Nature Plants：农科院蔬菜所团队系统阐述多倍体与植物进化和作物驯化的关系

不断地多倍化继而二倍化是植物演化和新物种形成的最重要方式之一。植物多倍化是植物基因组在进化过程中发生加倍的过程，形成了遗传物质是原有物种两倍（或两倍以上）的多倍体新物种。多倍体包括古多倍体和新多倍体。古多倍体指物种的祖先在进化历史中经历了基因组多倍化，但随后通过基因的丢失和基因组重排重新二倍化，也即由多套亚基因组组合形成的二倍体；而新多倍体是指新形成的，基因组未发生重排，仍然保持多倍体形式的物种。研究显示所有植物都经历了基因组古多倍化事件，且有相当比例的作物都在较近的时期里发生过多倍化。因此，多倍体的多套亚基因组以及多拷贝基因的进化对于植物的进化和作物的驯化具有重要意义。随着基因组学的发展，植物多倍化的研究取得了许多重要进展，是目前植物学研究的一个重要热点领域。

近日，中国农业科学院蔬菜花卉研究所王晓武团队与美国加州大学伯克利分校合作在Nature Plants发表了题为“Gene retention, fractionation and subgenome differences in polyploid plants”的综述，对植物多倍体研究进行了系统阐述，提出了相关的新理论和研究展望。

王晓武团队联合加州大学伯克利分校Michael Freeling院士，通过系统综述植物多倍体研究的最新进展，以及多倍体与古多倍体演化的最新理论，提出了多倍体进化的框架模型，将相关假说和理论置于多倍体进化的各个时期内，使我们能够在整体水平上更全面地认识多倍体的进化特点。多倍体基因组常表现出亚基因组差异，最典型的就是分化出优势亚基因组，即一套亚基因组相对于其他亚基因组在进化上具有优势的现象。在阐述亚基因组优势现象的相关机制时，针对异源多倍体杂交优势现象形成，提出了基因通路效率平衡（Pathway efficiency balance）的模型。该模型阐释了植物异源多倍体中亚基因组优势形成的潜在机制，并提出其与杂交优势可能具有一套相似的调控机制。这一假说为植物异源多倍体的研究提出了新的研究方向和思路。

基因通路效率平衡假说阐释杂交优势和亚基因组优势的关系，及潜在的调控机制模型。

王晓武团队多年从事芸薹属物种的研究，主导了白菜基因组的测序工作。芸薹属包括古多倍体和新多倍体等多个重要的蔬菜和油用作物，是植物多倍体进化研究的模型系统。据了解，本研究是因该课题组前期相关工作而受邀撰写的本领域的重点综述文章。

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Abstract

All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality. Polyploidization has happened repeatedly in plant evolution and, we conclude, is important for crop domestication. Once duplicated, the effect of purifying selection on any one duplicated gene is relaxed, permitting duplicate gene and regulatory element loss (fractionation). We review the general topic of fractionation, and how some gene categories are retained more than others. Several explanations, including neofunctionalization, subfunctionalization and gene product dosage balance, have been shown to influence gene content over time. For allopolyploids, genetic differences between parental lines immediately manifest as subgenome dominance in the wide-hybrid, and persist and propagate for tens of millions of years. While epigenetic modifications are certainly involved in genome dominance, it has been difficult to determine which came first, the chromatin marks being measured or gene expression. Data support the conclusion that genome dominance and heterosis are antagonistic and mechanically entangled; both happen immediately in the synthetic wide-cross hybrid. Also operating in this hybrid are mechanisms of ‘paralogue interference’. We present a foundation model to explain gene expression and vigour in a wide hybrid/new allotetraploid. This Review concludes that some mechanisms operate immediately at the wide-hybrid, and other mechanisms begin their operations later. Direct interaction of new paralogous genes, as measured using high-resolution chromatin conformation capture, should inform future research and single cell transcriptome sequencing should help achieve specificity while studying gene sub- and neo-functionalization.