Transcriptome and proteome wide identification of genes that are related to heterosis manifestion in maize seedling roots

杂种优势描述了杂种与其亲本近交系的平均值相比的上级表现，并且归因于相当数量的遗传位点的相互作用。对这些基因座的分子鉴定和表征将是理解杂种优势的一个重要步骤。因此，我们建议在转录组和蛋白质组范围内表征玉米幼苗根系中杂种优势相关基因的表达和蛋白质积累。分析将包括四个不同近交系的六个组合，包括一个flint/flint（A x B）和一个dent/dent（C x D）组内杂交以及这些近交系的四个可能的flint/dent组间杂交（A x C、A x D、B x C和B x D）。这将允许在三个不同的杂交组合中研究每个基因的四个等位基因。在我们的实验中包括正反交将允许研究亲本的起源效应。在该项目的初始阶段，将在表型和组织学水平上对选定的自交系和杂交种的早期根发育进行定量分析。然后将在一个确定的发育阶段用所有六个正反交的幼苗根进行微阵列实验。这些相互杂种中的三个的相同发育阶段也将进行蛋白质组学分析。我们的目标是确定一个子集的基因/蛋白质，这是在近交系与杂交种的差异表达，并测试这些基因的表达根据遗传模型的优势或超显性假说。在这些差异表达基因中，我们希望能够鉴定出其相对表达水平与杂种优势程度相关的基因。组织数据库中的分析数据和整合的分子数据到一个建模框架可能有助于预测未来的杂交生产合适的近交组合。总之，通过这种方法，我们希望有助于从分子水平上理解杂种优势中复杂的遗传网络。

Heterosis describes the superior performance of hybrids compared to the average of their parental inbred lines and is attributed to the interaction of a considerable number of genetic loci. A major step towards the understanding of heterosis will be the molecular identification and characterization of these loci. We suggest therefore a transcriptome- and proteome wide characterization of heterosis related gene expression and protein accumulation in roots of young seedlings of maize. The analyses will comprise six combinations of four different inbred lines including one flint/flint (A x B) and one dent/dent (C x D) intra-group cross and the four possible flint/dent inter-group crosses of these inbred lines (A x C, A x D, B x C and B x D). This will allow to study four alleles of each gene in three different hybrid combinations. Inclusion of reciprocal crosses in our experiments will allow to study parent of origin effects. In the initial phase of the project, early root development of selected inbred lines and hybrids will be quantitatively analyzed on the phenotypical and on the histological level. Microarray experiments will then be conducted with young seedling roots of all six reciprocal crosses at one defined developmental stage. The same developmental stage of three of these reciprocal hybrids will also be subjected to a proteomic analysis. Our objective is to identify a subset of genes/proteins which is differentially expressed in inbred lines versus hybrids and to test which of these genes are expressed according to the genetic models of the dominance or overdominance hypothesis. Among the differentially expressed genes we hope to identify genes whose relative expression level can be correlated with the degree of heterosis of a given hybrid. Organization of profiling data in databases and integration of the molecular data into a modeling framework might help to predict suitable inbred combinations for future hybrid production. In summary with this approach we hope to contribute to the molecular understanding of the complex genetic networks involved in heterosis.