Transcriptome modification to the BBAA subgenomes of common wheat since allohexaploidization is largely irreversible. Transcriptome modification to the BBAA subgenomes of common wheat since allohexaploidization is largely irreversible

The three subgenomes (B, A and D) of common wheat (2n=6x=42) are largely intact, which makes extraction of the BBAA subgenomes as organismally independent genomes possible. Availability of such novel extracted tetraploid wheat (Extracted-tetra) provides a unique opportunity to study whether and to what extent the BBAA subgenomes of common wheat have been irreversibly modified, as well as its attendant biological consequences, during their evolutionary trajectory as allohexaploidy. We report here that the extracted-tetra is stable in karyotype but with severely deteriorated phenotypes. Microarray-based transcriptome analysis revealed a substantial portion of differentially expressed genes (down- or up-regulation) between extracted and natural tetraploid wheat, Triticum turgidum, which exceeded the transcriptome divergence at tetraploid level, implying reinforced effects of allopolyploidization and domestication at the allohexaploid level. Great majority of the differentially expressed genes showed additive expression in a resynthesized allohexaploid wheat (parented by Extracted-tetra), indicating transcriptome modifications to the BBAA subgenomes are largely irreversible. Analysis of a newly synthesized allohexaploid wheat (parented by T. turgidum) suggests that whereas most of the modified genes are accrued evolutionary changes, some showed immediate regulation post-allohexaploidization and evolutionary perseverance. Homeologue-specific pyrosequencing of 44 genes revealed either concordant or independent expression changes to the B and A homeologues. The Extracted-tetra vs.T. turgidum down-regulated genes showed enrichment for distinct GO categories. Overall design: Structurally, the three constituent subgenomes of common wheat, BB, AA and DD, are largely intact with only a few inter-subgenomic translocations. Because of these unique attributes, it is feasible to extract the BBAA subgenomes from the common wheat BBAADD genome by hybridization to a durum line and repeated back-crossing to the hexaploid parent, restituting a novel type of extracted tetraploid wheat, namely Extracted-tetr, with a genome constitution BBAA, virtually identical to the subgenomes BBAA of its common wheat donor. Availability of the extracted-tetra, the resynthesized allohexaploid wheat parented by the extracted-tetra, and newly synthesized allohexaploid wheat parented by natural tetraploid wheat, T. turgidum, provides an excellent system to address the issues of whether and to what extent transcriptome modifications to the BBAA subgenomes of common wheat have occurred since its formation ca. 10,000 years ago, timing of the modifications, and their biological consequences. Here, we have addressed these issues by microarray-based transcriptome analysis.

普通小麦（2n=6x=42）的三个亚基因组（B、A和D）大多保持完整，这使得将BBAA亚基因组作为独立生物体基因组进行提取成为可能。新型提取型四倍体小麦（Extracted-tetra）的获得，为探究普通小麦的BBAA亚基因组在作为异源六倍体（allohexaploidy）的进化历程中是否、以及在多大程度上发生了不可逆修饰，及其伴随的生物学效应，提供了独特的研究契机。本研究报道，提取型四倍体小麦的核型保持稳定，但表型严重衰退。基于基因芯片（microarray）的转录组分析显示，提取型四倍体小麦与自然四倍体小麦硬粒小麦（Triticum turgidum）之间存在大量差异表达基因（上调或下调），其转录组差异程度超过了四倍体水平本身的转录组分化，这暗示异源多倍化与驯化在异源六倍体水平上产生了更强的调控效应。绝大多数差异表达基因在以提取型四倍体小麦为亲本构建的人工合成异源六倍体小麦中表现为加性表达，这表明BBAA亚基因组的转录组修饰在很大程度上是不可逆的。对以硬粒小麦为亲本构建的新合成异源六倍体小麦的分析表明，尽管大多数修饰基因属于累积的进化改变，但部分基因在异源多倍化后会受到即时调控并在进化中持续保留。对44个基因的部分同源基因特异性焦磷酸测序（pyrosequencing）显示，B和A部分同源基因的表达变化既可能协同一致，也可能独立发生。提取型四倍体小麦与硬粒小麦的下调差异表达基因富集于特定的基因本体（Gene Ontology, GO）类别。总体实验设计：从结构上看，普通小麦的三个组成亚基因组BB、AA和DD大多保持完整，仅存在少量亚基因组间易位。凭借这些独特属性，可通过将普通小麦BBAADD基因组与硬粒品系杂交，并反复回交于六倍体亲本，从中提取BBAA亚基因组，从而重建一种新型提取型四倍体小麦，即提取型四倍体小麦（Extracted-tetra），其基因组组成为BBAA，与供体普通小麦的BBAA亚基因组几乎完全一致。提取型四倍体小麦、以提取型四倍体小麦为亲本的人工合成异源六倍体小麦，以及以自然四倍体小麦硬粒小麦为亲本的新合成异源六倍体小麦的获得，为解决以下核心问题提供了绝佳的研究系统：普通小麦的BBAA亚基因组自约1万年前形成以来，是否、以及在多大程度上发生了转录组修饰，这些修饰发生的时间节点，以及它们的生物学效应。本研究通过基于基因芯片的转录组分析对上述问题进行了探究。