Cotton Characterization

Expression bias exists between duplicated genes of polyploid plant genomes. Recent research in allotetraploid cotton petal tissue show a conservation of expression bias.  This conservation of bias suggested there was a mechanism controlling this bias, including cis and trans acting mechanisms.  Recent studies in other plant species suggest cis acting mechanisms play an important role in polyploid expression bias.

In this study, the structures of the cis acting mechanisms in biased genes were quantified.  This includes the number and size of indels in the upstream 5’ region, the downstream 3’ region, and in introns and exons within Illumina WGS data and Sanger sequencing reads.

Differences in indels in the promoter regions of biased genes appeared to be more associated with biased gene expression than other quantified differences..  Genes that have a higher expression level appear to have more deletions than then duplicate homoeolog. This suggests that expression biases in polyploids are a product of cis-acting mechanisms that diverged during speciation of the A- and D-genomes of cotton.