Universality and regulation of gene expression complementation and its association with the phenotypic manifestation of heterosis in maize hybrids

观察到F1杂交种比它们的亲本更有活力的现象通常被称为杂种优势或杂种优势。玉米是全球谷物品种中年产量最高的，是主要玉米生产国独有的杂交种。杂交优势的开发被认为是现代农业最重要的创新之一，因为它具有显著的经济意义。然而，潜在的分子机制在很大程度上仍然是个谜。在以前的工作中，我们观察到了杂交中数百个基因的一种极端形式的基因表达互补，我们称之为单亲表达(SPE)。显示这种表达模式的基因只在一个亲本中活跃，但在杂交种中总是活跃的，因此符合杂种优势的显性模型。作为这些表达模式的结果，与其亲本近交系相比，杂交种表现出数百个额外的活性基因。在本项目的第一部分，我们将应用RNA-Seq来证明SPE互补是普遍观察到的，并在一组不同的基因型中，在地下与地上、幼苗与成熟组织以及营养组织与生殖组织中显示出显著的可塑性。随后，我们将应用基因组进化率谱来检验SPE模式中的非活跃等位基因代表一般有害等位基因的假设，这将符合杂种优势的显性模型。在本项目的第二部分，我们旨在了解SPE互补的调节及其在杂种优势表型表现中的作用。为此，我们将利用一个与其亲本自交系回交的玉米重组自交系群体，通过RNA-SEQ确定跨eQTL调控网络来识别SPE基因的关键调控因子。与双亲回交的重组自交系平均含有50%的杂合基因，而与两个亲本的杂交相比，这些类型的SPE图谱平均只有75%。因此，在这些群体中，杂合性和极端显性对杂种优势的影响是可以分开的。不同重组自交系的SPE图谱数目的差异将有助于测试它们对所研究性状的表型表现的影响。最后，通过RNA-SEQ实验获得的高分辨率SNP标记将被用来通过QTL定位来识别本项目中量化的一些杂种性状的潜在基因座。综上所述，这些实验将有助于从机理上理解杂种优势的分子基础，并将提供有助于在育种中利用杂种优势从而促进玉米改良的知识。

The observation that F1-hybrids are more vigorous than their parents is commonly referred to as heterosis or hybrid vigor. Maize, which provides the highest annual global kernel yield of all cereal species, is exclusively hybrid based in the major corn producing countries. The exploitation of hybrid vigor is considered as one of the most important innovations in modern agriculture because of its eminent economic importance. Nevertheless, the underlying molecular mechanisms remain largely enigmatic. In previous work, we observed an extreme form of gene expression complementation in hybrids for hundreds of genes that we designated single parent expression (SPE). Genes displaying such expression patterns are only active in one parent but always in the hybrid and thus are consistent with the dominance model of heterosis. As a consequence of these expression patterns, hybrids display hundreds of additionally active genes compared to their parental inbred lines. In the first part of this project, we will apply RNA-Seq to demonstrate that SPE complementation is universally observed and displays significant plasticity in belowground versus aboveground, seedling compared to mature and vegetative versus generative tissues in a distinct panel of genotypes. Subsequently, we will apply genomic evolutionary rate profiling to test the hypothesis that the inactive alleles in SPE patterns represent in general deleterious alleles, which would be in accordance with the dominance model of heterosis. In the second part of this project, we aim to understand the regulation of SPE complementation and its role in the phenotypic manifestation of heterosis. To this end we will take advantage of a maize recombinant inbred line population backcrossed to their parental inbred lines to identify key regulators of SPE genes by the determination of trans-eQTL regulatory networks via RNA-seq. Recombinant inbred lines backcrossed to their parents contain on average 50% heterozygous genes, whereas SPE patterns are expected to be reduced on average to only 75% in these genotypes compared to crosses of the two parental lines. Hence, in these populations the influence of heterozygosity and extreme dominance on heterosis can be separated. The variation of the number of SPE patterns in different recombinant inbred lines will allow testing their influence on phenotypic performance of the studied traits. Finally, high-resolution SNP markers obtained by the RNA-seq experiment will be used to identify loci underlying some of the heterotic traits quantified in this project by QTL mapping. In summary, these experiments will contribute to the mechanistic understanding of the molecular basis of heterosis and will provide knowledge that will facilitate the exploitation of heterosis in breeding and thus maize improvement.