Distantly related maize (Zea mays L.) inbred lines exhibit an exceptional degree of structural genomic diversity, which is probably unique among plants. This study systematically investigated the developmental and genotype-dependent regulation of the primary root transcriptomes of a genetically diverse panel of maize F1-hybrids and their parental inbred lines. While we observed substantial transcriptomic changes during primary root development, we demonstrated that hybrid-associated gene expression patterns, including differential, non-additive, and allele-specific transcriptome profiles, are particularly robust to these developmental fluctuations. For instance, differentially expressed genes with preferential expression in hybrids were highly conserved during development in comparison to their parental counterparts. Similarly, in hybrids a major proportion of non-additively expressed genes with expression levels between the parental values were particularly conserved during development. Importantly, in these expression patterns non-syntenic genes that evolved after the separation of the maize and sorghum lineages were systemically enriched. Furthermore, non-syntenic genes were substantially linked to the conservation of all surveyed gene expression patterns during primary root development. Among all F1-hybrids, between ~40% of the non-syntenic genes with unexpected allelic expression ratios and ~60% of the non-syntenic differentially and non-additively expressed genes were conserved and therefore robust to developmental changes. Hence, the enrichment of non-syntenic genes during primary root development might be involved in the developmental adaptation of maize roots and thus the superior performance of hybrids.

中文翻译：

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根发育过程中，不同玉米杂交种中的稳健非同步基因表达模式。

远缘玉米（Zea mays L.）自交系表现出异常的结构基因组多样性，这在植物中可能是独特的。这项研究系统地研究了玉米F1杂种及其亲本近交系的遗传多样性面板初级根转录组的发育和基因型依赖性调控。虽然我们观察到在初生根发育过程中转录组发生了实质性变化，但我们证明了与杂交相关的基因表达模式，包括差异，非加性和等位基因特异性转录组谱，对这些发育波动特别有力。例如，与亲本相比，在杂种中优先表达的差异表达基因在发育过程中高度保守。相似地，在杂种中，在发育过程中，绝大部分非加性表达基因的表达水平在亲本值之间是特别保守的。重要的是，在这些表达方式中，玉米和高粱谱系分离后进化的非同系基因被系统地富集。此外，在原根发育过程中，非同位基因与所有调查的基因表达模式的保守性基本相关。在所有F1杂种中，约40％的具有非等位基因等位基因表达比的非同步基因和约60％的非同步差异表达和非累加表达基因得到了保守，因此对发育变化具有鲁棒性。因此，