The Role That Transposable Elements May Play in Differential Expression Levels of Maize Paralogs

Allotetraploid plants inherit two distinct genomes with two distinct evolutionary histories.  One factor that can distinguish, or mark, those genomes is the number of transposable elements (TEs) near genes.  Previous work indicates that silencing of transposable elements has a repressive effect on nearby genes, suggesting that TE silencing involves a compromise between TE control and optimal levels of gene expression.  Further, the available data suggest that differences between the progenitors of allotetraploids in the degree of that compromise can result in global differences in gene expression between duplicate genes.  This in turn may lead to relaxed selection on genes from the “recessive” subgenome.  In many cases, this results in differential rates of duplicate gene loss, or fractionation.  However, even when both homeologs are retained, relaxed selection on one of the two retained homeologs has long term and ongoing consequences.  Using maize as an example, we will describe some of those consequences.