Mechanisms of polyploid formation. For simplicity, the A and D genomes of the diploid species are represented by only two chromosomes, in white and black, respectively. An allopolyploid (AADD) may form as a result of hybridization of the two species (hybrid AD), followed by whole-genome duplication (WGD). Alternatively, the two diploid species may give rise directly to the allopolyploid by fusion of their unreduced gametes.

Additive and non-additive gene regulation in hybrids. Alleles from parental genomes A and D (a.k.a. homoeologs) are shown at the top in black and white, respectively. Additive gene expression in the hybrid occurs when the A and D alleles are expressed in the same fashion as they were in the parents (bottom left). Two basic mechanisms can contribute to non-additivity. In trans-regulation (center) the hybrid overexpresses (top row) or underexpresses (bottom row) positive regulators that act similarly on both alleles. In cis by trans regulation (bottom right) the hybrid expresses a negative regulator that acts specifically on one allele because of differences in the cis-regulatory regions in the A and D genes. Such a regulator could be novel to the hybrid, or be produced from the unaffected parental genome. In the case illustrated here, a 'D-contributed' repressor (open square) acting on a cis-region unique to allele A results in repression of A and thus non-additive expression in the AD hybrid.