Summary
The genome-wide pattern of purifying selection on deleterious variants has attracted broad interest in breeding and evolutionary biology. Little is known about purifying selection in polyploid species with potential functional redundancy of duplicated homoeologs. Here, we examine the pattern of polymorphisms and the combined effects of both subgenome and gene expression on estimates of purifying selection in the allohexaploid bread wheat. We utilize the de novo annotated assemblies and transcriptome data of the 10+ Wheat Genome Project. Purifying selection is detected after filtering chromosomes harboring segregating foreign introgression by modern breeding. Interestingly, strong purifying selection is observed in the category of genes that are highly expressed in root tissues and are in the D subgenome, which is thought to contribute to the range expansion after allopolyploidization. We suggest that the combination of expressed tissues and subgenomes will inform the target of future wheat breeding to mitigate the effect of deleterious variants.