Epigenetic insights into the domestication of tetraploid peanut

Polyploidization is a crucial evolutionary mechanism driving species domestication that promotes species formation and adaptation by providing additional genetic information to accelerate the functional differentiation of genes and evolution of new traits. Despite its importance as a key epigenetic modification, the role of DNA methylation in polyploid domestication through the regulation of gene expression remains unclear. Here, we performed whole-genome bisulfite sequencing and RNA-seq analysis on the cultivated allotetraploid peanut (Arachis hypogaea L.) and its 2 ancestral diploids to investigate the epigenetic regulatory mechanisms of DNA methylation in the formation of peanut polyploids and in peanut domestication. Our findings unveiled substantial differences in DNA methylation between peanut subgenomes, particularly in non-CG contexts. Specifically, CHG methylation is a key factor regulating the expression bias of homoeologs and dominant subgenome expression, as well as stress-responsive gene expression. Additionally, CHH methylation plays a role in peanut seed development by regulating genes associated with fatty acid biosynthesis and lipid metabolism. In conclusion, our study provides a vital theoretical foundation and perspective on the epigenetics underlying cultivated peanut domestication, especially related to the formation of agronomic traits.