Orphan crops can play an essential role in future food security. Although they often have excellent nutritious composition and are able to grow in unfavourable conditions, they have been understudied in the last decades, and key improvement technologies are lacking. One promising orphan crop is grain amaranth, an ancient pseudo-cereal from the Americas with high nutritional value and excellent amino acid composition. During three independent domestications, the seed colour of grain amaranth has changed from dark to pale due to a change in secondary metabolite accumulation. My thesis aims (i) to establish transformation and genome editing for the non-model plant amaranth and (ii) to combine molecular biology and evolutionary genetic approaches to understand the cause and effect of the seed colour change.