Single Nucleotide Polymorphism Discovery via Genotyping-by-Sequencing to Assess Population Genetic Structure and Recurrent Polyploidization in Andropogon gerardii

Autopolyploidy is genome duplication within a lineage and can result in multiple cytotypes within a species. In this study, we explore the geographic distributions and evolutionary origins of cytotypes in the widespread, dominant tallgrass prairie species Andropogon gerardii. We conducted population-level sampling from across the geographic range of the species and used genotyping by sequencing to generate single nucleotide polymorphisms (SNPs) for A. gerardii individuals with known cytotypes. We used two distinct approaches to SNP calling: a reference-free approach, the UNEAK pipeline and a reference-guided approach using the sequenced Sorghum bicolor genome. Independent analyses of the two data sets showed similar patterns of clustering of A. gerardii individuals. Individuals originating from geographically proximate populations, regardless of their cytotype, tended to cluster together. Our data sets suggest that, in A. gerardii, higher-order polyploids (individuals with the 9 x cytotype) likely evolved multiple times from 6 x progenitors.