State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
Plant J. 2024 Sep;119(5):2450-2463. doi: 10.1111/tpj.16932. Epub 2024 Jul 14.
Polyploidy is a prominent driver of plant diversification, accompanied with dramatic chromosomal rearrangement and epigenetic changes that affect gene expression. How chromatin interactions within and between subgenomes adapt to ploidy transition remains poorly understood. We generate open chromatin interaction maps for natural hexaploid wheat (AABBDD), extracted tetraploid wheat (AABB), diploid wheat progenitor Aegilops tauschii (DD) and resynthesized hexaploid wheat (RHW, AABBDD). Thousands of intra- and interchromosomal loops are de novo established or disappeared in AB subgenomes after separation of D subgenome, in which 37-95% of novel loops are lost again in RHW after merger of D genome. Interestingly, more than half of novel loops are formed by cascade reactions that are triggered by disruption of chromatin interaction between AB and D subgenomes. The interaction repressed genes in RHW relative to DD are expression suppressed, resulting in more balanced expression of the three homoeologs in RHW. The interaction levels of cascade anchors are decreased step-by-step. Leading single nucleotide polymorphisms of yield- and plant architecture-related quantitative trait locus are significantly enriched in cascade anchors. The expression of 116 genes interacted with these anchors are significantly correlated with the corresponding traits. Our findings reveal trans-regulation of intrachromosomal loops by interchromosomal interactions during genome merger and separation in polyploid species.
多倍体是植物多样化的主要驱动因素，伴随着剧烈的染色体重排和表观遗传变化，影响基因表达。亚基因组内部和之间的染色质相互作用如何适应倍性转变仍知之甚少。我们为天然六倍体小麦（AABBDD）、提取的四倍体小麦（AABB）、二倍体小麦祖先节节麦（DD）和重新合成的六倍体小麦（RHW，AABBDD）生成了开放染色质相互作用图谱。在 D 亚基因组分离后，AB 亚基因组中数千个染色体内和染色体间环被重新建立或消失，其中 37-95%的新环在 D 基因组合并后在 RHW 中再次丢失。有趣的是，超过一半的新环是由 AB 和 D 亚基因组之间染色质相互作用中断引发的级联反应形成的。与 DD 相比，RHW 中受抑制的基因受到抑制，导致 RHW 中三个同源基因的表达更加平衡。级联锚的相互作用水平逐步降低。与产量和植物结构相关的数量性状基因座的单核苷酸多态性显著富集在级联锚中。与这些锚相互作用的 116 个基因的表达与相应的性状显著相关。我们的研究结果揭示了在多倍体物种的基因组合并和分离过程中，染色体间相互作用对染色体内环的转录调控。
