Over the last decade, it has become apparent that polyploid genomes are not always a simple sum of their constituent genomes, but products of dynamic genetic and epigenetic changes that occur upon, or shortly after, polyploid formation. Epigenetic changes, which involve alterations of gene expression without a change in DNA sequence, are particularly intriguing because they play essential roles in plant development and plant defense against viruses and transposons. In nascent polyploids, observed epigenetic phenomena include nucleolar dominance, changes in DNA methylation and chromatin structure, triggering silencing or activation of genes and (retro)transposons, and novel phenotypes (reviewed in Matzke et al., 1999; Comai, 2000; Wendel, 2000; Liu and Wendel, 2002, 2003; Osborn et al. 2003).

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