Abstract：
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.
摘要：
多倍体是植物多样化的突出驱动力，伴随着影响基因表达的巨大染色体重排和表观遗传变化。亚基因组内部和之间的染色质相互作用如何适应倍性转换仍然知之甚少。我们为天然六倍体小麦（AABBDD）生成开放的染色质相互作用图，提取的四倍体小麦（AABB），二倍体小麦祖细胞Aegilopstauschii（DD）和重新合成的六倍体小麦（RHW，AABBDD).在分离D亚基因组后，AB亚基因组中从头建立或消失了数千个染色体内和染色体间环，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的破坏触发的级联反应形成的。RHW中的相互作用抑制基因相对于DD的表达被抑制，导致三个同系物在RHW中的表达更平衡。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主要单核苷酸多态性在级联锚中显着富集。与这些锚相互作用的116个基因的表达与相应的性状显着相关。我们的发现揭示了多倍体物种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反式调节。
