Evolution of duplicate gene expression

One of the important realizations to emerge from numerous studies of polyploid plants is that polyploid creates massive alterations in gene expression.  In every allopolyploid examined to date, some fraction of the duplicate gene pairs are expressed unequally, and this suite of unequally expressed genes may itself favor one of the co-resident genomes, leading to a transcriptome that is unequally expressed with respect to the component genomes. This can vary quantitatively and qualitatively among species, tissues, and even cell lines and single cells, and is a fundamental feature of allopolyploids.

Biased homoeolog expression in polyploids 

Figure from Grover et al., 2012

In addition to this genome bias, polyploids almost always show expression level dominance, where, for a given gene, the total expression of homoeologs is statistically the same as only one of the polyploid parents. Originally described by Rapp et al. (2009) using cotton, this work has been confirmed and extended by Flagel & Wendel (2010), Yoo et al., (2013) and many others (see Grover et al., 2012 for perspective and review; all citations on publication page). Now that the phenomenon has been described, we are undertaking efforts to understand the mechanistic bases of both homoeolog bias and expression level dominance, using a combination of molecular biological tools including high throughput sequencing, monococcal nuclease assays, and chromatin immunoprecipitation. This work holds promise for helping us understand, for example, why some duplicate gene pairs are co-regulated, whereas other homoeolog pairs behave independently of one another.  See Hu and Wendel, 2018 for perspectives on genomic architecture, cis-trans relationships, and duplicate gene expression.

Co-regulation of duplicated genes

Modified from Yoo et al., 2013