Chenopodium polyploidy inferences from Salt Overly Sensitive 1 ( SOS1 ) data

• Premise of the study: Single‐copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50–75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single‐copy nuclear locus Salt Overly Sensitive 1 ( SOS1 ) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. • Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid‐mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. • Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A–D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. • Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum , was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa , and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium , groups with American diploid species, which suggests a transoceanic dispersal.