Identification of single nucleotide polymorphism markers for population genetic studies in Zizania palustris L.

Northern wild rice (NWR; Zizania palustris L.) is an annual, aquatic grass native to North America. Minnesota is a center of diversity for NWR where the plant provides food and shelter to a number of species and is an important indicator of water quality. In addition to its ecological functions, NWR is an important food source for humans and has been hand-harvested by canoe for centuries by indigenous peoples who consider it sacred. Since the 1950s, the species has also been cultivated in paddies. The species does not tolerate dry storage, so genetic diversity cannot be preserved in ex-situ gene banks. Knowledge of the genetic constitution of NWR is crucial towards the preservation of NWR in the wild. Reductions in the cost of next-generation sequencing have enabled novel genotyping methods, including genotyping-by-sequencing (GBS). The goal of this research was to test the utility of GBS in generating single nucleotide polymorphism (SNP) markers on a small number of NWR genotypes from natural stands as well as breeding lines. A sequencing depth of 2 M reads per genotype was identified as sufficient to generate ~ 2500 genome-wide SNP markers and conduct genetic diversity analyses.