Towards Stewardship of Wild Species and Their Domesticated Counterparts:
A Case Study in Northern Wild Rice (Zizania palustris L.)
Abstract
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 North America. In this study, we assembled and
genotyped a diverse collection of 839 NWR individuals using
genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide
polymorphisms (SNPs). Our collection consisted of samples from 12 wild
NWR populations collected across Minnesota and Western Wisconsin, some
of which were collected over two time points; a representative
collection of cultivated NWR varieties and breeding populations; and a
Zizania aquatica 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 geographical location, with some clustering
patterns likely influenced by historical ecosystem management.
Cultivated populations were genetically distinct from wild populations,
suggesting limited gene flow between the semi-domesticated crop and its
wild counterparts. The first genome-wide scans of putative selection
events in cultivated NWR suggest that the crop is undergoing heavy
selection pressure for traits conducive to irrigated paddy conditions.
Overall, this study presents a large set of SNP markers for use in NWR
genetic studies and provides new insights into the gene flow, history,
and complexity of wild and cultivated populations of NWR.