Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

Abstract

Effects of polyploidy in allohexaploid wheat (Triticum aestivum L.) have primarily been ascribed to increases in coding sequence variation and potential to acquire new gene functions through mutation of redundant loci. However, regulatory variation that arises through new promoter and transcription factor combinations or epigenetic events may also contribute to the effects of polyploidization. In this study, gene expression was characterized in a synthetic T. aestivum line and the T. turgidum and Aegilops tauschii parents to establish a timeline for such regulatory changes and estimate the frequency of nonadditive expression of homoeologous transcripts in newly formed T. aestivum. Large-scale analysis of nonadditive gene expression was assayed by microarray expression experiments, where synthetic T. aestivum gene expression was compared to additive model values (mid-parent) calculated from parental T. turgidum and Ae. tauschii expression levels. Approximately 16% of genes were estimated to display nonadditive expression in synthetic T. aestivum. A certain fraction of the genes (2.9%) showed overdominance or underdominance. cDNA-single strand conformation polymorphism analysis was applied to measure expression of homoeologous transcripts and further verify microarray data. The results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and nonadditive gene expression in T. aestivum.

Genomically Biased Accumulation of Seed Storage Proteins in Allopolyploid Cotton

“…In the recently formed natural allotetraploid Tragopogon miscellus, higher levels of expression have been reported for homoeologs originating in T. dubius vs. those originating in T. pratensis (Buggs et al 2010). Similar studies in allopolyploid wheat have also demonstrated nonequivalent expression patterns among homoeologs (Bottley et al 2006Pumphrey et al 2009). In cotton, biased expression of D-genome homoeologs has been reported for petal and fiber tissues in G. hirsutum Hovav et al 2008).…”

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

“…Therefore, this type of rapid genetic instability likely has played some roles in the initial establishment and eventual speciation of T. aestivum (Levy and Feldman 2004;Feldman and Levy 2005;Feldman and Levy 2009). Similarly, genome-wide changes in gene expression in the early generations of nascent allohexaploid wheat have also been documented as a general occurrence in multiple independent lines (Pumphrey et al 2009;Akhunova et al 2010;Chague et al 2010;our unpublished data), so were in other studied plant taxa (reviewed in Osborn et al 2003;Adams and Wendel 2005b;Comai 2005;Chen and Ni 2006;Adams 2007;Chen 2007;Doyle et al 2008;Hegarty and Hiscock 2008;Flagel and Wendel 2009;Jackson and Chen 2009;Soltis and Soltis 2009).…”

The legacy of diploid progenitors in allopolyploid gene expression patterns

“…Thus, the only measure of parental legacies was whether or not overall expression was equal to or different from the 'mid-parent value' (MPV), the mean expression of the two parental species (often represented by sister genomes of the allopolyploid subgenomes; figure 1) at that locus. Such studies were conducted on several allopolyploids, including Arabidopsis [35], Gossypium [36,37], Senecio [26,38], Brassica [39], Triticum [40][41][42] and Spartina [23,43].…”