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.

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