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Out of the almost 2,000 plants that have been selected as crops, only a few are fully domesticated, and many intermediates between wild plants and domesticates exist. Genetic constraints might be the reason why incompletely domesticated plants have few characteristic crop traits, and retained numerous wild plant features. Here, we investigate the incomplete domestication of an ancient grain from the Americas, amaranth. We sequenced 121 genomes of the crop and its wild ancestors to show that grain amaranth has been selected three times independently from a single wild ancestor, but has not been fully domesticated. While only few domestication traits have been adapted during amaranth domestication, the seed color converted from dark seeds to white seeds between the ancestor and the crops. To investigate the seed color adaptation in amaranth we produced a mapping population between wild and domesticated amaranth, a whole genome sequenced bulked segregant population and perform genome wide association mapping in our divers panel. All three methods agree on two quantitative trait loci controlling the trait. We identify a MYB-like transcription factor gene, a known regulator for seed color variation in other plant species, within one of the significant regions and shows that the trait was independently converted in Central and South America. We propose that a low effective population size at the time of domestication might have contributed to the lack of adaptation of complex domestication traits. Our results show how genetic constraints influenced domestication and might have set the fate of hundreds of crops. Significance Early farmers cultivated hundreds of plant species and altered their morphological and physiological characteristics during domestication to be well suited for human consumption. Despite long cultivation histories, many crops remained of minor importance, because they were limited in their adaptation to agro-ecological systems. We investigate the domestication history of the ancient minor crop amaranth and show that it was independently domesticated three times from the same ancestor. In all three domesticates, white seed color, which is controlled by only two genes, was independently selected. In contrast, more complex domestication traits like seed size were not changed during domestication, and our analyses suggest that this may have resulted from a lack of functional genetic variation in the ancestor during domestication. |
