Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus
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DOI：
10.1101/814491
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发表时间：
2019-10
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影响因子：
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通讯作者：
Kevin A. Bird;Chad Niederhuth;Shujun Ou;Malia A. Gehan;J. C. Pires;Zhiyong Xiong;R. VanBuren;
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作者：
Kevin A. Bird;Chad Niederhuth;Shujun Ou;Malia A. Gehan;J. C. Pires;Zhiyong Xiong;R. VanBuren;
与细胞核中的其他亚基因组相比，异源多倍体中的亲本二倍体基因组（亚基因组）之一通常表现出更高的基因表达水平。然而，亚基因组表达优势的遗传基础和决定性命运仍然知之甚少。我们检查了前十代中六个同基因再合成甘蓝型油菜（油菜）异源多倍体品系中亚基因组表达优势的建立，并发现了每个独立品系和世代中偏向于甘蓝“C”亚基因组的一致表达优势模式。同源交换（HE）引起的基因剂量变化的数量和方向在品系和世代之间变化很大，然而，我们恢复了与多个天然甘蓝型油菜品种中的HE热点重叠的HE热点。此外，我们发现在重新合成的品系中，更多的“C”亚基因组区域取代了“A”亚基因组区域，花粉数量和活力迅速下降。此外，亚基因组之间的 DNA 甲基化差异反映了在所有品系和世代中观察到的基因表达偏向于“C”亚基因组。基因相互作用网络分析表明，“C”亚基因组偏向对的网络相互作用和多种生物学功能有所富集，但“A”亚基因组偏向对没有观察到富集。这些发现表明，异源多倍体中的“重放进化磁带”会根据亲本物种之间预先存在的遗传差异产生可重复和可预测的亚基因组表达优势模式。意义 种间杂交将进化上不同的亲本基因组（亚基因组）合并到一个核中。一个常见的观察结果是，一个亚基因组比其他亚基因组“占主导地位”，包括更高的基因表达水平。哪种亚基因组在异源多倍体中占主导地位表达仍知之甚少。在这里，我们用六个同基因重新合成的异源多倍体甘蓝型油菜品系“重播了进化磁带”，并研究了前十代的亚基因组优势模式。我们发现相同的亲本亚基因组在所有品系和世代中始终更显着地表达。这表明亚基因组表达优势很大程度上是根据亲本二倍体基因组之间的差异预先确定的。这些发现对于生态和农业环境中植物杂交后观察到的基因型和表型多样性具有重大意义。
One of the parental diploid genomes (subgenomes) in an allopolyploid often exhibits higher gene expression levels compared to the other subgenome(s) in the nucleus. However, the genetic basis and deterministic fate of subgenome expression dominance remains poorly understood. We examined the establishment of subgenome expression dominance in six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines over the first ten generations, and uncovered consistent expression dominance patterns that were biased towards the Brassica oleracea ‘C’ subgenome across each of the independent lines and generations. The number and direction of gene dosage changes from homoeologous exchanges (HEs) was highly variable between lines and generations, however, we recovered HE hotspots overlapping with those in multiple natural B. napus cultivars. Additionally, we found a greater number of ‘C’ subgenome regions replacing ‘A’ subgenome regions among resynthesized lines with rapid reduction in pollen counts and viability. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the ‘C’ subgenome in all lines and generations. Gene-interaction network analysis indicated an enrichment for network interactions and several biological functions for ‘C’ subgenome biased pairs, but no enrichment was observed for ‘A’ subgenome biased pairs. These findings demonstrate that “replaying the evolutionary tape” in allopolyploids results in repeatable and predictable subgenome expression dominance patterns based on preexisting genetic differences among the parental species. Significance Interspecific hybridization merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is “dominant” over the other subgenome(s) including higher gene expression levels. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized allopolyploid Brassica napus lines and investigated subgenome dominance patterns over the first ten generations. We found that the same parental subgenome was consistently more dominantly expressed in all lines and generations. This suggests that subgenome expression dominance is largely predetermined based on differences among the parental diploid genomes. These findings have major implications regarding the genotypic and phenotypic diversity observed following plant hybridization in both ecological and agricultural contexts.