Partial redundancy buffers deleterious effects of mutating <i>DNA methyltransferase 1-1</i> (<i>MET1-1</i>) in polyploid wheat

DNA methylation plays important roles in gene expression, transposable element silencing, and genome stability. Altering DNA methylation could generate additional phenotypic variation for crop breeding, however the lethality of epigenetic mutants in crop species has hindered its investigation. Here, we exploit partial redundancy between homoeologues in polyploid wheat to generate viable mutants in the DNA methyltransferase 1-1 (MET1-1) gene with altered methylation profiles. In Triticum turgidum (tetraploid wheat) and Triticum aestivum (hexaploid wheat), we found under-representation of higher order mutants (5/6 and 6/6 mutant met1-1 copies in hexaploid wheat and 3/4 and 4/4 copies in tetraploid wheat) when genotyping segregating seeds and seedlings, due to reduced transmission of null mutant gametes from the paternal and maternal side. The loss of four or more functional copies of MET1-1 results in decreased CG methylation in hexaploid wheat. Changes to gene expression increase stepwise with the number of mutant alleles, suggesting a dosage-dependent effect. We identified heritable changes to flowering and awn phenotypes which segregate independently of MET1-1. Together our results demonstrate that polyploidy can be leveraged to generate quantitative changes to CG methylation without the lethal consequences observed in other crops.