INRAE/UCA UMR 1095, 5 Chemin de Beaulieu, Clermont Ferrand, 63100, France.
Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, 46 allée d'Italie, Lyon, 69364, France.
BMC Genomics. 2023 May 11;24(1):255. doi: 10.1186/s12864-023-09324-2.
Bread wheat is a recent allohexaploid (genomic constitution AABBDD) that emerged through a hybridization between tetraploid Triticum turgidum (AABB) and diploid Aegilops tauschii (DD) less than 10,000 years ago. The hexaploidization can be re-created artificially, producing synthetic wheat that has been used to study immediate genomic responses to polyploidization. The scale of the consequences of polyploidization, and their mechanism of establishment, remain uncertain.
Here we sampled several synthetic wheats from alternative parental genotypes and reciprocal crosses, and examined transcriptomes from two different tissues and successive generations. We did not detect any massive reprogramming in gene expression, with only around 1% of expressed genes showing significant differences compared to their lower-ploidy parents. Most of this differential expression is located on the D subgenome, without consistency in the direction of the expression change. Homoeolog expression bias in synthetic wheat is similar to the pattern observed in the parents. Both differential expression and homoeolog bias are tissue-specific. While up to three families of transposable elements became upregulated in wheat synthetics, their position and distance are not significantly associated with expression changes in proximal genes.
While only a few genes change their expression pattern after polyploidization, they can be involved in agronomically important pathways. Alternative parental combinations can lead to opposite changes on the same subset of D-located genes, which is relevant for harnessing new diversity in wheat breeding. Tissue specificity of the polyploidization-triggered expression changes indicates the remodelling of transcriptomes in synthetic wheat is plastic and likely caused by regulome interactions rather than permanent changes. We discuss the pitfalls of transcriptomic comparisons across ploidy levels that can inflate the de-regulation signal.
Transcriptomic response to polyploidization in synthetic AABBDD wheat is modest and much lower than some previous estimates. Homoeolog expression bias in wheat allohexaploids is mostly attributed to parental legacy, with polyploidy having a mild balancing effect.
栽培小麦是一种新近的异源六倍体（基因组组成 AABBDD），由约 1 万年前四倍体硬质小麦（Triticum turgidum，AABB）与二倍体节节麦（Aegilops tauschii，DD）杂交形成。六倍体化可以人为地重新创造，产生已被用于研究多倍体化即刻基因组反应的合成小麦。多倍体化的后果规模及其建立机制仍不确定。
在这里，我们从不同的亲本基因型和正反交中选择了几种合成小麦，并检查了来自两个不同组织和连续几代的转录组。我们没有检测到任何大规模的基因表达重编程，只有大约 1%的表达基因与它们的低倍体亲本相比表现出显著差异。这种差异表达的大部分位于 D 亚基因组上，表达变化的方向没有一致性。合成小麦中同源基因表达偏向与亲本中观察到的模式相似。差异表达和同源基因偏向都是组织特异性的。虽然多达三个转座元件家族在小麦合成物中上调，但它们的位置和距离与近端基因的表达变化没有显著关联。
虽然多倍体化后只有少数基因改变了它们的表达模式，但它们可能参与了具有重要农艺意义的途径。不同的亲本组合可以导致同一组 D 位基因的相反变化，这对于在小麦育种中利用新的多样性具有重要意义。多倍体化触发的表达变化的组织特异性表明，合成小麦的转录组重塑是可塑性的，可能是由调控组相互作用引起的，而不是永久性变化。我们讨论了跨倍性水平进行转录组比较可能夸大去调控信号的陷阱。
合成 AABBDD 小麦对多倍体化的转录组反应是适度的，远低于一些先前的估计。小麦异源六倍体中的同源基因表达偏向主要归因于亲本遗传，多倍体化具有轻微的平衡效应。
