Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands.
Plant Physiol. 2010 Nov;154(3):1067-78. doi: 10.1104/pp.110.159996. Epub 2010 Sep 10.
Gene expression differences between individuals within a species can be largely explained by differences in genetic background. The effect of genetic variants (alleles) of genes on expression can be studied in a multifactorial way by the application of genetical genomics or expression quantitative trait locus mapping. In this paper, we present a strategy to construct regulatory networks by the application of genetical genomics in combination with transcript profiling of mutants that are disrupted in single genes. We describe the network identification downstream of the receptor-like kinase ERECTA in Arabidopsis (Arabidopsis thaliana). Extending genetical genomics on the Landsberg erecta/Cape Verde Islands (Ler/Cvi) recombinant inbred population with expression profiling of monogenic mutants enabled the identification of regulatory networks in the so far elusive ERECTA signal transduction cascade. We provide evidence that ERECTA is the causal gene for the major hotspot for transcript regulation in the Arabidopsis Ler/Cvi recombinant inbred population. We further propose additional genetic variation between Ler and Cvi in loci of the signaling pathway downstream of ERECTA and suggest candidate genes underlying these loci. Integration of publicly available microarray expression data of other monogenic mutants allowed us to link ERECTA to a downstream mitogen-activated protein kinase signaling cascade. Our study shows that microarray data of monogenic mutants can be effectively used in combination with genetical genomics data to enhance the identification of genetic regulatory networks.
物种内个体之间的基因表达差异很大程度上可以用遗传背景的差异来解释。通过应用遗传基因组学或表达数量性状基因座作图，可以以多因素的方式研究基因的遗传变异（等位基因）对表达的影响。在本文中，我们提出了一种通过应用遗传基因组学结合突变体的转录谱分析来构建调控网络的策略，这些突变体在单个基因中被破坏。我们描述了在拟南芥（Arabidopsis thaliana）中受体样激酶 ERECTA 下游的网络识别。在 Landsberg erecta/Cape Verde Islands（Ler/Cvi）重组自交系群体上扩展遗传基因组学，并对单基因突变体进行表达谱分析，使我们能够鉴定出迄今为止难以捉摸的 ERECTA 信号转导级联中的调控网络。我们提供的证据表明，ERECTA 是拟南芥 Ler/Cvi 重组自交系群体中转录调控主要热点的因果基因。我们进一步提出了 ERECTA 下游信号通路中 Ler 和 Cvi 之间的其他遗传变异，并提出了这些基因座下的候选基因。整合其他单基因突变体的公共微阵列表达数据，使我们能够将 ERECTA 与下游丝裂原激活的蛋白激酶信号级联联系起来。我们的研究表明，单基因突变体的微阵列数据可以与遗传基因组学数据有效结合，以增强遗传调控网络的识别。
