Genetic Analysis of Wild and Cultivated Populations of Northern Wild Rice (Zizania palustris L.) Reveal New Insights into Gene Flow and Domestication

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of the United States and Canada. Understanding the genetic diversity of NWR is essential to conservation efforts. In this study, we assembled and genotyped a diverse collection of 789 NWR individuals using genotyping-by-sequencing and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations, some of which were collected temporally, a representative sampling of cultivated NWR germplasm, and a Zizania aquatica population (outgroup). Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their lake or river of origin as well as larger clustering patterns based on watershed assignment. Contextualizing some clustering patterns with historical knowledge of ecosystem management helped to unravel some of the complexity of the population structure of wild populations. Cultivated materials were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. Estimates of linkage disequilibrium (LD) in NWR demonstrated that LD decays quickly across the genome and provided insights into the quality of the reference genome assembly of NWR. The first genome-wide scans of putative selection events in cultivated NWR were also evaluated. Overall, this study presents a large set of new SNP markers for use in NWR genetic studies as well as new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR. ### Competing Interest Statement The authors have declared no competing interest.