LAUSR

Abstract Waterlogging is a global abiotic stress that seriously restricts the growth and yield of wheat. DNA methylation is the most common epigenetic modification and plays an important role in plant responses to adverse conditions. In this study, the methylation-sensitive amplification polymorphism (MSAP) sequencing approach was used to detect the methylation levels and pattern changes under hypoxia stress in different waterlogging tolerance wheat ( Triticum aestivum L.) genotypes. Methyltransferase gene expression and protein levels were higher in the tolerant wheat genotype. Although demethylation occurred predominantly in both wheat genotypes, waterlogging-related genes, such as ERF1 , ACC1 , and CKX2.3 , were significantly upregulated only in the tolerant genotype by demethylation, whereas other genes, such as RGA2 , were significantly downregulated only in the sensitive genotype. N 6 -Methyladenosine (m 6 A) content decreased significantly in the leaves of the sensitive genotype but remained unchanged in the tolerant genotype. Our results showed that both DNA and RNA methylations play a regulatory role in wheat response to waterlogging stress.