Description |
Wheat is a powerful genetic model for studying polyploid evolution and crop domestication. Hexaploid bread wheat was formed by two rounds of interspecific hybridization and polyploidization. However, genetic and epigenetic effects on tetraploid-hexaploid wheat evolution remain elusive. Here we report genome-wide DNA methylation landscapes in Extracted Tetraploid Wheat (ETW, AABB), natural hexaploid wheat (NHW, AABBDD), resynthesized hexaploidy wheat (RHW, AABBDD), natural diploid (DD) and tetraploid wheats (AABB). In the endosperm, levels of DNA methylation, especially in CHG (H=A, T or C) context, were dramatically decreased in the ETW relative to natural hexaploid wheat, and those demethylated regions were re-methylated in resynthesized hexaploid wheat upon adding back of the D-genome. Hypo-differentially methylated regions (DMRs) (880,273) are 26-fold more than hyper-DMRs (33,567) in ETW, which were correlated with gene and TE expression dynamics. Moreover, hypo-DMRs in ETW were associated with reduced H3K9me2 levels and increased expression of histone genes. In natural hexaploid wheat, TEs correlated with DNA methylation changes, which in turn altered expression of TE-associated genes. These results indicate a dynamic role for DNA methylation in mediating gene and TE expression in response to genome merger and separation during tetraploid-hexaploid wheat formation and evolution. |