Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11878-83. doi: 10.1073/pnas.1201961109. Epub 2012 Jul 2.
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
通过驯化，人类极大地改变了 Zea mays ssp. parviglumis（墨西哥类蜀黍）的形态，使其成为我们现在所认识的玉米。这个系统是研究适应、基因组进化以及复杂性状的遗传学和进化的模型。为了研究驯化如何重塑玉米幼苗的转录组，我们对 38 个不同玉米基因型和 24 个墨西哥类蜀黍基因型的 18242 个基因进行了表达谱分析。我们发现了 600 多个在玉米中表达水平与墨西哥类蜀黍显著不同的基因。此外，1100 多个基因的共表达谱发生了显著改变，这反映了自驯化以来转录组的大量重布线。表达发生改变的基因在种群遗传分析中被认为是玉米驯化和改良过程中可能的选择目标的基因中显著富集；46 个先前被鉴定为可能的选择目标的基因也表现出改变的表达水平和共表达关系。我们还鉴定了 45 个在自交玉米中表达水平升高的基因，这些基因在自交玉米中发生了改变，而在异交玉米中则没有。这些基因主要富集了与生物胁迫相关的功能，可能反映了自交的影响。本研究不仅记录了玉米驯化后转录组的改变，鉴定了几个可能对玉米进化有贡献的基因，而且强调了通过将基因表达与种群遗传分析相结合可以获得的互补信息。
