Wang Zheng, Yang Jinghua, Cheng Feng, Li Peirong, Xin Xiaoyun, Wang Weihong, Yu Yangjun, Zhang Deshuang, Zhao Xiuyun, Yu Shuancang, Zhang Fenglan, Dong Yang, Su Tongbing
Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing 100097, China.
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.
Hortic Res. 2022 Apr 22;9:uhac090. doi: 10.1093/hr/uhac090. eCollection 2022.
Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the 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 , a typical allopolyploid with subgenome dominance. Polyploidization provides the genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in . Above and beyond the fundamental understanding of WGD and subgenome dominance in and other plants, however, it 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 acceleration of 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 of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.
多倍体化或全基因组复制（WGD）是被子植物中一种广为人知的物种形成和适应机制，而亚基因组优势是异源多倍体中的一个关键现象，它在多倍体化之后确立。占主导地位的亚基因组对基因组进化和同源基因表达偏向的贡献更大，这两者都为短期表型适应和长期驯化带来优势。在本综述中，我们首先总结了亚基因组优势可能的机制基础，包括遗传因素（转座子、遗传不相容性和同源交换（HE））、表观遗传因素（DNA甲基化和组蛋白修饰）以及发育和环境因素对这一进化过程的影响。然后我们转向[具体物种名称]，一个具有亚基因组优势的典型异源多倍体。多倍体化不仅为[具体物种名称]基因组提供了适应多变环境的基因组可塑性，还为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”，[具体物种名称]在全基因组复制过程中经历了两次基因组精简，其中大多数响应环境信号和植物激素的基因被过度保留，增强了亚基因组优势及随之而来的适应性。不仅如此，最近构建的18个具有不同形态类型的[具体物种名称]种质的泛基因组提供了进一步的证据，以揭示多倍体化和亚基因组优势对[具体物种名称]种内多样化的影响。然而，除了对[具体物种名称]和其他植物中全基因组复制和亚基因组优势的基本理解之外，为什么亚基因组优势具有组织和时空特异性特征，并且在异源多倍体中能够因环境因素在不同亚基因组的同源区域之间转换，这仍然难以捉摸。我们最后提议加速合成异源多倍体、组学技术和基因组编辑工具的联合应用，以加深对各种物种和环境中亚基因组优势的遗传和表观遗传机制的研究。我们相信，与亚基因组优势相关的各种具有生态、进化和农业意义的性状的基因组和遗传基础的意义将被揭示，并有助于做出新的发现和作物育种。
