Transcriptomic plasticity of maize hybrids and their parental inbred lines at the interface of genotype and development

商业玉米生产几乎完全是以杂交为基础的，因为玉米杂交种的表现明显好于其纯合子亲本。然而，这种现象的分子基础，即所谓的杂种优势，在很大程度上仍然是个谜。在第一个资助期，我们发现了一种特定的基因表达互补形式，我们称之为单亲表达(SPE)。SPE基因只在两个亲本自交系中的一个中表达，但在两个正反交组合中都有表达。在玉米根组织中，我们发现了2.300个spe基因。作为SPE的结果，在所有被分析的根组织中，杂交种的活跃基因总数比其亲本自交系中表达的基因数量多400个。此外，只有在玉米最后一次全基因组复制后才出现的非共线基因在SPE基因中的表达明显过高。在第二个资助期，我们计划通过RNA测序实验来考察基因型和发育对玉米杂交种转录可塑性的影响，从而扩大这些分析范围。以轮回母本B73与自交系A554、H84、H99、OH43、W64A和Mo17杂交，研究轮回母本B73与自交系OH43、W64A和Mo17杂交对玉米初级根转录可塑性的遗传控制。在由初生根长度定义的三个发育阶段，将监测这些基因类型对转录复杂性的发育控制。计划中的实验的一个主要焦点将是进一步探索SPE模式在玉米初生根杂种优势表现中的普遍程度和作用，并鉴定新的基因型特异性SPE模式。此外，还将对这些基因的进化起源、由其可见的突变表型鉴定的经典玉米基因中的ter流行情况、它们的调控和功能进行综述。此外，还将确定差异、非加性和等位基因特异的基因表达模式，以确定这些基因组合在发育过程中的保守和独特模式。最后，这些表达模式将与表型和组织学数据相关联，以初步了解基因表达模式在玉米根杂种优势发育表现中的作用。这些与相对较少的基因类型的相关性预计相对较弱，但可能为未来利用更大的基因型板进行研究提供第一线索。综上所述，对玉米杂交种及其亲本自交系转录可塑性的基因和发育控制的分析将为深入了解导致玉米根系杂种优势表现的复杂分子过程提供深入的见解。

Commercial maize production is almost exclusively hybrid-based, because maize hybrids perform significantly better than their homozygous parents. Nevertheless, the molecular basis of this phenomenon, known as heterosis, remains largely enigmatic.In the first funding period we discovered a specific form of complementation of gene expression that we designated single parent expression (SPE). SPE-genes are expressed in only one of the two parental inbred lines but in both reciprocal hybrids. In maize root tissues we discovered >2.300 SPE-genes. As a consequence of SPE, in all root tissues under analysis, the total number of active genes in hybrids exceeded the number of genes expressed in their parental inbred lines by >400. Moreover, non-syntenic genes which emerged only after the last whole genome duplication of maize were significantly overrepresented among SPE genes.In the second funding period, we plan to extend these analyses by surveying the influence of genotype and development on the transcriptomic plasticity of maize hybrids by RNA-Sequencing experiments. The genotype-dependent control of transcriptomic plasticity in maize primary roots will be studied in six crosses of the recurrent female parent B73 with the inbred lines A554, H84, H99, OH43, W64A and Mo17. Developmental control of transcriptomic complexity will be monitored in these genotypes at three developmental stages defined by the length of primary roots. A major focus of the planned experiments will be to further explore the prevalence and role of SPE patterns during the manifestation of heterosis in maize primary roots and the identification of novel genotype specific SPE patterns. Moreover, the evolutionary origin of these genes, teir prevalence among classical maize genes identified by their visible mutant phenotype, their regulation and their function will be surveyed. Furthermore, differential, non-additive and allele-specific gene expression patterns will be determined to identify conserved and unique patterns between these genotype combinations during development. Finally, these expression patterns will be correlated with phenotypic and histological data to gain initial insights into the role of gene expression patterns in the developmental manifestation of heterosis in maize roots. These correlations with a relative small number of genotypes are expected to be relatively weak but might provide first cues for future research directions using larger panels of genotypes.In summary, the analysis of the genotypic and developmental control of the transcriptomic plasticity of maize hybrids and their parental inbred lines will provide insights into the complex molecular processes leading to heterosis manifestation in maize roots.