Homoeolog expression in polyploid wheat mutants shows limited transcriptional compensation

Here, we assessed whether transcriptional compensation is prevalent between homoeologs in hexaploid and tetraploid wheat using ethyl methanesulfonate (EMS) mutagenised Targeting Induced Local Lesions in Genomes (TILLING) lines (Krasileva et al., 2017). Each wheat TILLING line has a large number of mutations (>?5000 in the hexaploid cultivar Cadenza; Krasileva et al., 2017), allowing us to simultaneously screen the effect of many mutations. We performed RNA-sequencing and differential gene expression analysis to determine whether genes are frequently upregulated in response to a loss-of-function mutation in one of their homoeologs. We found no evidence for widespread active transcriptional compensation between homoeologs, with a rate of c. 3% in hexaploid and tetraploid wheat, indicating that such a mechanism is unlikely to be the primary cause of functional redundancy between homoeologs in polyploid wheat.