Gene Expression Dominance in Allopolyploids: Hypotheses and Models

The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets. Here, we explore quantitative models of regulatory mismatches leading to gene expression dominance. We also suggest that, when pairs of merged genomes are similar from one allopolyploidization event to another, gene-level and genome dominance patterns should also be similar. An increasing number of studies are addressing the molecular bases of nonadditive contributions of the two parents to allopolyploids. Gene expression dominance can be a genome-wide trend called genome dominance, which leaves an evolutionary footprint. The prevailing explanation for genome dominance is that the two genomes differ in their complements of TEs, which can repress nearby genes. Regulatory mismatches between trans effectors and their target genes can contribute to gene expression dominance.