Introduction
Northern Wild Rice (NWR; Zizania palustris L.) is an annual, diploid (2n =2x =30), aquatic grass native to the Eastern Temperate and Northern Forest ecoregions of North America1,2. Predominantly found in shallow, slow-moving waters surrounding the Great Lakes region of North America, NWR’s regional significance in these areas is vast and complex3–8. To begin, NWR is a natural resource that provides food and substantial habitat for a wide range of wildlife9,10 as well as important ecosystem services such as anchoring riparian soils and inhibiting algal blooms11. For centuries, this nutritious grain has been hand-harvested from regional lakes and rivers by Dakota and Anishinaabe Peoples 2,12, and ‘psin’ (Dakota) or ‘manoomin’ (Ojibwe, Anishinaabe) remains an integral component of their cultures and lives today. The species has also become a high-value commodity crop that includes hand-harvested grain from regional waters, and cultivated grain from irrigated paddies, grown primarily in Minnesota (MN) and California (CA) 13. As a part of the Oryzae tribe in the Poaceae family, Zizania species are also considered crop wild relatives of Oryza sativa L. (white rice). Given the many roles described above, we contend that the conservation of NWR serves as an important intersection between our ecosystems, our cultures and food, and our economies.
Worldwide, plant species are experiencing declines and extinction events as a result of human activities altering natural ecosystems. For at least the last century, NWR has been experiencing such declines in its native habitats 14,15, and the species appears to be slowly migrating northward 16. Recent reports have stated that NWR is at high risk of loss, and the International Union for Conservation of Nature has added NWR to their red list of threatened species 17. Hydrological changes due to damming and channelization, recreational water activity, shoreline development, and water pollution from industrial activities have all been associated with the decline of NWR in its natural habitats 6,15. The species is particularly sensitive to high levels of sulfates in its water supply and acts as an important indicator species of water quality6,18. In addition to these conservation challenges, NWR seed is intermediately recalcitrant or desiccation intolerant, which reduces seed longevity in storage to 1-2 years 19 and reduces the feasibility of preservation in ex-situ seed banks. Therefore, the genetic diversity of NWR is currently only preservedin-situ within its natural range (Porter, 2019).
Genetic diversity represents the extent of heritable variation within and among populations of a species, and its preservation is vital for the maintenance of long-term viability in the face of continual environmental change 20,21. A 2008 MN Department of Natural Resources (MN DNR) report on the health of NWR natural stands concluded that the species’ greatest threat was an overall state-wide decline in genetic diversity 15. Biologists and conservationists have widely recognized the value of characterizing genome-wide diversity within a species for use in conservation efforts22,23. However, few such studies have been conducted for NWR, and molecular studies have heavily relied on obsolete marker systems 5,24,25, which are laborious to produce and often limited in number 26. The advent of low-cost high-throughput sequencing, such as genotyping-by-sequencing (GBS), which provides genome-wide coverage of co-dominant, single-nucleotide polymorphism (SNP) markers, has improved the genetic diversity characterization of extensive and complex germplasm collections27. In 2019, a study with limited sample size demonstrated the potential for GBS to be applied to NWR28.
The cultivation of NWR in irrigated man-made paddies, similar to white rice production, began in the 1950s to create an industry capable of supplying a consistent source of the grain to agricultural markets. As such, the production of cultivated NWR (cNWR) is a fairly new endeavor and only ~60 cycles of targeted selection separate cNWR from its wild counterparts. Breeders of cNWR have focused primarily on adapting the species to agronomic production in paddies, and on fixing seed-shattering resistance in the crop 2. However, concerns regarding the potential impact of gene flow between cNWR and natural stands of NWR have been raised given the species’ outcrossing nature 12,29–31. The Great Lakes region is the center of both origin and diversity of Z. palustris ; therefore, it is important to understand the potential impact of domesticating and cultivating cNWR in those areas. As plant breeders, we have a responsibility to be good stewards of our natural and domesticated plants. Thus, an understanding of how cNWR fits into local landscapes, and particularly, to what extent gene flow is occurring among natural stands and cNWR is essential to overall germplasm preservation.
In this study, we generated a genome-wide SNP dataset via GBS for a NWR diversity collection to study the population structure and gene flow within and among wild and cultivated populations. We aimed to improve our understanding of the genetic variability within the species and provide new information regarding the selective pressures applied to cNWR germplasm.