Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton

A putative advantage of allopolyploidy is the possibility of differential selection of duplicated (homeologous) genes originating from two different progenitor genomes. In this note we explore this hypothesis using a high throughput, SNP-specific microarray technology applied to seed trichomes (cotton) harvested from three developmental time points in wild and modern accessions of two independently domesticated cotton species, Gossypium hirsutum and G. barbadense. We show that homeolog expression ratios are dynamic both developmentally and over the several-thousand-year period encompassed by domestication and crop improvement, and that domestication increased the modulation of homeologous gene expression. In both species, D-genome expression was preferentially enhanced under human selection pressure, but for nonoverlapping sets of genes for the two independent domestication events. Our data suggest that human selection may have operated on different components of the fiber developmental genetic program in G. hirsutum and G. barbadense, leading to convergent rather than parallel genetic alterations and resulting morphology.