型之间的基因表达水平多态性（ELP）是解释表型变异的很有前景的数量性状基因座（QTL）候选者。据推测，此类ELP绝大多数代表调控元件多态性。然而，目前尚缺乏将表达水平、调控序列和基因结构变异联系起来的全基因组综合分析，因而无法对这一推测进行明确验证。在此，我们分析了在Eil-0和Lc-0生态型之间观察到的ELP。与无变异的对照相比，相应基因中的5'调控序列变异确实增加了。然而，通过基因组平铺阵列发现，所有ELP基因中约42%在一个亲本中还存在主要转录单元缺失，这比对照富集了4倍以上。在具有简单遗传的ELP子集中，这一比例更高，且缺失通常更严重。使用其他技术方法对Bay-0和Sha生态型进行分析也得到了类似结果。总体而言，我们的结果表明，剧烈的结构变化是具有简单遗传的ELP的主要原因，这证实了在克隆的拟南芥QTL中实验观察到的插入缺失优势。
