Description of the F0/F1 ASE test for cis- and trans-acting gene expression regulation. (A) Each inbred parent possesses only the cis and trans factors associated with that genotype, while the F1 hybrid possesses both. (B) In the simplest case where ASE patterns are affected by a single cis element, allelic imbalance ratios are identical across generations. (C) In the case where a single trans factor causes ASE variation, the F1 ASE counts should be identical for both alleles since both trans factors are acting on each allele. To illustrate the effects of cis- and trans-by-treatment interactions, take the case where an experimental treatment induces the expression of a HAL2-specific cis- or trans-acting repressor (green symbol, dashed lines). The resultant expression patterns would shift so that the difference between alleles (cis-by-treatment, D) or the slope of the genotype*generation interaction depends on the treatment (trans-by-treatment, E). The scheme presented here is a simplification, and all combinations of cis, trans additive effects and interactions with the environment are possible.
