Abstract
Allopolyploidy is a prevalent process in plants, having important physiological, ecological, and evolutionary consequences. Massive, genome-wide transcriptomic rewiring in response to genomic merger and doubling has been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression-level dominance, and revamping of co-expression networks. Here we present an analytical framework to investigate expression change in allopolyploids as governed by distinct sets of intra- and inter-subgenome cis-trans relationships. The analytical framework devised is a novel extension of classic allele-specific expression analysis to incorporate and distinguish the separate effects of parental regulatory as well as expression differences in cis or trans, while providing the conceptual basis and tools to reconcile various patterns of regulatory novelty following hybridization and allopolyploidy.