Patterns of genetic variation in a prairie wildflower, Silphium integrifolium, suggest a non-prairie origin and untapped variation available for improved breeding
Understanding the relationship between genetic structure and geography provides information about a species' evolutionary history and can be useful to breeders interested in de novo domestication. Silphium integrifolium is an iconic perennial American prairie wildflower that is targeted for domestication as an oilseed crop. Germplasm in the existing breeding program is derived from accessions collected in restricted geographic regions. We present the first application of population genetic data
... lation genetic data in this species to address the following goals (1) improve existing breeding programs by characterizing genetic structure and (2) identify the species geographic origin and potential targets and drivers of natural selection as the range has expanded. We developed a reference transcriptome to use as a genotyping reference for dozens of samples from throughout the species range. Population genetic analyses were used to describe the distribution of genetic variation and demographic inference modeling was used to characterize potential processes that have shaped variation. Divergence outlier scans for selection and associations with environmental variables were used to identify loci linked to putative targets and drivers of natural selection. Genetic variation partitions samples into three geographic clusters. Patterns of variation and demographic modeling suggests that the geographic origin of the species is in the American southeast. Breeding program accessions are from the region with lowest observed genetic variation. This iconic prairie species did not originate within the modern prairie. Breeding programs can be improved by including accessions from outside of the germplasm founding region, which has relatively little genetic variation compared to the south and east. The observed geographic structuring of variation coupled with the identified targets and environmental drivers of adaptation during range expansion can guide future collecting efforts towards wild populations with beneficial agronomic traits.