Abstract
SummaryBread wheat (Triticum aestivum L.) is an allopolyploid species containing three ancestral genomes. Therefore, three homoeologous copies exist for the majority of genes in the wheat genome. Whether different homoeologs are differentially expressed (homoeolog expression bias) in response to biotic and abiotic stresses is poorly understood. In this study, we applied a RNA‐seq approach to analyse homoeolog‐specific global gene expression patterns in wheat during infection by the fungal pathogen Fusarium pseudograminearum, which causes crown rot disease in cereals. To ensure specific detection of homoeologs, we first optimized read alignment methods and validated the results experimentally on genes with known patterns of subgenome‐specific expression. Our global analysis identified widespread patterns of differential expression among homoeologs, indicating homoeolog expression bias underpins a large proportion of the wheat transcriptome. In particular, genes differentially expressed in response to Fusarium infection were found to be disproportionately contributed from B and D subgenomes. In addition, we found differences in the degree of responsiveness to pathogen infection among homoeologous genes with B and D homoeologs exhibiting stronger responses to pathogen infection than A genome copies. We call this latter phenomenon as ‘homoeolog induction bias’. Understanding how homoeolog expression and induction biases operate may assist the improvement of biotic stress tolerance in wheat and other polyploid crop species.
Highlights
The vast majority of extant plants species either currently exist in a state of polyploidy or have been affected by polyploidization events during their evolutionary history
We investigated homoeolog-specific gene expression patterns of bread wheat infected with F. pseudograminearum, a necrotrophic fungal pathogen (Akinsanmi et al, 2006), to determine whether different subgenomes respond to pathogen attack differently
Our analyses suggest that individual wheat subgenomes contribute disproportionately to the overall response to F. pseudograminearum with B and D subgenomes displaying a greater contribution than the A subgenome
Summary
The vast majority of extant plants species either currently exist in a state of polyploidy (neopolyploidy) or have been affected by polyploidization events during their evolutionary history (paleopolyploidy; Blanc and Wolfe, 2004; Wood et al, 2009). Plants undergo dramatic alterations to global gene expression immediately after a polyploidization event followed by a gradual reversion on an evolutionary timescale to a diploid state (Feldman and Levy, 2009). Without such correction, increased dosage may be detrimental to plant fitness in newly formed polyploids due to the risk of unbalancing the fine-tuned regulation of many biological functions in progenitor species (Bekaert et al, 2011; Birchler et al, 2005). This process has been shown to occur in a nonrandom fashion, resulting in uneven contribution of particular biological processes and molecular functions from specific subgenomes, a phenomenon termed functional compartmentalization or subfunctionalization (Bekaert et al, 2011)
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