Gene Fractionation and Function in the Ancient Subgenomes of Maize

The maize genome experienced an ancient whole genome duplication ∼10 MYA and the duplicate subgenomes have since experienced reciprocal gene loss such that many genes have returned to single-copy status. This process has not affected the subgenomes equally; reduced gene expression in one of the subgenomes mitigates the consequences of mutations and gene deletions and is thought to drive higher rates of fractionation. Here, we use published data to show that, in accordance with predictions of this model, paralogs with greater expression contribute more to phenotypic variation compared with their lowly expressed counterparts. Furthermore, paralogous genes in the least-fractionated subgenome account for a greater degree of phenotypic diversity than those resident on the more-fractionated subgenome. Intriguingly, analysis of singleton genes reveals this difference persists even after fractionation is complete. Additionally, we show that the two subgenomes of maize may differ in their epigenetic profiles.