Abstract
Plant domestication has had profound impacts on the morphology and genetic diversity of crops. Beyond sequence diversity, changes in chromatin structure can play an important role in plant adaptation. However, the interplay between the chromatin landscape and plant domestication remains unclear. Here, we present a high-quality genome assembly and chromatin landscape map of the ancient pseudo-cereal, amaranth. ATAC-sequencing of multiple accessions of three grain amaranth species and two wild relatives, shows that the overall amount of accessible chromatin is highly conserved, but about 2.5% of all chromatin switched states, with a higher fraction of the genome repeatedly opening during domestication processes. These differentially accessible chromatin regions, between the crops and their wild ancestor, are species-specific and significantly associated with selective sweeps - reflecting the repeated independent domestication of amaranth. Our findings reveal the dynamic interplay between domestication and the chromatin landscape, highlighting an additional layer of diversity in crops.