Foxtail millet (Setaria italica) is the second most important millet species globally, adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail (S. viridis), it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops.

We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to wild S. viridis. Further, we aimed to identify genes involved in environmental stress tolerance, that have undergone differential selection between geographical and genetic groups.

328 S. italica landrace accessions and 12 S. viridis accessions were sequenced by genotyping-by-sequencing (GbS). After filtering, 5677 single nucleotide polymorphisms (SNPs) were retained for the combined S. italica/S. viridis dataset, and 5020 SNPs for the S. italica dataset. We extended geographic coverage of S. viridis by including previously published GbS sequence tags, yielding an 825-SNP dataset for phylogenetic reconstruction.

All S. italica samples were monophyletic relative to S. viridis, suggesting a single origin of foxtail millet, although no group of S. italica was clearly the most ancestral. Four genetic clusters were found within S. italica, with distinctive geographical distributions. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes in comparisons between clusters potentially involved in environmental adaptations, particularly to novel climates encountered as domesticated foxtail millet spread to new altitudes and latitudes.