Incomplete domestication of South American grain amaranth (Ama- ranthus caudatus) from its wild relatives

1 Grain amaranth is a pseudo-cereal and an ancient crop of Central and South America. Of the 2 three species of grain amaranth, Amaranthus caudatus is mainly grown in the Andean region. 3 Several models of domestication were proposed including a domestication from the wild rela4 tives A. hybridus or A. quitensis. To investigate the domestication history of A. caudatus and 5 its relationship to the two wild relatives, we used genotyping-by-sequencing (GBS) to geno6 type 119 amaranth accessions from the Andean region. We determined the genome sizes of 7 the three species and compared phenotypic variation in two domestication-related traits, seed 8 size and seed color. We show that the population genetic analysis based on 9,485 SNPs 9 revealed very little genetic differentiation between the two wild species, suggesting they are 10 the same species, but a strong differentiation between wild and domesticated amaranths. A. 11 caudatus has a higher genetic diversity than its wild relatives and about 10% of accessions 12 showed a strong admixture between the wild and cultivated species suggesting recent gene 13 flow. Genome sizes and seed sizes were not significantly different between wild and domesti14 cated amaranths, although a genetically distinct cluster of Bolivian accessions had significantly 15 larger seeds. Taken together our analysis suggests that grain amaranth is an incompletely do16 mesticated species, either because it was not strongly selected or because high levels of gene 17 flow from its sympatric wild relatives counteract the fixation of key domestication traits in the 18 domesticated A. caudatus. 19 Page 2 not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/025866 doi: bioRxiv preprint first posted online Sep. 1, 2015;