Polyploidization or whole genome duplications (WGD) is a well-known speciation and adaptation mechanism in angiosperm, while subgenome dominance is a crucial phenomenon of allopolyploids established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which benefit short-term phenotypic adaptation and long-term domestication advantages. In the review, we firstly summarized probable mechanistic basis for subgenome dominance, including the effects of genetic (transposon, genetic incompatibility, and homoeologous exchange (HE)), epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa (B. rapa), a typical allopolyploid with subgenome dominance. The polyploidization provides the B. rapa genomes with not only the genomic plasticity for adapting the changeable environments, but also the abundant of genetic basis for the morphological variation, making it to be a representative species for subgenome dominance study. According to the “two-step theory”, the B. rapa experienced genome fractionation twice during WGD in which most of genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than that, the pan-genome of 18 B.rapa accessions with different morphotypes recently constructed postulated further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it still remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids. We lastly propose to accelerate the combined application of resynthesized allopolyploids, “omics” technology and genome editing tools to deepen mechanistic investigations of subgenome dominance both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis for a variety of ecologically, evolutionarily and agriculturally interesting traits coupling with subgenome dominance will be uncovered and aid in new discoveries and crop breeding.

中文翻译：

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亚基因组优势及其在作物驯化和育种中的进化意义

多倍化或全基因组重复（WGD）是被子植物中众所周知的物种形成和适应机制，而亚基因组优势是多倍化后建立的异源多倍体的关键现象。优势亚基因组对基因组进化和同源基因表达偏差的贡献更大，这两者都有利于短期表型适应和长期驯化优势。在综述中，我们首先总结了亚基因组优势的可能机制基础，包括遗传（转座子、遗传不相容和同源交换（HE））、表观遗传（DNA甲基化和组蛋白修饰）以及发育和环境因素对这种进化的影响。过程。然后我们转向芸苔属（B. rapa），一种具有亚基因组优势的典型异源多倍体。多倍化为油菜基因组提供了适应多变环境的基因组可塑性，也为其形态变异提供了丰富的遗传基础，使其成为亚基因组优势研究的代表性物种。根据“两步理论”，油菜在 WGD 期间经历了两次基因组分离，其中大多数响应环境线索和植物激素的基因被过度保留，增强了亚基因组优势和随之而来的适应。更重要的是，最近构建的具有不同形态型的 18 个 B.rapa 种质的泛基因组假设了进一步的证据来揭示多倍化和亚基因组优势对 B. rapa 种内多样化的影响。超越对 WGD 和 B 中亚基因组优势的基本理解。然而，为什么亚基因组优势具有组织和时空特异性特征并且可以通过异源多倍体中的环境在不同亚基因组的同源区域之间改组仍然难以捉摸。最后，我们建议加速再合成的异源多倍体、“组学”技术和基因组编辑工具的组合应用，以深化对各种物种和环境中遗传和表观遗传亚基因组优势的机制研究。我们相信，基因组和遗传基础对与亚基因组优势相结合的各种生态、进化和农业有趣性状的影响将被揭示，并有助于新发现和作物育种。为什么亚基因组优势具有组织和时空特异性特征并且可以通过异源多倍体中的环境在不同亚基因组的同源区域之间洗牌仍然难以捉摸。最后，我们建议加速再合成的异源多倍体、“组学”技术和基因组编辑工具的组合应用，以深化对各种物种和环境中遗传和表观遗传亚基因组优势的机制研究。我们相信，基因组和遗传基础对与亚基因组优势相结合的各种生态、进化和农业有趣性状的影响将被揭示，并有助于新发现和作物育种。为什么亚基因组优势具有组织和时空特异性特征并且可以通过异源多倍体中的环境在不同亚基因组的同源区域之间洗牌仍然难以捉摸。最后，我们建议加速再合成的异源多倍体、“组学”技术和基因组编辑工具的组合应用，以深化对各种物种和环境中遗传和表观遗传亚基因组优势的机制研究。我们相信，基因组和遗传基础对与亚基因组优势相结合的各种生态、进化和农业有趣性状的影响将被揭示，并有助于新发现和作物育种。最后，我们建议加速再合成的异源多倍体、“组学”技术和基因组编辑工具的组合应用，以深化对各种物种和环境中遗传和表观遗传亚基因组优势的机制研究。我们相信，基因组和遗传基础对与亚基因组优势相结合的各种生态、进化和农业有趣性状的影响将被揭示，并有助于新发现和作物育种。最后，我们建议加速再合成的异源多倍体、“组学”技术和基因组编辑工具的组合应用，以深化对各种物种和环境中遗传和表观遗传亚基因组优势的机制研究。我们相信，基因组和遗传基础对与亚基因组优势相结合的各种生态、进化和农业有趣性状的影响将被揭示，并有助于新发现和作物育种。