DNA methylation in cotton evolution

Polyploidy, accompanied by reorganization of genomic structure and regulatory networks, is recognized as pervasive force in plant evolution . DNA methylation is a conserved epigenetic mark participating in gene expression regulation and transposable elements (TEs) silencing. However, roles of DNA methylation in polyploidy are not well understood. Here we show DNA methylation patterns during polyploidy and domestication in cotton. The effects of hybridization on DNA methylation changes were conserved during subsequent polyploidy and evolution. Homoeologous DNA methylation exchanges without DNA sequence variation were involved in homoeolog expression bias in polyploidy. The expression of GhCOL2_D, homolog of Arabidopsis CONSTANS, was elevated due to DNA methylation loss in cotton domestication. In addition, knocking down of GhCOL2 delayed flowering of cultivated cotton, suggesting demethylation of GhCOL2_D contributed to loss of photoperiod sensitive in cotton domestication. Our results provide new insights about roles of DNA methylation in polyploidy and domestication of plant.