Comparative Proteomics of Diploid and Polyploid Cotton

Polyploidy has played a spectacular role in plant evolution. Through allopolyploidization, two or more divergent genomes are combined into a common nucleus, which is often followed by rapid as well as longer-term genomic and epigenetic responses. Little is known, however, about how genomic merger and doubling reverberate through the various “omics” to ultimately affect phenotypes or evolutionary trajectories. Recent application of proteomic approaches to polyploid plants suggest that genomic merger and doubling have consequences that extend beyond the transcriptome into the realm of the proteome, providing a promising experimental arena for enhancing understanding of plant adaptation and function. Using the model polyploid system provided by the cotton genus (Gossypium) as an example, we will demonstrate several approaches for interspecific comparisons of protein composition and expression among diploid and polyploid species. In addition, we will describe patterns of non-additive expression, expression level dominance and homoeolog expression bias at the proteome level. We discuss prospects and challenges inherent in characterizing protein products of duplicated genes, as well as the combined use of the different -omics approaches in polyploid plants.