Models for transcriptional and post-transcriptional regulation of nonadditive gene expression in allopolyploids. (a) Cis- and trans-acting effects on transcriptional regulation of nonadditive gene expression in allotetraploids. I. During evolution, changes in cis-regulatory elements may confer “strong/dominant” and “weak/recessive” loci. II. Combination of these loci in the same allotetraploid cells induces cis- and trans-acting effects. Because A. thaliana FRI (AtFRI) is nonfunctional, A. arenosa FRI (AaFRI) trans-activates A. thaliana FLC (AtFLC) and cis-regulates one of the A. arenosa FLC (AaFLC1) loci, leading to overdominance or very late flowering in resynthesized allotetraploids. The cis-regulation and trans-activation are maintained by histone acetylation (Ac in a small purple circle) and methylation (Me in a small orange circle). Functional AaFRI is in a large red circle, and nonfunctional A. thaliana FRI (atflc) is in a white small circle with a slash line. The straight and inclined red arrows indicate cis- and trans-acting effects, respectively, by AaFRI. FLC loci are in oval circles. Blue and green indicates active AtFLC1 and AaFLC1, respectively, and gray indicates silenced AaFLC2. The differences in the expression of three FLC loci may reflect cis-regulatory variation (). III. Cis- and trans-acting interactions and epigenetic regulation of FRI and FLC loci may facilitate selection for flowering-time variation in resynthesized allotetraploids (indicated by a circular wheel). IV. In A. suecica, additional selection forces may enhance the expression of AaFLC1 (color change from dark green in II to yellow green in IV) and related genes such as MAFs (), which facilitate adaptation to cold climate. This simple model may be generalized to explain a mechanism for regulatory interactions between divergent loci in other pathways in the allotetraploids (see text for details). (b) Nonadditive accumulation of mRNAs and small RNAs in allotetraploids (null hypothesis Ho: 2 + 1 = 3). There is evidence that 15–40% of the genes are expressed differently between two closely related species of Arabidopsis (), and a subset of those genes are subjected to nonadditive expression in the allotetraploids. Up- or downregulation of mRNAs may be caused by activation of genes originating in parent A, B, or both. We exclude the situation in which the expression of one locus is compensated by its corresponding homoeologous locus. If the nonadditively accumulated transcripts are small RNAs, such as microRNAs (miRNAs), heterochromatic and transposon-related siRNAs (ht-siRNAs), trans-acting siRNAs (ta-siRNAs), and natural anti-sense (nat-siRNAs), they typically negatively regulate the expression of their target genes. The red and blue wave lines indicate RNA transcripts or small RNAs produced in species A and B, respectively. We hypothetically assign two RNA molecules for species A and one RNA molecule for species B. Note that the number of RNAs in the nascent allotetraploids (F1) is not equal to 3 (2 + 1), suggesting nonadditive regulation (dominance and overdominance if larger than 3 or repression if smaller than 3). Possible changes (dashed arrows) in RNA composition and accumulation (column X) may occur in self-pollinating progeny, which are indicated by orange and green wave lines, respectively. According to the hypothetical outcome, the origins of small RNA upregulation (red in 1–3) and repression (blue in 4–6) are shown in the last column.