Decoding gene expression in polyploid wheat

Many globally important crops are polyploids, for example cotton, sugar cane, potato and wheat. However, the regulation of polyploid genomes is complicated because there are multiple copies of most genes. We have limited knowledge about the molecular mechanisms regulating these gene copies. In this project we will take advantage of the recent revolution in wheat genomics to study how multiple gene copies are regulated polyploid genomes using wheat as a model system.
The most widely grown wheat is hexaploid bread wheat (Triticum aestivum) which has on average three highly similar copies of every gene (homoeologs). The A, B and D homoeologs of each gene are typically >95% identical within coding sequences and can be functionally redundant, i.e. if one homoeolog is mutated no phenotypic effect will be observed due to compensation by the other homoeologs. However, we do not know how common functional redundancy is between homoeologs or understand the molecular mechanisms controlling redundancy. This lack of knowledge limits our ability to control phenotype and hence improve polyploid crops.
Homoeolog expression levels were studied as a first step towards understanding homoeolog redundancy and it was found that 30% of wheat genes show different expression levels between the A, B and D homoeologs suggesting that the homoeologs may be non-redundant. The hypothesis is that the ability to manipulate the relative expression levels of homoeologs may provide a route to reduce functional redundancy and more easily alter phenotypes in wheat. Therefore, this project will investigate the mechanisms that control homoeolog expression levels including epigenetic and nonsense-mediate decay pathways, and their effects on phenotype.