Standing between us and global food shortage are high yielding varieties of wheat, oilseed rape, potato, maize and sugarcane. These come from diverse plant families, but share the fact that they have undergone recent hybridisation and whole genome duplication (that is, they are allopolyploids). How the possession of two complete sub-genomes from different parental species might contribute to their high yields is not fully understood, but it certainly does contribute to complexity in bioinformatic analyses of the genomes and transcriptomes of these crops (for example, Harper et al., 2012).
Few laboratories have studied the complexities of allopolyploid crops as intently as the group of Jonathan Wendel at Iowa State University. Taking cotton as their study system over the past decade, the Wendel lab have applied a portfolio of newly emerging technologies to characterise patterns of gene expression in wild and cultivated species of diploid and allopolyploid cotton. Starting with single-stranded conformation polymorphism analysis (Adams et al., 2003), they moved on to two generations of Nimblegen microarrays (Udall et al., 2006, 2007; Flagel et al., 2008; Hovav et al., 2008; Rapp et al., 2009), Sequenom MassARRAYs (Chaudhary et al., 2009), proteomics (Hu et al., 2011), and as reported by Yoo et al. (2012), high coverage Illumina sequencing.