Genome‐wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids

Abstract

Summary The present study aims to understand regulation of gene expression in synthetic and natural wheat (Triticum aestivum) allohexaploids, that combines the AB genome of Triticum turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome‐wide analysis of gene expression that allowed characterization of the effect of variability of the D genome progenitor, the intergenerational stability as well as the comparison with natural wheat allohexaploid. We used the Affymetrix GeneChip Wheat Genome Array, on which 55 049 transcripts are represented. Additive expression was shown to represent the majority of expression regulation in the synthetic allohexaploids, where expression for more than c. 93% of transcripts was equal to the mid‐parent value measured from a mixture of parental RNA. This leaves c. 2000 (c. 7%) transcripts, in which expression was nonadditive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high intergenerational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is established early upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids.

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as a general occurrence in multiple independent lines (Pumphrey et al 2009;Akhunova et al 2010;Chague et al 2010;our unpublished data), so were in other studied plant taxa (reviewed in Osborn et al 2003;Adams and Wendel 2005b;Comai 2005;Chen and Ni 2006;Adams 2007;Chen 2007;Doyle et al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).…”

Quantitative trait locus analysis for flowering-related traits using two F₂ populations derived from crosses between Japanese common wheat cultivars and synthetic hexaploids

“…tauschii (DD) genomes affects gene expression profiles in synthetic hexaploid wheat (Pumphrey et al, 2009;Chagué et al, 2010). This alteration of gene expression is considered to be due to epistatic interaction between the AB and D genomes and genetic and epigenetic modification of the chromatin structure (Khasdan et al, 2010;Mestiri et al, 2010;Feldman et al, 2012).…”

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].…”