Genetic and Epigenetic Mechanisms for Polyploidy and Hybridity

Polyploidy can be classified as autopolyploidy (whole-genome duplication within a species) and allopolyploidy (duplication of genomes between species). While changes in autopolyploids are primarily dependent on genome dosage, allopolyploidy generates both effects of whole-genome duplication and hybridization or merger between species or genera. Barbara McClintock coined the term "genome shock" to describe some of these effects in interspecific hybrids. The genomes from related species have to sense each other and reconcile their differences in organization, structure, and gene expression in order to overcome postzygotic barriers or hybrid incompatibility, giving rise to successful allopolyploid progeny. This process involves genetic changes through gain or loss of DNA and through chromosomal rearrangements as well as epigenetic changes in the expression of small RNAs, transposons, and protein factors that are divergent between the species. Divergent maternal and paternal genomes are predicted to cause hybrid incompatibilities. Allopolyploids that overcome the incompatibility display a wide range of transgressive phenotypes, including hybrid vigor and novel traits that are selected and maintained in the new allopolyploid species. This chapter reviews the progress and advancements toward the understanding of mechanistic roles for gene expression and small RNA changes in morphological diversity and adaptive evolution of the allopolyploids.