Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so‐called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post‐polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

中文翻译：

---

六倍体小麦基因组同源拷贝数变异的新见解

面包小麦是一种异源六倍体物种，起源于三个二倍体物种之间连续和最近的两轮杂交，这三个二倍体物种在染色体数量、基因组大小、TE 含量、基因含量和同线性方面非常相似。因此，长期以来人们一直认为大多数基因存在于三对同源拷贝中。然而，这些所谓的三联体只代表了一半的小麦基因，而剩下的一半属于同源组，跨亚基因组的拷贝数不同。在这项研究中，我们检查并比较了三联体的分布、保守性、功能、表达和表观遗传谱，其中同源组在一个亚基因组中经历了缺失（二分体）或重复（四分体）。我们表明，二元体和四元体主要位于远端区域，并且比三元体具有较低的表达水平和广度。此外，它们富含与适应相关的功能，并且与抑制性 H3K27me3 修饰更相关。总之，这些结果表明，三联体主要对应于看家基因，是核心基因组的一部分，而二联体和四联体属于小麦科可有可无的基因组。此外，通过比较不同类别的二分体和四分体，我们假设，与大多数异源多倍体物种不同，六倍体小麦不存在亚基因组优势和偏向分离。由于六倍体小麦的进化史，三个亚基因组之间观察到的差异更可能与两个连续且持续的多倍体后二倍体化浪潮有关，这对 A 和 B 的影响比对 D 的影响更大。