Polyploidy: genome obesity and its consequences.

Polyploidy is a major evolutionary feature of many plants and some animals (Grant, 1981; Otto & Whitton, 2000). Allopolyploids (e.g. wheat, cotton, and canola) were formed by combination of two or more distinct genomes, whereas autopolyploids (e.g. potato, sugarcane, and banana) resulted from duplication of a single genome. Both allopolyploids and autopolyploids are prevalent in nature (Tate et al., 2004). Recent research has shown that polyploid genomes may undergo rapid changes in genome structure and function via genetic and epigenetic changes (Fig. 1) (Levy & Feldman, 2002; Osborn et al., 2003; Chen, 2007). The former include chromosomal rearrangements (e.g. translocation, deletion, and transposition) and DNA sequence elimination and mutations, whereas epigenetic modifications (chromatin and RNA-mediated pathways) give rise to gene expression changes that are not associated with changes in DNA sequence. Over time, polyploids may become ‘diploidized’ so that they behave like diploids cytogenetically and genetically. Comparative and genome sequence analyses indicate that many plant species, including maize, rice, poplar, and Arabidopsis, are recent or ancient diploidized (paleo-) polyploids. Fig. 1 Diagram of allopolyploid formation and evolution The consequences of polyploidy have been of long-standing interest in genetics, evolution, and systematics (Wendel, 2000; Soltis et al., 2003). Research interest in polyploids has been renewed in the past decade following the discovery of multiple origins and patterns of polyploid formation (Soltis et al., 2003) and rapid genetic changes in resynthesized allotetraploids in Brassica (Song et al., 1995) and wheat (Feldman et al., 1997). Rapid technological advances have also facilitated genomic-scale investigation of polyploids and hybrids (Wang et al., 2006). Many ongoing studies are focused on investigation of: (i) the evolutionary consequence of gene and genome duplications in polyploids; (ii) genomic and gene expression changes in resynthesized allotetraploids; (iii) genetic and gene expression variation in natural populations of polyploids; and (iv) comparison of genetic and gene expression changes in resynthesized and natural polyploids (Wendel, 2000; Osborn et al., 2003; Soltis et al., 2003; Comai, 2005; Chen, 2007). The presentations given at the Polyploidy workshop, Plant and Animal Genome XV Conference (http://www.intl-pag.org/), reflected these current research themes, reporting on ancient polyploidy events in Glycine, expression evolution of duplicate genes in Arabidopsis, gene expression changes in resynthesized Brassica and wheat allopolyploids, hybridization barriers in Arabidopsis, and tissue-specific and stress-induced expression patterns of duplicate genes in cotton and hybrid Populus. ‘… expression of duplicate genes in response to developmental programs is more strongly correlated than that of duplicate genes in response to environmental stresses, suggesting rapid evolution of duplicate genes in response to external factors’