Characterization of South American Grain Amaranth (Amaranthus caudatus) Domestication with Genotyping By Sequencing and Whole Genome Sequencing

Grain amaranth is a pseudo-cereal and an ancient crop of Central and South America.  Of the three species of grain amaranth, Amaranthus caudatus is mainly cultivated in the Andean region. To investigate the domestication history of A. caudatus and its relationship to the two wild relatives A. quitensis and A. hybridus, we used genotyping-by-sequencing (GBS) to genotype 119 amaranth accessions from the Andean region. We determined the genome sizes of the three species and compared phenotypic variation in two domestication-related traits, seed size and seed color. A population genetic analysis based on 9,485 SNPs revealed very little genetic differentiation between the two wild species, suggesting they are the same species, but showed a strong differentiation between wild and domesticated amaranths despite evidence for a significant level of recent gene flow. Genome sizes and seed sizes were not significantly different between wild and domesticated amaranths, although a genetically distinct cluster of Bolivian accessions had significantly larger seeds. The analysis of phenotypic traits like seed size and seed color indicates that grain amaranth is an incompletely domesticated species, either because it was not strongly selected or because high levels of gene flow from its sympatric wild relatives counteract the fixation of key domestication traits in the domesticated A. caudatus. We have initiated the resequencing of A. caudatus and wild relativ accessions to resolve the domestication history at greater detail, and first results of this work will be presented.