Polyploidy is an exceptionally common phenomenon, with most, if not all, plants having experienced polyploidization sometime in their genomic history. Much research has been devoted to the genetic, genomic, and transcriptomic consequences of genome merger and doubling. These have revealed a great diversity in responses to polyploidy (e.g., sequence elimination, gene silencing/loss, intergenomic sequence conversion, activation of retroelements, etc) and contributed significantly to our understanding of the consequences of genome merger and doubling. A limitation of the majority of this research, however, is that it focuses on single response components (e.g., genes) that do not act in isolation, but rather often function in highly complex and connected functional pathways and networks that may be sensitive to perturbations. A next step, then, in improving our understanding of polyploidy and the consequences of polyploidy, would be to improve our understanding of the evolutionary dynamics involved not simply in duplicating genes, but in understanding the evolutionary dynamics involved in duplicating entire networks.
Our current project involves just this, i.e., understanding the evolutionary consequences of allopolyploid speciation on pathways and networks. Using the cotton genus (Gossypium) as a well-developed model for studies of polyploidy, we will measure and describe the effects of genome merger and doubling on several interconnected components of the anthocyanin biosynthetic pathway, on three levels: genomic, transcriptomic, and metabolomic. In addition, using the more complex flowering time network, we will describe the responses of an entire network to both to genomic merger and doubling, and to intense directional selection, practiced by early domesticators as cotton was transformed from a wild, photoperiod-sensitive, perennial antecedent into a day-length neutral, annualized row crop. More remarkably, this process was replicated for two different species, providing the unique opportunity to test the repeatability of the evolutionary process and to generate detailed information on the levels at which parallelisms and convergences operate. Together, these studies will provide a novel perspective on an important evolutionary process.